; This file contains extended force field parameters for the GROMOS force field 45A3 parameters set ; GROMACS 4.5.x format - files: aminoacids.rtp, aminoacids.n.tdb, aminoacids.c.tdb and aminoacids.hdb ; Authors: Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink & Bojan Zagrovic ; Parameter files in GROMACS 4.3.x and 4.4.x, and GROMOS formats available at http://vienna-ptm.univie.ac.at/ ; aminoacids.rtp file (backbone and side chain parameters) [ bondedtypes ] ; bonds angles dihedrals impropers 2 2 1 2 ; phosphoserine (-1) [ S1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OG OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PD P 0.63000 2 ; to add up to -1 net charge OE1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE3 OA -0.54800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) HE3 H 0.39800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG gb_17 OG PD gb_27 PD OE1 gb_23 PD OE2 gb_23 PD OE3 gb_27 OE3 HE3 gb_1 [ exclusions ] ; ai aj OE1 HE3 OE2 HE3 OG HE3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG ga_12 CB OG PD ga_25 OG PD OE1 ga_13 OG PD OE2 ga_13 OG PD OE3 ga_4 OE1 PD OE2 ga_28 OE1 PD OE3 ga_13 OE2 PD OE3 ga_13 PD OE3 HE3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG gd_17 CA CB OG PD gd_12 CB OG PD OE3 gd_9 CB OG PD OE3 gd_11 OG PD OE3 HE3 gd_9 OG PD OE3 HE3 gd_11 ; phosphoserine (-2) [ S2P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OG OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PD P 0.11500 2 ; to add up to -2 net charge OE1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE3 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG gb_17 OG PD gb_27 PD OE1 gb_23 PD OE2 gb_23 PD OE3 gb_23 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG ga_12 CB OG PD ga_25 OG PD OE1 ga_13 OG PD OE2 ga_13 OG PD OE3 ga_13 OE1 PD OE2 ga_13 OE1 PD OE3 ga_13 OE2 PD OE3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG gd_17 CA CB OG PD gd_12 CB OG PD OE1 gd_9 CB OG PD OE1 gd_11 ; phosphothreonine (-1) [ T1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OG1 OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PD P 0.63000 2 ; to add up to -1 net charge OE1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE3 OA -0.54800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) HE3 H 0.39800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) CG2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 PD gb_27 PD OE1 gb_23 PD OE2 gb_23 PD OE3 gb_27 OE3 HE3 gb_1 [ exclusions ] ; ai aj OE1 HE3 OE2 HE3 OG1 HE3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_14 OG1 CB CG2 ga_14 CB OG1 PD ga_25 OG1 PD OE1 ga_13 OG1 PD OE2 ga_13 OG1 PD OE3 ga_4 OE1 PD OE2 ga_28 OE1 PD OE3 ga_13 OE2 PD OE3 ga_13 PD OE3 HE3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG1 gd_17 CA CB OG1 PD gd_12 CB OG1 PD OE3 gd_9 CB OG1 PD OE3 gd_11 OG1 PD OE3 HE3 gd_9 OG1 PD OE3 HE3 gd_11 ; phosphothreonine (-2) [ T2P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OG1 OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PD P 0.11500 2 ; to add up to -2 net charge OE1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OE3 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) CG2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 PD gb_27 PD OE1 gb_23 PD OE2 gb_23 PD OE3 gb_23 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_14 OG1 CB CG2 ga_14 CB OG1 PD ga_25 OG1 PD OE1 ga_13 OG1 PD OE2 ga_13 OG1 PD OE3 ga_13 OE1 PD OE2 ga_13 OE1 PD OE3 ga_13 OE2 PD OE3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG1 gd_17 CA CB OG1 PD gd_12 CB OG1 PD OE1 gd_9 CB OG1 PD OE1 gd_11 ; phosphotyrosine (-1) [ Y1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C 0.15000 6 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OH OA -0.36000 6 ; from the phosphate group of nucleotides (e.g. ATP) PT P 0.63000 6 ; to add up to -1 net charge OI1 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OA -0.54800 6 ; from the hydroxyl group of nucleotides (e.g. ATP) HI3 H 0.39800 6 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 CZ OH gb_12 OH PT gb_27 PT OI1 gb_23 PT OI2 gb_23 PT OI3 gb_27 OI3 HI3 gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 HE1 HD1 CZ CD2 CE1 CD2 OH HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OH HE2 OH OH HI3 OI1 HI3 OI2 HI3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CE1 CZ CE2 ga_26 CE1 CZ OH ga_26 CE2 CZ OH ga_26 CZ OH PT ga_25 OH PT OI1 ga_13 OH PT OI2 ga_13 OH PT OI3 ga_4 OI1 PT OI2 ga_28 OI1 PT OI3 ga_13 OI2 PT OI3 ga_13 HI3 OI3 PT ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ OH PT gd_2 CZ OH PT OI3 gd_9 CZ OH PT OI3 gd_11 OH PT OI3 HI3 gd_9 OH PT OI3 HI3 gd_11 ; phosphotyrosine (-2) [ Y2P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C 0.15000 6 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OH OA -0.36000 6 ; from the phosphate group of nucleotides (e.g. ATP) PT P 0.11500 6 ; to add up to -2 net charge OI1 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 CZ OH gb_12 OH PT gb_27 PT OI1 gb_23 PT OI2 gb_23 PT OI3 gb_23 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 HE1 HD1 CZ CD2 CE1 CD2 OH HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OH HE2 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CE1 CZ CE2 ga_26 CE1 CZ OH ga_26 CE2 CZ OH ga_26 CZ OH PT ga_25 OH PT OI1 ga_13 OH PT OI2 ga_13 OH PT OI3 ga_13 OI1 PT OI2 ga_13 OI1 PT OI3 ga_13 OI2 PT OI3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ OH PT gd_2 CZ OH PT OI1 gd_9 CZ OH PT OI1 gd_11 ; phosphoaspartate (-1) [ D1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.53000 2 ; to add up to -1 net charge OD1 O -0.38000 2 ; from the carbonyl oxygen (of e.g. the peptide bond) OD2 OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PE P 0.63000 2 ; from the phosphate group (of e.g. S1P) OZ1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OZ2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OZ3 OA -0.54800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) HZ3 H 0.39800 2 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG OD2 gb_12 OD2 PE gb_27 PE OZ1 gb_23 PE OZ2 gb_23 PE OZ3 gb_27 OZ3 HZ3 gb_1 [ exclusions ] ; ai aj OZ1 HZ3 OZ2 HZ3 OD2 HZ3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_21 CB CG OD2 ga_18 OD1 CG OD2 ga_32 CG OD2 PE ga_25 OD2 PE OZ1 ga_13 OD2 PE OZ2 ga_13 OD2 PE OZ3 ga_4 OZ1 PE OZ2 ga_28 OZ1 PE OZ3 ga_13 OZ2 PE OZ3 ga_13 PE OZ3 HZ3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG OD2 gd_20 CB CG OD2 PE gd_3 CG OD2 PE OZ3 gd_9 CG OD2 PE OZ3 gd_11 OD2 PE OZ3 HZ3 gd_9 OD2 PE OZ3 HZ3 gd_11 ; phosphoaspartate (-2) [ D2P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.53000 2 ; to add up to -2 net charge OD1 O -0.38000 2 ; from the carbonyl oxygen (of e.g. the peptide bond) OD2 OA -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) PE P 0.11500 2 ; from the phosphate group (of e.g. S2P) OZ1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OZ2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OZ3 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG OD2 gb_12 OD2 PE gb_27 PE OZ1 gb_23 PE OZ2 gb_23 PE OZ3 gb_23 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_21 CB CG OD2 ga_18 OD1 CG OD2 ga_32 CG OD2 PE ga_25 OD2 PE OZ1 ga_13 OD2 PE OZ2 ga_13 OD2 PE OZ3 ga_13 OZ1 PE OZ2 ga_13 OZ1 PE OZ3 ga_13 OZ2 PE OZ3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG OD2 gd_20 CB CG OD2 PE gd_3 CG OD2 PE OZ1 gd_9 CG OD2 PE OZ1 gd_11 ; phospholysine (-1) [ K1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ NE -0.28000 4 ; from NE of ARGN HZ H 0.28000 4 ; from HE of ARGN PH P 0.42000 5 ; to add up to -1 net charge OI1 OM -0.63500 5 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 5 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OA -0.54800 5 ; from the hydroxyl group of nucleotides (e.g. ATP) HI3 H 0.39800 5 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ PH gb_23 PH OI1 gb_23 PH OI2 gb_23 PH OI3 gb_27 OI3 HI3 gb_1 [ exclusions ] ; ai aj OI1 HI3 OI2 HI3 NZ HI3 HZ OI1 HZ OI2 HZ OI3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_19 HZ NZ PH ga_22 CE NZ PH ga_32 NZ PH OI1 ga_13 NZ PH OI2 ga_13 NZ PH OI3 ga_4 OI1 PH OI2 ga_28 OI1 PH OI3 ga_13 OI2 PH OI3 ga_13 HI3 OI3 PH ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CE PH HZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ PH gd_19 CE NZ PH OI3 gd_19 NZ PH OI3 HI3 gd_9 NZ PH OI3 HI3 gd_11 ; phospholysine (-2) [ K2P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ NE -0.28000 4 ; from NE of ARGN HZ H 0.28000 4 ; from HE of ARGN PH P -0.09500 5 ; to add up to -2 net charge OI1 OM -0.63500 5 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 5 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OM -0.63500 5 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ PH gb_23 PH OI1 gb_23 PH OI2 gb_23 PH OI3 gb_23 [ exclusions ] ; ai aj HZ OI1 HZ OI2 HZ OI3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_19 HZ NZ PH ga_22 CE NZ PH ga_32 NZ PH OI1 ga_13 NZ PH OI2 ga_13 NZ PH OI3 ga_13 OI1 PH OI2 ga_13 OI1 PH OI3 ga_13 OI2 PH OI3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CE PH HZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ PH gd_19 CE NZ PH OI1 gd_19 ; phosphoarginine (0) [ R0P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD CH2 0.09000 2 NE NE -0.11000 2 HE H 0.24000 2 CZ C 0.43000 2 ; to add up to 1 net charge NH1 NZ -0.26000 2 HH11 H 0.24000 2 HH12 H 0.24000 2 NH2 NE -0.11000 2 ; from NE nitrogen atom of ARG HH2 H 0.24000 2 ; from terminal hydrogen atoms of ARG PT P 0.42000 3 ; to add up to -1 net charge OI1 OM -0.63500 3 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 3 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OA -0.54800 3 ; from the hydroxyl group of nucleotides (e.g. ATP) HI3 H 0.39800 3 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH11 gb_2 NH1 HH12 gb_2 NH2 HH2 gb_2 NH2 PT gb_23 PT OI1 gb_23 PT OI2 gb_23 PT OI3 gb_27 OI3 HI3 gb_1 [ exclusions ] ; ai aj HH2 OI1 HH2 OI2 HH2 OI3 HI3 OI1 HI3 OI2 HI3 NH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH11 ga_22 CZ NH1 HH12 ga_22 HH11 NH1 HH12 ga_23 CZ NH2 HH2 ga_22 HH2 NH2 PT ga_19 CZ NH2 PT ga_32 NH2 PT OI1 ga_13 NH2 PT OI2 ga_13 NH2 PT OI3 ga_4 OI1 PT OI2 ga_28 OI1 PT OI3 ga_13 OI2 PT OI3 ga_13 PT OI3 HI3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH1 HH11 HH12 CZ gi_1 NH2 CZ PT HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH2 gd_4 NE CZ NH1 HH11 gd_4 NE CZ NH2 PT gd_4 CZ NH2 PT OI3 gd_19 NH2 PT OI3 HI3 gd_9 NH2 PT OI3 HI3 gd_11 ; phosphoarginine (-1) [ R1P ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD CH2 0.09000 2 NE NE -0.11000 2 HE H 0.24000 2 CZ C 0.43000 2 ; to add up to 1 net charge NH1 NZ -0.26000 2 HH11 H 0.24000 2 HH12 H 0.24000 2 NH2 NE -0.11000 2 ; from NE nitrogen atom of ARG HH2 H 0.24000 2 ; from terminal hydrogen atoms of ARG PT P -0.09500 3 ; to add up to -2 net charge OI1 OM -0.63500 3 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 3 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OM -0.63500 3 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH11 gb_2 NH1 HH12 gb_2 NH2 HH2 gb_2 NH2 PT gb_23 PT OI1 gb_23 PT OI2 gb_23 PT OI3 gb_23 [ exclusions ] ; ai aj HH2 OI1 HH2 OI2 HH2 OI3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH11 ga_22 CZ NH1 HH12 ga_22 HH11 NH1 HH12 ga_23 CZ NH2 HH2 ga_22 HH2 NH2 PT ga_19 CZ NH2 PT ga_32 NH2 PT OI1 ga_13 NH2 PT OI2 ga_13 NH2 PT OI3 ga_13 OI1 PT OI2 ga_13 OI1 PT OI3 ga_13 OI2 PT OI3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH1 HH11 HH12 CZ gi_1 NH2 CZ PT HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH2 gd_4 NE CZ NH1 HH11 gd_4 NE CZ NH2 PT gd_4 CZ NH2 PT OI1 gd_19 ; 1-phosphohistidine (-1) [ H11 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.29000 2 ND1 NR -0.58000 2 CE1 CR1 0.29000 2 CD2 CR1 0.00000 3 NE2 NR 0.00000 3 PZ P 0.42000 4 ; to add up to -1 net charge OH1 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OH2 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OH3 OA -0.54800 4 ; from the hydroxyl group of nucleotides (e.g. ATP) HH3 H 0.39800 4 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 NE2 PZ gb_23 PZ OH1 gb_23 PZ OH2 gb_23 PZ OH3 gb_27 OH3 HH3 gb_1 [ exclusions ] ; ai aj CB CE1 CB NE2 PZ CD2 PZ NE2 HH3 NE2 HH3 OH1 HH3 OH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE1 ga_6 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CD2 NE2 PZ ga_36 CE1 NE2 PZ ga_36 NE2 PZ OH1 ga_13 NE2 PZ OH2 ga_13 NE2 PZ OH3 ga_4 OH1 PZ OH2 ga_28 OH1 PZ OH3 ga_13 OH2 PZ OH3 ga_13 PZ OH3 HH3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 NE2 CD2 CE1 PZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 CD2 NE2 PZ OH3 gd_19 NE2 PZ OH3 HH3 gd_9 NE2 PZ OH3 HH3 gd_11 ; 1-phosphohistidine (-2) [ H12 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.29000 2 ND1 NR -0.58000 2 CE1 CR1 0.29000 2 CD2 CR1 0.00000 3 NE2 NR 0.00000 3 PZ P -0.09500 4 ; to add up to -2 net charge OH1 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OH2 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OH3 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 NE2 PZ gb_23 PZ OH1 gb_23 PZ OH2 gb_23 PZ OH3 gb_23 [ exclusions ] ; ai aj CB CE1 CB NE2 PZ CD2 PZ NE2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE1 ga_6 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CD2 NE2 PZ ga_36 CE1 NE2 PZ ga_36 NE2 PZ OH1 ga_13 NE2 PZ OH2 ga_13 NE2 PZ OH3 ga_13 OH1 PZ OH2 ga_13 OH1 PZ OH3 ga_13 OH2 PZ OH3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 NE2 CD2 CE1 PZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 CD2 NE2 PZ OH1 gd_19 ; 3-phosphohistidine (-1) [ H31 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 2 ND1 NR 0.00000 2 CD2 CR1 0.29000 3 CE1 CR1 0.29000 3 NE2 NR -0.58000 3 PE3 P 0.42000 4 ; to add up to -1 net charge OZ1 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OZ2 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OZ3 OA -0.54800 4 ; from the hydroxyl group of nucleotides (e.g. ATP) HZ3 H 0.39800 4 ; from the hydroxyl group of nucleotides (e.g. ATP) C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 ND1 PE3 gb_23 CD2 NE2 gb_9 CE1 NE2 gb_9 PE3 OZ1 gb_23 PE3 OZ2 gb_23 PE3 OZ3 gb_27 OZ3 HZ3 gb_1 [ exclusions ] ; ai aj CB CE1 CB NE2 CB PE3 PE3 CD2 PE3 NE2 HZ3 ND1 HZ3 OZ1 HZ3 OZ2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE1 ga_6 CG ND1 PE3 ga_36 CE1 ND1 PE3 ga_36 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 ND1 PE3 OZ1 ga_13 ND1 PE3 OZ2 ga_13 ND1 PE3 OZ3 ga_4 OZ1 PE3 OZ2 ga_28 OZ1 PE3 OZ3 ga_13 OZ2 PE3 OZ3 ga_13 PE3 OZ3 HZ3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 ND1 CG CE1 PE3 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 CG ND1 PE3 OZ3 gd_19 ND1 PE3 OZ3 HZ3 gd_9 ND1 PE3 OZ3 HZ3 gd_11 ; 3-phosphohistidine (-2) [ H32 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 2 ND1 NR 0.00000 2 CD2 CR1 0.29000 3 CE1 CR1 0.29000 3 NE2 NR -0.58000 3 PE3 P -0.09500 4 ; to add up to -2 net charge OZ1 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OZ2 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) OZ3 OM -0.63500 4 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 ND1 PE3 gb_23 CD2 NE2 gb_9 CE1 NE2 gb_9 PE3 OZ1 gb_23 PE3 OZ2 gb_23 PE3 OZ3 gb_23 [ exclusions ] ; ai aj CB CE1 CB NE2 CB PE3 PE3 CD2 PE3 NE2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE1 ga_6 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CG ND1 PE3 ga_36 CE1 ND1 PE3 ga_36 ND1 PE3 OZ1 ga_13 ND1 PE3 OZ2 ga_13 ND1 PE3 OZ3 ga_13 OZ1 PE3 OZ2 ga_13 OZ2 PE3 OZ3 ga_13 OZ1 PE3 OZ3 ga_13 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 ND1 CG CE1 PE3 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 CG ND1 PE3 OZ1 gd_19 ; N6-methyllysine (0) [ KMN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.21000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NZ NT -0.83000 3 ; from NZ of LYS HZ H 0.41000 3 ; derived from terminal hydrogen atoms of LYS CH CH3 0.21000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_10 HZ NZ CH ga_10 CE NZ CH ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_14 ; N6-methyllysine (+1) [ KMC ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NZ NL 0.10400 3 ; to add up to +1 net charge HZ1 H 0.24800 3 HZ2 H 0.24800 3 CH CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ1 gb_2 NZ HZ2 gb_2 NZ CH gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ1 ga_10 CE NZ HZ2 ga_10 HZ1 NZ HZ2 ga_9 HZ1 NZ CH ga_10 HZ2 NZ CH ga_10 CE NZ CH ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_14 ; N6,N6-dimethyllysine (0) [ K2M ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.21000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NZ NT -0.63000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CH1 CH3 0.21000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CH2 CH3 0.21000 3 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ CH1 gb_20 NZ CH2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ CH1 ga_12 CE NZ CH2 ga_12 CH1 NZ CH2 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH1 gd_14 ; N6,N6-dimethyllysine (+1) [ K2C ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NZ NL 0.15200 3 ; to add up to +1 net charge HZ H 0.24800 3 CH1 CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CH2 CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH1 gb_20 NZ CH2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_10 HZ NZ CH1 ga_10 HZ NZ CH2 ga_10 CE NZ CH1 ga_12 CE NZ CH2 ga_12 CH1 NZ CH2 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH1 gd_14 ; N6,N6,N6-trimethyllysine [ K3C ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NZ NL 0.20000 3 ; to add up to +1 net charge CH1 CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CH2 CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CH3 CH3 0.20000 3 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ CH1 gb_20 NZ CH2 gb_20 NZ CH3 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ CH1 ga_12 CE NZ CH2 ga_12 CE NZ CH3 ga_12 CH1 NZ CH2 ga_12 CH1 NZ CH3 ga_12 CH2 NZ CH3 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH1 gd_14 ; omega-N-methylarginine (0) [ RMN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 NE NE -0.28000 3 HE H 0.28000 3 CZ C 0.18000 4 ; 0.36 charge divided between CZ and CT to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) NH1 NE -0.36000 4 ; from ring nitrogen atoms of nucleotides (e.g. ATP) CT CH3 0.18000 4 ; 0.36 charge divided between CZ and CT to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) NH2 NZ -0.83000 5 HH21 H 0.41500 5 HH22 H 0.41500 5 C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 CT gb_20 NH2 HH21 gb_2 NH2 HH22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 CT ga_26 CZ NH2 HH21 ga_22 CZ NH2 HH22 ga_22 HH21 NH2 HH22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH2 HH21 HH22 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 CT gd_4 NE CZ NH2 HH21 gd_4 ; omega-N-methylarginine (+1) [ RMC ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD CH2 0.09000 2 NE NE -0.11000 2 HE H 0.24000 2 CZ C 0.34000 2 NH1 NZ -0.26000 2 HH11 H 0.24000 2 HH12 H 0.24000 2 NH2 NZ -0.11000 2 ; from NE atom of ARG HH2 H 0.24000 2 CT CH3 0.09000 2 ; from CD atom of ARG C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH11 gb_2 NH1 HH12 gb_2 NH2 HH2 gb_2 NH2 CT gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH11 ga_22 CZ NH1 HH12 ga_22 HH11 NH1 HH12 ga_23 CZ NH2 HH2 ga_22 HH2 NH2 CT ga_19 CZ NH2 CT ga_32 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH1 HH11 HH12 CZ gi_1 NH2 HH2 CT CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 HH11 gd_4 NE CZ NH2 CT gd_4 ; symmetric-dimethylarginine (0) [ RSM ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 NE NE -0.28000 3 HE H 0.28000 3 CZ C 0.18000 4 ; 0.36 charge divided between CZ and CT1 to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) NH1 NE -0.36000 4 ; from ring nitrogen atoms of nucleotides (e.g. ATP) CT1 CH3 0.18000 4 ; 0.36 charge divided between CZ and CT1 to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) NH2 NE -0.28000 5 ; from NE atom of ARGN HH2 H 0.28000 5 ; from HE atom of ARGN CT2 CH3 0.00000 6 ; from CD atom of ARGN C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 CT1 gb_20 NH2 HH2 gb_2 NH2 CT2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 CT1 ga_26 CZ NH2 HH2 ga_22 HH2 NH2 CT2 ga_19 CZ NH2 CT2 ga_32 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH2 HH2 CT2 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 CT1 gd_4 NE CZ NH2 CT2 gd_4 ; symmetric-dimethylarginine (+1) [ RMS ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD CH2 0.09000 2 NE NE -0.11000 2 HE H 0.24000 2 CZ C 0.34000 2 NH1 NZ -0.11000 2 ; from NE atom of ARG HH1 H 0.24000 2 CT1 CH3 0.09000 2 ; from CD atom of ARG NH2 NZ -0.11000 2 ; from NE atom of ARG HH2 H 0.24000 2 CT2 CH3 0.09000 2 ; from CD atom of ARG C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH1 gb_2 NH1 CT1 gb_20 NH2 HH2 gb_2 NH2 CT2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH1 ga_22 HH1 NH1 CT1 ga_19 CZ NH1 CT1 ga_32 CZ NH2 HH2 ga_22 HH2 NH2 CT2 ga_19 CZ NH2 CT2 ga_32 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH1 HH1 CT1 CZ gi_1 NH2 HH2 CT2 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 CT1 gd_4 NE CZ NH2 CT2 gd_4 ; asymmetric-dimethylarginine (0) [ RAM ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 NE NE -0.28000 3 HE H 0.28000 3 CZ C 0.15000 4 NH1 NE -0.54800 4 HH1 H 0.39800 4 NH2 NZ -0.20000 5 ; from ring nitrogen atoms of nucleotides (e.g. ATP) CT1 CH3 0.10000 5 ; 0.2 charge divided between CT1 and CT2 to add up to 0 net charge, also similar to methyl groups of methyl-arginine modifications and used for ring carbons in nucleotides (e.g. DCYT) CT2 CH3 0.10000 5 ; 0.2 charge divided between CT1 and CT2 to add up to 0 net charge, also similar to methyl groups of methyl-arginine modifications and used for ring carbons in nucleotides (e.g. DCYT) C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH1 gb_2 NH2 CT1 gb_20 NH2 CT2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH1 ga_22 CZ NH2 CT1 ga_27 CZ NH2 CT2 ga_27 CT1 NH2 CT2 ga_27 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH2 CT1 CT2 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 HH1 gd_4 NE CZ NH2 CT1 gd_4 ; asymmetric-dimethylarginine (+1) [ RMA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD CH2 0.09000 2 NE NE -0.11000 2 HE H 0.24000 2 CZ C 0.43000 2 ; from CZ of R1P NH1 NZ -0.26000 2 HH11 H 0.24000 2 HH12 H 0.24000 2 NH2 NZ -0.05000 2 ; to add up to +1 net charge, also used for nitrogen atoms in histidine building blocks CT1 CH3 0.09000 2 ; from CD atom of ARG CT2 CH3 0.09000 2 ; from CD atom of ARG C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_10 CZ NH1 gb_10 CZ NH2 gb_10 NH1 HH11 gb_2 NH1 HH12 gb_2 NH2 CT1 gb_20 NH2 CT2 gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_19 HE NE CZ ga_22 CD NE CZ ga_32 NE CZ NH1 ga_27 NE CZ NH2 ga_27 NH1 CZ NH2 ga_27 CZ NH1 HH11 ga_22 CZ NH1 HH12 ga_22 HH11 NH1 HH12 ga_23 CZ NH2 CT1 ga_27 CZ NH2 CT2 ga_27 CT1 NH2 CT2 ga_27 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ NH1 NH2 NE gi_1 NH1 HH11 HH12 CZ gi_1 NH2 CT1 CT2 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH1 gd_4 NE CZ NH1 HH11 gd_4 NE CZ NH2 CT1 gd_4 ; 1-methylhistidine (0) [ H1M ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.13000 2 ND1 NR -0.58000 2 CD2 CR1 0.00000 2 CE1 CR1 0.26000 2 NE2 NR 0.00000 2 CZ CH3 0.19000 2 ; from HE2 in HISB C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 NE2 CZ gb_21 [ exclusions ] ; ai aj CB CE1 CB NE2 CG CZ ND1 CZ [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE1 ga_6 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CD2 NE2 CZ ga_36 CE1 NE2 CZ ga_36 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 NE2 CD2 CE1 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 ; 1-methylhistidine (+1) [ H1C ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.05000 2 ND1 NR 0.38000 2 HD1 H 0.30000 2 CD2 CR1 0.00000 2 CE1 CR1 -0.14000 2 NE2 NR 0.31000 2 CZ CH3 0.20000 2 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 HD1 gb_2 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 NE2 CZ gb_21 [ exclusions ] ; ai aj CB HD1 CB CE1 CB NE2 CG CZ ND1 CZ HD1 CD2 HD1 NE2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 HD1 ga_35 CG ND1 CE1 ga_6 HD1 ND1 CE1 ga_35 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CD2 NE2 CZ ga_36 CE1 NE2 CZ ga_36 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 ND1 CG CE1 HD1 gi_1 NE2 CD2 CE1 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 ; 3-methylhistidine (0) [ H3M ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 2 ND1 NR 0.00000 2 CD2 CR1 0.13000 2 CE1 CR1 0.26000 2 CE3 CH3 0.19000 2 ; from HD1 in HISA NE2 NR -0.58000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE1 gb_9 ND1 CE3 gb_21 CD2 NE2 gb_9 CE1 NE2 gb_9 [ exclusions ] ; ai aj CB CE3 CB CE1 CB NE2 CE3 CD2 CE3 NE2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE3 ga_36 CG ND1 CE1 ga_6 CE3 ND1 CE1 ga_36 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 ND1 CG CE1 CE3 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 ; 3-methylhistidine (+1) [ H3C ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.05000 2 ND1 NR 0.38000 2 CD2 CR1 0.00000 2 CE1 CR1 -0.14000 2 CE3 CH3 0.20000 2 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 NE2 NR 0.31000 2 HE2 H 0.30000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 CE3 gb_21 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 NE2 HE2 gb_2 [ exclusions ] ; ai aj CB CE3 CB CE1 CB NE2 CG HE2 ND1 HE2 CE3 CD2 CE3 NE2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 CE3 ga_36 CG ND1 CE1 ga_6 CE3 ND1 CE1 ga_36 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 CD2 NE2 CE1 ga_6 CD2 NE2 HE2 ga_35 CE1 NE2 HE2 ga_35 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 ND1 CG CE1 CE3 gi_1 NE2 CD2 CE1 HE2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 ; N5-methylglutamine [ QME ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.10000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 CD C 0.28000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OE1 O -0.38000 2 NE2 N -0.28000 3 ; from the peptide bond HE2 H 0.28000 3 ; from the peptide bond CZ CH3 0.00000 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_4 CD NE2 gb_9 NE2 HE2 gb_2 NE2 CZ gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_29 CG CD NE2 ga_18 OE1 CD NE2 ga_32 CD NE2 HE2 ga_31 HE2 NE2 CZ ga_17 CD NE2 CZ ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD OE1 NE2 CG gi_1 NE2 CZ CD HE2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE2 gd_20 CG CD NE2 CZ gd_4 ; N4-methylasparagine [ NME ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.10000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 CG C 0.28000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OD1 O -0.38000 2 ND2 N -0.28000 3 ; from the peptide bond HD2 H 0.28000 3 ; from the peptide bond CE CH3 0.00000 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG ND2 gb_9 ND2 HD2 gb_2 ND2 CE gb_20 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_29 CB CG ND2 ga_18 OD1 CG ND2 ga_32 CG ND2 HD2 ga_31 HD2 ND2 CE ga_17 CG ND2 CE ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG OD1 ND2 CB gi_1 ND2 CE CG HD2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND2 gd_20 CB CG ND2 CE gd_4 ; glutamate methyl ester [ EME ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD C 0.56000 2 ; from the carbonyl group (of e.g. GLU) with the partial charge increased by 0.18 - see the comment of CZ atom OE1 O -0.38000 2 ; from the carbonyl group (of e.g. GLU) OE2 OA -0.36000 2 ; from the ring oxygen atom of nucleotides (e.g. ATP) CZ CH3 0.18000 2 ; 0.36 charge divided between CD and CZ to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_4 CD OE2 gb_12 OE2 CZ gb_17 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_29 CG CD OE2 ga_18 OE1 CD OE2 ga_32 CD OE2 CZ ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD OE1 OE2 CG gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD OE2 gd_20 CG CD OE2 CZ gd_3 ; aspartate methyl ester [ DMA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.56000 2 ; from the carbonyl group (of e.g. GLU) with the partial charge increased by 0.18 - see the comment of CE atom OD1 O -0.38000 2 ; from the carbonyl group (of e.g. GLU) OD2 OA -0.36000 2 ; from the ring oxygen atom of nucleotides (e.g. ATP) CE CH3 0.18000 2 ; 0.36 charge divided between CG and CE to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG OD2 gb_12 OD2 CE gb_17 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_29 CB CG OD2 ga_18 OD1 CG OD2 ga_32 CG OD2 CE ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG OD2 gd_20 CB CG OD2 CE gd_3 ; S-methylcysteine [ CYM ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 ; from MET SG S 0.00000 2 ; from MET CD CH3 0.00000 2 ; from MET C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG CD gb_29 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG CD ga_3 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG CD gd_13 ; N6-acetyllysine [ KAC ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ N -0.28000 4 ; from the peptide bond HZ H 0.28000 4 ; from the peptide bond CH C 0.28000 5 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OI2 O -0.38000 5 ; from the carbonyl group (of e.g. GLN) CI1 CH3 0.10000 5 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH gb_9 CH OI2 gb_4 CH CI1 gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_17 HZ NZ CH ga_31 CE NZ CH ga_30 NZ CH OI2 ga_32 NZ CH CI1 ga_18 OI2 CH CI1 ga_29 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CH CE HZ gi_1 CH CI1 NZ OI2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_19 CE NZ CH CI1 gd_4 ; 3-hydroxyproline (R) [ PH3 ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 CH2 0.00000 3 CD CH2 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 OG1 HG1 gb_1 CB CG2 gb_26 CG2 CD gb_26 CD N gb_20 [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 CB OG1 HG1 ga_11 OG1 CB CG2 ga_12 CB CG2 CD ga_12 CG2 CD N ga_12 CD N CA ga_20 -C N CD ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CG2 CA OG1 gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 CD gd_17 CB CG2 CD N gd_17 CG2 CD N CA gd_19 ; 3-hydroxyproline (S) [ P3H ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 CH2 0.00000 3 CD CH2 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 OG1 HG1 gb_1 CB CG2 gb_26 CG2 CD gb_26 CD N gb_20 [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 CB OG1 HG1 ga_11 OG1 CB CG2 ga_12 CB CG2 CD ga_12 CG2 CD N ga_12 CD N CA ga_20 -C N CD ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CA CG2 OG1 gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 CD gd_17 CB CG2 CD N gd_17 CG2 CD N CA gd_19 ; 4-hydroxyproline (S) [ HY2 ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH1 0.15000 2 ; from the hydroxyl group of THR OD1 OA -0.54800 2 ; from the hydroxyl group of THR HD1 H 0.39800 2 ; from the hydroxyl group of THR CD2 CH2 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_17 OD1 HD1 gb_1 CG CD2 gb_26 CD2 N gb_20 [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_12 CB CG OD1 ga_12 CB CG CD2 ga_12 CG OD1 HD1 ga_11 OD1 CG CD2 ga_12 CG CD2 N ga_12 CD2 N CA ga_20 -C N CD2 ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD2 gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CB CD2 OD1 gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_17 CB CG OD1 HD1 gd_12 CB CG CD2 N gd_17 CG CD2 N CA gd_19 ; 3,4-dihydroxyproline [ PHH ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 CH1 0.15000 3 ; from the hydroxyl group of THR OD1 OA -0.54800 3 ; from the hydroxyl group of THR HD1 H 0.39800 3 ; from the hydroxyl group of THR CD2 CH2 0.00000 4 C C 0.380 5 O O -0.380 5 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 OG1 HG1 gb_1 CB CG2 gb_26 CG2 OD1 gb_17 OD1 HD1 gb_1 CG2 CD2 gb_26 CD2 N gb_20 [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 CB OG1 HG1 ga_11 OG1 CB CG2 ga_12 CB CG2 OD1 ga_12 CB CG2 CD2 ga_12 CG2 OD1 HD1 ga_11 OD1 CG2 CD2 ga_12 CG2 CD2 N ga_12 CD2 N CA ga_20 -C N CD2 ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD2 gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CA CG2 OG1 gi_2 CG2 CB CD2 OD1 gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 CD2 gd_17 CB CG2 OD1 HD1 gd_12 CB CG2 CD2 N gd_17 CG2 CD2 N CA gd_19 ; 5-hydroxylysine (0,R) [ KH5 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE1 OA -0.54800 3 ; from the hydroxyl group of THR HE1 H 0.39800 3 ; from the hydroxyl group of THR CE2 CH2 0.00000 4 NZ NT -0.83000 5 HZ1 H 0.41500 5 HZ2 H 0.41500 5 C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_17 CD CE2 gb_26 OE1 HE1 gb_1 CE2 NZ gb_20 NZ HZ1 gb_2 NZ HZ2 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_12 CG CD CE2 ga_12 OE1 CD CE2 ga_12 CD OE1 HE1 ga_11 CD CE2 NZ ga_14 CE2 NZ HZ1 ga_10 CE2 NZ HZ2 ga_10 HZ1 NZ HZ2 ga_9 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD CE2 OE1 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE2 gd_17 CG CD OE1 HE1 gd_12 CG CD CE2 NZ gd_17 CD CE2 NZ HZ1 gd_14 ; 5-hydroxylysine (0,S) [ K5H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE1 OA -0.54800 3 ; from the hydroxyl group of THR HE1 H 0.39800 3 ; from the hydroxyl group of THR CE2 CH2 0.00000 4 NZ NT -0.83000 5 HZ1 H 0.41500 5 HZ2 H 0.41500 5 C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_17 CD CE2 gb_26 OE1 HE1 gb_1 CE2 NZ gb_20 NZ HZ1 gb_2 NZ HZ2 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_12 CG CD CE2 ga_12 OE1 CD CE2 ga_12 CD OE1 HE1 ga_11 CD CE2 NZ ga_14 CE2 NZ HZ1 ga_10 CE2 NZ HZ2 ga_10 HZ1 NZ HZ2 ga_9 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD OE1 CE2 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE2 gd_17 CG CD OE1 HE1 gd_12 CG CD CE2 NZ gd_17 CD CE2 NZ HZ1 gd_14 ; 5-hydroxylysine (+1,R) [ KPH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE1 OA -0.54800 3 ; from the hydroxyl group of THR HE1 H 0.39800 3 ; from the hydroxyl group of THR CE2 CH2 0.12700 4 NZ NL 0.12900 4 HZ1 H 0.24800 4 HZ2 H 0.24800 4 HZ3 H 0.24800 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_17 CD CE2 gb_26 OE1 HE1 gb_1 CE2 NZ gb_20 NZ HZ1 gb_2 NZ HZ2 gb_2 NZ HZ3 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_12 CG CD CE2 ga_12 OE1 CD CE2 ga_12 CD OE1 HE1 ga_11 CD CE2 NZ ga_14 CE2 NZ HZ1 ga_10 CE2 NZ HZ2 ga_10 CE2 NZ HZ3 ga_10 HZ1 NZ HZ2 ga_9 HZ1 NZ HZ3 ga_9 HZ2 NZ HZ3 ga_9 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD CE2 OE1 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE2 gd_17 CG CD OE1 HE1 gd_12 CG CD CE2 NZ gd_17 CD CE2 NZ HZ1 gd_14 ; 5-hydroxylysine (+1,S) [ KHP ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE1 OA -0.54800 3 ; from the hydroxyl group of THR HE1 H 0.39800 3 ; from the hydroxyl group of THR CE2 CH2 0.12700 4 NZ NL 0.12900 4 HZ1 H 0.24800 4 HZ2 H 0.24800 4 HZ3 H 0.24800 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE1 gb_17 CD CE2 gb_26 OE1 HE1 gb_1 CE2 NZ gb_20 NZ HZ1 gb_2 NZ HZ2 gb_2 NZ HZ3 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD OE1 ga_12 CG CD CE2 ga_12 OE1 CD CE2 ga_12 CD OE1 HE1 ga_11 CD CE2 NZ ga_14 CE2 NZ HZ1 ga_10 CE2 NZ HZ2 ga_10 CE2 NZ HZ3 ga_10 HZ1 NZ HZ2 ga_9 HZ1 NZ HZ3 ga_9 HZ2 NZ HZ3 ga_9 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD OE1 CE2 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE2 gd_17 CG CD OE1 HE1 gd_12 CG CD CE2 NZ gd_17 CD CE2 NZ HZ1 gd_14 ; 3,4-dihydroxyphenylalanine [ HTY ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.15000 4 ; from the hydroxyl group of TYR OZ1 OA -0.54800 4 ; from the hydroxyl group of TYR HZ1 H 0.39800 4 ; from the hydroxyl group of TYR CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C 0.15000 6 ; from the hydroxyl group of TYR OH OA -0.54800 6 ; from the hydroxyl group of TYR HH H 0.39800 6 ; from the hydroxyl group of TYR C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 CZ2 gb_15 CE1 OZ1 gb_12 OZ1 HZ1 gb_1 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 OH gb_12 OH HH gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG OZ1 CG HE2 CG CZ2 CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 OZ1 HD1 CZ2 CD2 CE1 CD2 OH HD2 HE2 HD2 CZ2 CE1 HE2 OZ1 CE2 OZ1 OH HE2 OH HH OZ1 HH HZ1 HZ1 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 OZ1 ga_26 CD1 CE1 CZ2 ga_26 OZ1 CE1 CZ2 ga_26 CE1 OZ1 HZ1 ga_11 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 CE2 ga_26 CE1 CZ2 OH ga_26 CE2 CZ2 OH ga_26 CZ2 OH HH ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 OZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CD1 CE1 OZ1 HZ1 gd_2 CE1 CZ2 OH HH gd_2 ; 7-hydroxytryptophan [ W7H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C 0.15000 4 ; from the hydroxyl group of TYR OH2 OA -0.54800 4 ; from the hydroxyl group of TYR HH2 H 0.39800 4 ; from the hydroxyl group of TYR CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH3 C -0.10000 6 HH3 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 CZ2 OH2 gb_12 CZ2 CH3 gb_15 CZ3 HZ3 gb_3 CZ3 CH3 gb_15 OH2 HH2 gb_1 CH3 HH3 gb_3 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ3 CD2 OH2 CD2 CH3 NE1 CE3 NE1 OH2 NE1 CH3 HE1 CZ2 CE2 HE3 CE2 CZ3 CE2 HH3 CE3 CZ2 CE3 HH3 HE3 HZ3 HE3 CH3 CZ2 HZ3 CZ3 OH2 HZ3 HH3 OH2 HH3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CE2 CZ2 OH2 ga_26 CE2 CZ2 CH3 ga_26 OH2 CZ2 CH3 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH3 ga_24 CE3 CZ3 CH3 ga_26 CZ2 OH2 HH2 ga_11 CZ2 CH3 HH3 ga_24 HH3 CH3 CZ3 ga_24 CZ2 CH3 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH3 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH3 CZ3 gi_1 CD2 CE3 CZ3 CH3 gi_1 CE3 CZ3 CH3 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH3 OH2 gi_1 CZ3 CE3 CH3 HZ3 gi_1 CH3 CZ2 CZ3 HH3 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CE2 CZ2 OH2 HH2 gd_2 ; 3-hydroxyaspartate (-1,R) [ DH3 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.27000 3 OD1 OM -0.63500 3 OD2 OM -0.63500 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_5 CG2 OD2 gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_21 CB CG2 OD2 ga_21 OD1 CG2 OD2 ga_37 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CG2 OG1 CA gi_2 CG2 OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 OD1 gd_20 ; 3-hydroxyaspartate (-1,S) [ D3H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.27000 3 OD1 OM -0.63500 3 OD2 OM -0.63500 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_5 CG2 OD2 gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_21 CB CG2 OD2 ga_21 OD1 CG2 OD2 ga_37 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 CG2 OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 OD1 gd_20 ; 3-hydroxyaspartate (0,R) [ DN3 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.53000 3 OD1 O -0.38000 3 OD2 OA -0.54800 3 HD2 H 0.39800 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_4 CG2 OD2 gb_12 OD2 HD2 gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_29 CB CG2 OD2 ga_18 OD1 CG2 OD2 ga_32 CG2 OD2 HD2 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CG2 OG1 CA gi_2 CG2 OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 OD2 gd_20 CB CG2 OD2 HD2 gd_3 ; 3-hydroxyaspartate (0,S) [ D3N ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.53000 3 OD1 O -0.38000 3 OD2 OA -0.54800 3 HD2 H 0.39800 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_4 CG2 OD2 gb_12 OD2 HD2 gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_29 CB CG2 OD2 ga_18 OD1 CG2 OD2 ga_32 CG2 OD2 HD2 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 CG2 OD1 OD2 CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 OD2 gd_20 CB CG2 OD2 HD2 gd_3 ; 3-hydroxyasparagine (R) [ N3H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.38000 3 OD1 O -0.38000 3 ND2 NT -0.83000 4 HD21 H 0.41500 4 HD22 H 0.41500 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_4 CG2 ND2 gb_8 ND2 HD21 gb_2 ND2 HD22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG2 ga_12 CA CB OG1 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_29 CB CG2 ND2 ga_18 OD1 CG2 ND2 ga_32 CG2 ND2 HD21 ga_22 CG2 ND2 HD22 ga_22 HD21 ND2 HD22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CG2 OG1 CA gi_2 CG2 OD1 ND2 CB gi_1 ND2 HD21 HD22 CG2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 ND2 gd_20 CB CG2 ND2 HD21 gd_4 ; 3-hydroxyasparagine (S) [ NH3 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 C 0.38000 3 OD1 O -0.38000 3 ND2 NT -0.83000 4 HD21 H 0.41500 4 HD22 H 0.41500 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_17 CB CG2 gb_26 OG1 HG1 gb_1 CG2 OD1 gb_4 CG2 ND2 gb_8 ND2 HD21 gb_2 ND2 HD22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG2 ga_12 CA CB OG1 ga_12 OG1 CB CG2 ga_12 CB OG1 HG1 ga_11 CB CG2 OD1 ga_29 CB CG2 ND2 ga_18 OD1 CG2 ND2 ga_32 CG2 ND2 HD21 ga_22 CG2 ND2 HD22 ga_22 HD21 ND2 HD22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 CG2 OD1 ND2 CB gi_1 ND2 HD21 HD22 CG2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 ND2 gd_20 CB CG2 ND2 HD21 gd_4 ; 4-carboxyglutamate (-2) [ ECA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH1 0.00000 1 CD1 C 0.27000 2 OE1 OM -0.63500 2 OE2 OM -0.63500 2 CD2 C 0.27000 3 ; from GLU OE3 OM -0.63500 3 ; from GLU OE4 OM -0.63500 3 ; from GLU C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_26 CD1 OE1 gb_5 CD1 OE2 gb_5 CG CD2 gb_26 CD2 OE3 gb_5 CD2 OE4 gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_12 CB CG CD2 ga_12 CD1 CG CD2 ga_12 CG CD1 OE1 ga_21 CG CD1 OE2 ga_21 OE1 CD1 OE2 ga_37 CG CD2 OE3 ga_21 CG CD2 OE4 ga_21 OE3 CD2 OE4 ga_37 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_2 CD1 OE1 OE2 CG gi_1 CD2 OE3 OE4 CG gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_17 CB CG CD1 OE2 gd_20 CB CG CD2 OE4 gd_20 ; 4-carboxyglutamate (-1) [ ECN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH1 0.00000 1 CD1 C 0.53000 2 ; from GLUH OE1 O -0.38000 2 ; from GLUH OE2 OA -0.54800 2 ; from GLUH HE2 H 0.39800 2 ; from GLUH CD2 C 0.27000 3 OE3 OM -0.63500 3 OE4 OM -0.63500 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_26 CD1 OE1 gb_4 CD1 OE2 gb_12 OE2 HE2 gb_1 CG CD2 gb_26 CD2 OE3 gb_5 CD2 OE4 gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_12 CB CG CD2 ga_12 CD1 CG CD2 ga_12 CG CD1 OE1 ga_29 CG CD1 OE2 ga_18 OE1 CD1 OE2 ga_32 CD1 OE2 HE2 ga_11 CG CD2 OE3 ga_21 CG CD2 OE4 ga_21 OE3 CD2 OE4 ga_37 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_2 CD1 OE1 OE2 CG gi_1 CD2 OE3 OE4 CG gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_17 CB CG CD1 OE2 gd_20 CG CD1 OE2 HE2 gd_3 CB CG CD2 OE4 gd_20 ; sulfotyrosine [ YSU ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C 0.15000 6 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) OH OA -0.36000 6 ; from the phosphate group of nucleotides (e.g. ATP) ST S 1.11500 6 ; to add up to -1 net charge OI1 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI2 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) OI3 OM -0.63500 6 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 CZ OH gb_12 OH ST gb_24 ST OI1 gb_24 ST OI2 gb_24 ST OI3 gb_24 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 HE1 HD1 CZ CD2 CE1 CD2 OH HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OH HE2 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CE1 CZ CE2 ga_26 CE1 CZ OH ga_26 CE2 CZ OH ga_26 CZ OH ST ga_11 OH ST OI1 ga_12 OH ST OI2 ga_12 OH ST OI3 ga_12 OI1 ST OI2 ga_12 OI1 ST OI3 ga_12 OI2 ST OI3 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ OH ST gd_2 CZ OH ST OI1 gd_20 ; dehydroalanine [ SDH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH0 0.00000 1 ; from aliphatic carbon atoms CB CH2 0.00000 1 ; from aliphatic carbon atoms C C 0.380 2 O O -0.380 2 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_9 ; a shorter bond type to mimic double bond properties [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_26 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_26 C CA CB ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 ; 2,3-didehydrobutyrine [ TDH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH0 0.00000 1 ; from aliphatic carbon atoms CB CH1 0.00000 2 ; from aliphatic carbon atoms CG CH3 0.00000 2 C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_9 ; a shorter bond type to mimic double bond properties CB CG gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_26 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_26 C CA CB ga_26 CA CB CG ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_4 ; 6-bromotryptophan [ WBR ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH2 C 0.05500 6 ; from 8-bromo-guanosine reported by Hritz and Oostenbrink. DOI:10.1021/jp902968m BRT BR -0.05500 6 ; from 8-bromo-guanosine reported by Hritz and Oostenbrink. DOI:10.1021/jp902968m C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 CH2 BRT gb_39 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ2 CD2 HZ3 CD2 CH2 NE1 CE3 NE1 HZ2 NE1 CH2 HE1 CZ2 CE2 HE3 CE2 CZ3 CE2 BRT CE3 CZ2 CE3 BRT HE3 HZ3 HE3 CH2 CZ2 HZ3 HZ2 CZ3 HZ2 BRT HZ3 BRT [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE3 CZ3 CH2 ga_26 CZ2 CH2 BRT ga_26 BRT CH2 CZ3 ga_26 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 HZ3 gi_1 CH2 CZ2 CZ3 BRT gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 ; S-nitrosocysteine [ CSN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 SG S 0.10000 2 ; to add up to 0 net charge ND NR 0.28000 2 ; to add up to 0 net charge OE O -0.38000 2 ; from the carbonyl group (of e.g. the peptide bond) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG ND gb_29 ; from MET ND OE gb_4 ; from the carbonyl group (of e.g. the peptide bond) [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG ND ga_5 SG ND OE ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG ND gd_13 CB SG ND OE gd_10 ; citrulline [ RCI ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 NE N -0.28000 3 HE H 0.28000 3 CZ C 0.38000 4 ; from ASN/GLN OH1 O -0.38000 4 ; from ASN/GLN NH2 NT -0.83000 5 ; from ASN/GLN HH21 H 0.41500 5 ; from ASN/GLN HH22 H 0.41500 5 ; from ASN/GLN C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD NE gb_20 NE HE gb_2 NE CZ gb_9 CZ OH1 gb_4 CZ NH2 gb_8 NH2 HH21 gb_2 NH2 HH22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD NE ga_12 CD NE HE ga_17 HE NE CZ ga_31 CD NE CZ ga_30 NE CZ OH1 ga_21 NE CZ NH2 ga_29 OH1 CZ NH2 ga_21 CZ NH2 HH21 ga_22 CZ NH2 HH22 ga_22 HH21 NH2 HH22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NE CD CZ HE gi_1 CZ OH1 NH2 NE gi_1 NH2 HH21 HH22 CZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD NE gd_17 CG CD NE CZ gd_19 CD NE CZ NH2 gd_4 NE CZ NH2 HH21 gd_4 ; allysine (aminoadipic semialdehyde) [ KAL ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE C 0.28000 3 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OZ O -0.38000 3 ; from the carbonyl group (of e.g. GLN) HE HC 0.10000 3 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE HE gb_3 CE OZ gb_4 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE HE ga_24 HE CE OZ ga_24 CD CE OZ ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CE OZ CD HE gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE OZ gd_20 ; N-acetylglucosamine (N4-linked to ASN) [ NNG ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.38000 2 OD1 O -0.38000 2 ND2 N -0.28000 3 HD2 H 0.28000 3 C1 CH1 0.18000 4 ; 0.36 charge divided between C1 and C5 to add up to 0 net charge, also used in other building blocks (e.g. TMP) O5 OA -0.36000 4 ; from carbohydrates (e.g. GALB) C5 CH1 0.18000 4 ; 0.36 charge divided between C1 and C5 to add up to 0 net charge, also used in other building blocks (e.g. TMP) C6 CH2 0.15000 5 ; from carbohydrates (e.g. GALB) O6 OA -0.54800 5 ; from carbohydrates (e.g. GALB) HO6 H 0.39800 5 ; from carbohydrates (e.g. GALB) C2 CH1 0.00000 6 ; from aliphatic carbon atoms C4 CH1 0.15000 7 ; from carbohydrates (e.g. GALB) O4 OA -0.54800 7 ; from carbohydrates (e.g. GALB) HO4 H 0.39800 7 ; from carbohydrates (e.g. GALB) C3 CH1 0.15000 8 ; from carbohydrates (e.g. GALB) O3 OA -0.54800 8 ; from carbohydrates (e.g. GALB) HO3 H 0.39800 8 ; from carbohydrates (e.g. GALB) N2 N -0.28000 9 ; from the peptide bond HN2 H 0.28000 9 ; from the peptide bond C7 C 0.28000 10 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 O7 O -0.38000 10 ; from the carbonyl group (of e.g. GLN) C8 CH3 0.10000 10 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 C C 0.380 11 O O -0.380 11 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG ND2 gb_9 ND2 HD2 gb_2 ND2 C1 gb_20 C1 O5 gb_19 O5 C5 gb_19 C5 C6 gb_25 C6 O6 gb_19 O6 HO6 gb_1 C5 C4 gb_25 C4 O4 gb_19 O4 HO4 gb_1 C4 C3 gb_25 C3 O3 gb_19 O3 HO3 gb_1 C3 C2 gb_25 C2 C1 gb_25 C2 N2 gb_20 N2 HN2 gb_2 N2 C7 gb_9 C7 O7 gb_4 C7 C8 gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_29 CB CG ND2 ga_18 OD1 CG ND2 ga_32 CG ND2 HD2 ga_31 CG ND2 C1 ga_30 C1 ND2 HD2 ga_17 ND2 C1 O5 ga_8 ND2 C1 C2 ga_8 O5 C1 C2 ga_8 C5 O5 C1 ga_9 O5 C5 C6 ga_8 O5 C5 C4 ga_8 C6 C5 C4 ga_7 C5 C6 O6 ga_8 C6 O6 HO6 ga_11 C5 C4 O4 ga_8 C5 C4 C3 ga_7 O4 C4 C3 ga_8 C4 O4 HO4 ga_11 C4 C3 O3 ga_8 C4 C3 C2 ga_7 C2 C3 O3 ga_8 C3 O3 HO3 ga_11 C3 C2 C1 ga_7 C3 C2 N2 ga_8 C1 C2 N2 ga_8 C2 N2 HN2 ga_17 C2 N2 C7 ga_30 HN2 N2 C7 ga_31 N2 C7 O7 ga_32 N2 C7 C8 ga_18 O7 C7 C8 ga_29 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG OD1 ND2 CB gi_1 ND2 CG C1 HD2 gi_1 C1 O5 ND2 C2 gi_2 C5 O5 C6 C4 gi_2 C2 N2 C3 C1 gi_2 C3 O3 C2 C4 gi_2 C4 C3 O4 C5 gi_2 N2 C7 C2 HN2 gi_1 C7 C8 N2 O7 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND2 gd_20 CB CG ND2 C1 gd_4 CG ND2 C1 O5 gd_19 ND2 C1 C2 C3 gd_17 ND2 C1 C2 C3 gd_7 O5 C1 C2 C3 gd_7 O5 C1 C2 N2 gd_8 ND2 C1 C2 N2 gd_8 C1 C2 N2 C7 gd_19 C2 N2 C7 C8 gd_4 C1 C2 C3 C4 gd_17 C1 C2 C3 O3 gd_7 N2 C2 C3 C4 gd_7 N2 C2 C3 O3 gd_8 C2 C3 O3 HO3 gd_12 C2 C3 C4 C5 gd_17 C2 C3 C4 O4 gd_7 O3 C3 C4 C5 gd_7 O3 C3 C4 O4 gd_8 C3 C4 O4 HO4 gd_12 C2 C1 O5 C5 gd_14 C1 O5 C5 C4 gd_14 C4 C5 C6 O6 gd_17 C4 C5 C6 O6 gd_7 O5 C5 C6 O6 gd_8 C5 C6 O6 HO6 gd_12 C6 C5 C4 C3 gd_17 O5 C5 C4 C3 gd_7 C6 C5 C4 O4 gd_7 O5 C5 C4 O4 gd_8 ; 2,3-dihydroxyphenylalanine [ F23 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C 0.15000 2 ; from the hydroxyl group of TYR OE3 OA -0.54800 2 ; from the hydroxyl group of TYR HE3 H 0.39800 2 ; from the hydroxyl group of TYR CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.15000 4 ; from the hydroxyl group of TYR OZ1 OA -0.54800 4 ; from the hydroxyl group of TYR HZ1 H 0.39800 4 ; from the hydroxyl group of TYR CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C -0.10000 6 HZ2 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 CE1 gb_15 CD1 OE3 gb_12 OE3 HE3 gb_1 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 CZ2 gb_15 CE1 OZ1 gb_12 OZ1 HZ1 gb_1 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 HZ2 gb_3 [ exclusions ] ; ai aj CB HD2 CB CE1 CB CE2 CB OE3 CG OZ1 CG HE2 CG CZ2 CD1 HD2 CD1 CE2 CD1 HZ2 CD2 CE1 CD2 OE3 CD2 HZ2 HD2 HE2 HD2 CZ2 CE1 HE2 CE2 OZ1 HE2 HZ2 OE3 CZ2 OE3 OZ1 HZ2 OZ1 OE3 HZ1 HE3 OZ1 HE3 HZ1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 CE1 ga_26 CG CD1 OE3 ga_26 CE1 CD1 OE3 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 CZ2 ga_26 CD1 CE1 OZ1 ga_26 CZ2 CE1 OZ1 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CD1 OE3 HE3 ga_11 CE1 CZ2 HZ2 ga_24 CE2 CZ2 HZ2 ga_24 CE1 CZ2 CE2 ga_26 CE1 OZ1 HZ1 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 OE3 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 OZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 HZ2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CG CD1 OE3 HE3 gd_2 CD1 CE1 OZ1 HZ1 gd_2 ; 2-hydroxyphenylalanine [ F2H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C 0.15000 2 ; from the hydroxyl group of TYR OE3 OA -0.54800 2 ; from the hydroxyl group of TYR HE3 H 0.39800 2 ; from the hydroxyl group of TYR CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C -0.10000 4 HE1 HC 0.10000 4 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ C -0.10000 6 HZ HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 OE3 gb_12 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 HE1 gb_3 CE1 CZ gb_15 CE2 HE2 gb_3 CE2 CZ gb_15 OE3 HE3 gb_1 CZ HZ gb_3 [ exclusions ] ; ai aj CB HD2 CB CE1 CB CE2 CB OE3 CG HE1 CG HE2 CG CZ CD1 HD2 CD1 CE2 CD1 HZ CD2 OE3 CD2 CE1 CD2 HZ HD2 HE2 HD2 CZ CE1 HE2 HE1 CE2 HE1 OE3 HE1 HZ HE2 HZ OE3 CZ [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 CE1 ga_26 CG CD1 OE3 ga_26 CE1 CD1 OE3 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 HE1 ga_24 HE1 CE1 CZ ga_24 CD1 CE1 CZ ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ ga_24 CD2 CE2 CZ ga_26 CD1 OE3 HE3 ga_11 CE1 CZ HZ ga_24 CE2 CZ HZ ga_24 CE1 CZ CE2 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ gi_1 CG CD2 CE2 CZ gi_1 CD1 CE1 CZ CE2 gi_1 CD2 CE2 CZ CE1 gi_1 CD1 CG CE1 OE3 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ CD1 HE1 gi_1 CE2 CZ CD2 HE2 gi_1 CZ CE1 CE2 HZ gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CG CD1 OE3 HE3 gd_2 ; 3-hydroxyphenylalanine [ F3H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.15000 4 ; from the hydroxyl group of TYR OZ1 OA -0.54800 4 ; from the hydroxyl group of TYR HZ1 H 0.39800 4 ; from the hydroxyl group of TYR CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C -0.10000 6 HZ2 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 CZ2 gb_15 CE1 OZ1 gb_12 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 HZ2 gb_3 OZ1 HZ1 gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE2 CG CZ2 CG OZ1 CD1 HD2 CD1 CE2 CD1 HZ2 HD1 CD2 HD1 CZ2 HD1 OZ1 CD2 CE1 CD2 HZ2 HD2 HE2 HD2 CZ2 CE1 HE2 CE2 OZ1 HE2 HZ2 HZ2 OZ1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 CZ2 ga_26 CD1 CE1 OZ1 ga_26 CZ2 CE1 OZ1 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 HZ2 ga_24 CE2 CZ2 HZ2 ga_24 CE1 CZ2 CE2 ga_26 CE1 OZ1 HZ1 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 OZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 HZ2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CD1 CE1 OZ1 HZ1 gd_2 ; 6-hydroxytryptophan [ W6H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH2 C 0.15000 6 ; from the hydroxyl group of TYR OI OA -0.54800 6 ; from the hydroxyl group of TYR HI H 0.39800 6 ; from the hydroxyl group of TYR C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 CH2 OI gb_12 OI HI gb_1 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ2 CD2 HZ3 CD2 CH2 NE1 CE3 NE1 HZ2 NE1 CH2 HE1 CZ2 CE2 HE3 CE2 CZ3 CE2 OI CE3 CZ2 CE3 OI HE3 HZ3 HE3 CH2 CZ2 HZ3 HZ2 CZ3 HZ2 OI HZ3 OI [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE3 CZ3 CH2 ga_26 CZ2 CH2 CZ3 ga_26 CZ2 CH2 OI ga_26 CZ3 CH2 OI ga_26 CH2 OI HI ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 HZ3 gi_1 CH2 CZ2 CZ3 OI gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CZ2 CH2 OI HI gd_2 ; 5-hydroxytryptophan [ W5H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C 0.15000 5 ; from the hydroxyl group of TYR OH3 OA -0.54800 5 ; from the hydroxyl group of TYR HH3 H 0.39800 5 ; from the hydroxyl group of TYR CH2 C -0.10000 6 HH2 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 CH2 gb_15 CZ3 OH3 gb_12 CH2 HH2 gb_3 OH3 HH3 gb_1 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ2 CD2 OH3 CD2 CH2 NE1 CE3 NE1 HZ2 NE1 CH2 HE1 CZ2 CE2 HE3 CE2 CZ3 CE2 HH2 CE3 CZ2 CE3 HH2 HE3 OH3 HE3 CH2 CZ2 OH3 HZ2 CZ3 HZ2 HH2 OH3 HH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 OH3 ga_26 CH2 CZ3 OH3 ga_26 CZ3 OH3 HH3 ga_11 CE3 CZ3 CH2 ga_26 CZ2 CH2 HH2 ga_24 HH2 CH2 CZ3 ga_24 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 OH3 gi_1 CH2 CZ2 CZ3 HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CE3 CZ3 OH3 HH3 gd_2 ; 4-hydroxytryptophan [ W4H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C 0.15000 3 ; from the hydroxyl group of TYR OZ4 OA -0.54800 3 ; from the hydroxyl group of TYR HZ4 H 0.39800 3 ; from the hydroxyl group of TYR CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH2 C -0.10000 6 HH2 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 OZ4 gb_12 CE3 CZ3 gb_15 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 OZ4 HZ4 gb_1 CH2 HH2 gb_3 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG CZ2 CG CZ3 CG OZ4 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ2 CD2 HZ3 CD2 CH2 NE1 CE3 NE1 HZ2 NE1 CH2 HE1 CZ2 CE2 CZ3 CE2 HH2 CE2 OZ4 CE3 CZ2 CE3 HH2 CZ2 HZ3 HZ2 CZ3 HZ2 HH2 HZ3 OZ4 HZ3 HH2 OZ4 CH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 CZ3 ga_26 CD2 CE3 OZ4 ga_26 CZ3 CE3 OZ4 ga_26 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE3 CZ3 CH2 ga_26 CE3 OZ4 HZ4 ga_11 CZ2 CH2 HH2 ga_24 HH2 CH2 CZ3 ga_24 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 OZ4 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 HZ3 gi_1 CH2 CZ2 CZ3 HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CD2 CE3 OZ4 HZ4 gd_2 ; 2-hydroxytryptophan [ W2H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C 0.15000 2 ; from the hydroxyl group of TYR OE4 OA -0.54800 2 ; from the hydroxyl group of TYR HE4 H 0.39800 2 ; from the hydroxyl group of TYR CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH2 C -0.10000 6 HH2 HC 0.10000 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 OE4 gb_12 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 OE4 HE4 gb_1 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 CH2 HH2 gb_3 [ exclusions ] ; ai aj CB NE1 CB CE2 CB CE3 CB OE4 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 CD2 HE1 CD2 OE4 CD2 HZ2 CD2 HZ3 CD2 CH2 NE1 CE3 NE1 HE4 NE1 HZ2 NE1 CH2 HE1 OE4 HE1 CZ2 CE2 HE3 CE2 OE4 CE2 CZ3 CE2 HH2 CE3 CZ2 CE3 HH2 HE3 HZ3 HE3 CH2 CZ2 HZ3 HZ2 CZ3 HZ2 HH2 HZ3 HH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 NE1 ga_6 CG CD1 OE4 ga_36 NE1 CD1 OE4 ga_36 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CD1 OE4 HE4 ga_11 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE3 CZ3 CH2 ga_26 CZ2 CH2 HH2 ga_24 HH2 CH2 CZ3 ga_24 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 OE4 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 HZ3 gi_1 CH2 CZ2 CZ3 HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CG CD1 OE4 HE4 gd_2 ; 3-hydroxyleucine (R) [ L3H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 CH1 0.00000 3 CD1 CH3 0.00000 3 CD2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG2 gb_26 CB OG1 gb_17 OG1 HG1 gb_1 CG2 CD1 gb_26 CG2 CD2 gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB CG2 CD1 ga_14 CB CG2 CD2 ga_14 CD1 CG2 CD2 ga_14 CB OG1 HG1 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_2 CG2 CD2 CD1 CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 CD1 gd_17 ; 3-hydroxyleucine (S) [ LH3 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH1 0.15000 2 ; from the hydroxyl group of THR OG1 OA -0.54800 2 ; from the hydroxyl group of THR HG1 H 0.39800 2 ; from the hydroxyl group of THR CG2 CH1 0.00000 3 CD1 CH3 0.00000 3 CD2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG2 gb_26 CB OG1 gb_17 OG1 HG1 gb_1 CG2 CD1 gb_26 CG2 CD2 gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_12 CA CB CG2 ga_12 OG1 CB CG2 ga_12 CB CG2 CD1 ga_14 CB CG2 CD2 ga_14 CD1 CG2 CD2 ga_14 CB OG1 HG1 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB CG2 OG1 CA gi_2 CG2 CD2 CD1 CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG2 gd_17 CA CB OG1 HG1 gd_12 CA CB CG2 CD1 gd_17 ; 4-hydroxyleucine [ L4H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH0 0.15000 2 ; from the hydroxyl group of THR OD3 OA -0.54800 2 ; from the hydroxyl group of THR HD3 H 0.39800 2 ; from the hydroxyl group of THR CD1 CH3 0.00000 3 CD2 CH3 0.00000 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_26 CG CD2 gb_26 CG OD3 gb_17 OD3 HD3 gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_12 CB CG CD2 ga_12 CB CG OD3 ga_12 CD1 CG CD2 ga_12 CD1 CG OD3 ga_12 CD2 CG OD3 ga_12 CG OD3 HD3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG OD3 gd_17 CB CG OD3 HD3 gd_12 ; 5-hydroxyleucine (R) [ L5H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH1 0.00000 2 CD1 CH3 0.00000 2 CD2 CH2 0.15000 3 ; from the hydroxyl group of THR OE OA -0.54800 3 ; from the hydroxyl group of THR HE H 0.39800 3 ; from the hydroxyl group of THR C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_26 CG CD2 gb_26 CD2 OE gb_17 OE HE gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_14 CB CG CD2 ga_14 CD1 CG CD2 ga_14 CG CD2 OE ga_12 CD2 OE HE ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD2 CD1 CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_17 CB CG CD2 OE gd_17 CG CD2 OE HE gd_12 ; 5-hydroxyleucine (S) [ LH5 ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH1 0.00000 2 CD1 CH3 0.00000 2 CD2 CH2 0.15000 3 ; from the hydroxyl group of THR OE OA -0.54800 3 ; from the hydroxyl group of THR HE H 0.39800 3 ; from the hydroxyl group of THR C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_26 CG CD2 gb_26 CD2 OE gb_17 OE HE gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_14 CB CG CD2 ga_14 CD1 CG CD2 ga_14 CG CD2 OE ga_12 CD2 OE HE ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_17 CB CG CD2 OE gd_17 CG CD2 OE HE gd_12 ; 3-hyroxyvaline [ V3H ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH0 0.15000 2 ; from the hydroxyl group of THR OG3 OA -0.54800 2 ; from the hydroxyl group of THR HG3 H 0.39800 2 ; from the hydroxyl group of THR CG1 CH3 0.00000 3 CG2 CH3 0.00000 4 C C 0.380 5 O O -0.380 5 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG1 gb_26 CB CG2 gb_26 CB OG3 gb_17 OG3 HG3 gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG1 ga_12 CA CB CG2 ga_12 CA CB OG3 ga_12 CG1 CB CG2 ga_12 CG1 CB OG3 ga_12 CG2 CB OG3 ga_12 CB OG3 HG3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG3 gd_17 CA CB OG3 HG3 gd_12 ; cysteine sulfenic acid [ CYH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 SG S 0.15000 2 ; from the hydroxyl group of THR OD OA -0.54800 2 ; from the hydroxyl group of THR HD H 0.39800 2 ; from the hydroxyl group of THR C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG OD gb_27 OD HD gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG OD ga_12 SG OD HD ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG OD gd_13 CB SG OD HD gd_12 ; 5-hydroxyproline (R) [ PH5 ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE OA -0.54800 3 ; from the hydroxyl group of THR HE H 0.39800 3 ; from the hydroxyl group of THR C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE gb_17 OE HE gb_1 CD N gb_20 [ exclusions ] ; ai aj N HE [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_12 CB CG CD ga_12 CG CD OE ga_12 CG CD N ga_12 OE CD N ga_12 CD OE HE ga_11 CD N CA ga_20 -C N CD ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD gi_1 C CA +N O gi_1 CA N C CB gi_2 CD CG N OE gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD N gd_17 CG CD OE HE gd_12 CG CD N CA gd_19 ; 5-hydroxyproline (S) [ P5H ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH1 0.15000 3 ; from the hydroxyl group of THR OE OA -0.54800 3 ; from the hydroxyl group of THR HE H 0.39800 3 ; from the hydroxyl group of THR C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE gb_17 OE HE gb_1 CD N gb_20 [ exclusions ] ; ai aj N HE [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_12 CB CG CD ga_12 CG CD OE ga_12 CG CD N ga_12 OE CD N ga_12 CD OE HE ga_11 CD N CA ga_20 -C N CD ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD gi_1 C CA +N O gi_1 CA N C CB gi_2 CD N CG OE gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD N gd_17 CG CD OE HE gd_12 CG CD N CA gd_19 ; glutamic semialdehyde [ GSA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 CD C 0.28000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 HD HC 0.10000 2 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OE O -0.38000 2 ; from the carbonyl group (of e.g. GLN) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD HD gb_3 CD OE gb_4 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD HD ga_24 HD CD OE ga_24 CG CD OE ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD OE CG HD gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD OE gd_20 ; 2-amino-3-ketobutyric acid [ TOX ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB C 0.38000 2 ; from the carbonyl group (of e.g. GLN) OG1 O -0.38000 2 ; from the carbonyl group (of e.g. GLN) CG2 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB OG1 gb_4 CB CG2 gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB OG1 ga_26 CA CB CG2 ga_26 OG1 CB CG2 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CB OG1 CG2 CA gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB OG1 gd_20 ; pyroglutamic acid [ PGA ] [ atoms ] N N 0.00000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD C 0.38000 3 ; from the carbonyl group (of e.g. GLN) OE O -0.38000 3 ; from the carbonyl group (of e.g. GLN) C C 0.380 4 O O -0.380 4 [ bonds ] N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD OE gb_4 CD N gb_9 [ angles ] ; ai aj ak gromos type -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_12 CB CG CD ga_12 CG CD N ga_18 CG CD OE ga_29 N CD OE ga_32 CD N CA ga_20 -C N CD ga_30 [ impropers ] ; ai aj ak al gromos type N -C CA CD gi_1 C CA +N O gi_1 CA N C CB gi_2 CD CG N OE gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD N gd_20 CG CD N CA gd_4 ; 2-oxo-histidine [ H2X ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 2 ND1 NR -0.28000 3 HD1 H 0.28000 3 CD2 CR1 0.00000 4 NE2 NR -0.28000 5 HE2 H 0.28000 5 CE1 C 0.38000 6 ; from the carbonyl group (of e.g. GLN) OZ O -0.38000 6 ; from the carbonyl group (of e.g. GLN) C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG ND1 gb_9 CG CD2 gb_9 ND1 HD1 gb_2 ND1 CE1 gb_9 CD2 NE2 gb_9 CE1 NE2 gb_9 CE1 OZ gb_4 NE2 HE2 gb_2 [ exclusions ] ; ai aj CB HD1 CB CE1 CB NE2 CG HE2 CG OZ HD1 CD2 HD1 NE2 HD1 OZ ND1 HE2 CD2 OZ HE2 OZ [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG ND1 ga_36 CB CG CD2 ga_36 ND1 CG CD2 ga_6 CG ND1 HD1 ga_35 CG ND1 CE1 ga_6 HD1 ND1 CE1 ga_35 CG CD2 NE2 ga_6 ND1 CE1 NE2 ga_6 ND1 CE1 OZ ga_36 NE2 CE1 OZ ga_36 CD2 NE2 CE1 ga_6 CD2 NE2 HE2 ga_35 CE1 NE2 HE2 ga_35 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG ND1 CD2 CB gi_1 CD2 CG ND1 CE1 gi_1 ND1 CG CD2 NE2 gi_1 ND1 CG CE1 HD1 gi_1 CG ND1 CE1 NE2 gi_1 CG CD2 NE2 CE1 gi_1 CD2 NE2 CE1 ND1 gi_1 CE1 OZ NE2 ND1 gi_1 NE2 CD2 CE1 HE2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG ND1 gd_20 ; methionine sulfoxide (R) [ MSX ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 SD S 0.38000 2 ; to add up to 0 net charge OE2 O -0.38000 2 ; from the carbonyl group (e.g. GLN) CE1 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG SD gb_30 SD CE1 gb_30 SD OE2 gb_24 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG SD ga_15 CG SD CE1 ga_3 CG SD OE2 ga_5 CE1 SD OE2 ga_5 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 SD OE2 CE1 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG SD gd_17 CB CG SD CE1 gd_13 ; methionine sulfoxide (S) [ MXS ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 SD S 0.38000 2 ; to add up to 0 net charge OE2 O -0.38000 2 ; from the carbonyl group (e.g. GLN) CE1 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG SD gb_30 SD CE1 gb_30 SD OE2 gb_24 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG SD ga_15 CG SD CE1 ga_3 CG SD OE2 ga_5 CE1 SD OE2 ga_5 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 SD CE1 OE2 CG gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG SD gd_17 CB CG SD CE1 gd_13 ; methionine sulfone [ MES ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 1 SD S 0.72000 2 ; to add up to 0 net charge OE2 O -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) OE3 O -0.36000 2 ; from the phosphate group of nucleotides (e.g. ATP) CE1 CH3 0.00000 3 C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG SD gb_30 SD CE1 gb_29 SD OE2 gb_24 SD OE3 gb_24 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG SD ga_15 CG SD CE1 ga_12 CG SD OE2 ga_12 CG SD OE3 ga_12 OE2 SD OE3 ga_12 CE1 SD OE2 ga_12 CE1 SD OE3 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG SD gd_17 CB CG SD CE1 gd_13 ; cysteine sulfinic acid [ CSA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) SG S 0.12000 2 ; to add up to -1 net charge OD1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OD2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG OD1 gb_24 SG OD2 gb_24 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG OD1 ga_5 OD1 SG OD2 ga_5 CB SG OD2 ga_5 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 SG CB OD1 OD2 gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG OD1 gd_13 ; cysteic acid [ CSE ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.15000 2 ; from the carbon atom attached to the phosphate group of nucleotides (e.g. ATP) SG S 0.75500 2 ; to add up to -1 net charge OD1 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OD2 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) OD3 OM -0.63500 2 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG OD1 gb_24 SG OD2 gb_24 SG OD3 gb_24 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG OD1 ga_12 OD1 SG OD2 ga_12 CB SG OD2 ga_12 CB SG OD3 ga_12 OD1 SG OD3 ga_12 OD2 SG OD3 ga_12 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG OD1 gd_13 ; 3-nitrotyrosine (-1) [ YNI ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.10000 4 ; to add up to -1 net charge NZ1 NR 0.05500 4 ; to add up to -1 net charge OH1 O -0.36000 4 ; from the phosphate group of nucleotides (e.g. ATP) OH2 O -0.36000 4 ; from the phosphate group of nucleotides (e.g. ATP) CZ2 C 0.20000 4 ; to add up to -1 net charge OH3 OM -0.63500 4 ; from the carboxyl group (of e.g. GLU) CE2 C -0.10000 5 HE2 HC 0.10000 5 C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 NZ1 gb_11 NZ1 OH1 gb_5 NZ1 OH2 gb_5 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 OH3 gb_12 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE2 CG NZ1 CG CZ2 CD1 HD2 CD1 CE2 CD1 OH3 HD1 CD2 HD1 NZ1 HD1 CZ2 CD2 CE1 CD2 OH3 HD2 HE2 HD2 CZ2 CE1 HE2 HE2 OH3 NZ1 CE2 NZ1 OH3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 NZ1 ga_26 CD1 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CE1 NZ1 OH1 ga_26 CE1 NZ1 OH2 ga_26 OH1 NZ1 OH2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 CE2 ga_26 CE1 CZ2 OH3 ga_26 CE2 CZ2 OH3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 NZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 OH3 gi_1 NZ1 CE1 OH1 OH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ2 OH3 HH3 gd_2 CD1 CE1 NZ1 OH1 gd_4 ; 3-nitrotyrosine (0) [ YNN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.10000 4 ; newly developed parameters tp match the experimental HFE NZ1 NR 0.30000 4 ; newly developed parameters tp match the experimental HFE OH1 O -0.20000 4 ; newly developed parameters tp match the experimental HFE OH2 O -0.20000 4 ; newly developed parameters tp match the experimental HFE CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C 0.05000 6 ; newly developed parameters tp match the experimental HFE OH3 OA -0.36000 6 ; newly developed parameters tp match the experimental HFE HH3 H 0.31000 6 ; newly developed parameters tp match the experimental HFE C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 NZ1 gb_11 NZ1 OH1 gb_5 NZ1 OH2 gb_5 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 OH3 gb_12 OH3 HH3 gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE2 CG NZ1 CG CZ2 CD1 HD2 CD1 CE2 CD1 OH3 HD1 CD2 HD1 NZ1 HD1 CZ2 CD2 CE1 CD2 OH3 HD2 HE2 HD2 CZ2 CE1 HE2 HE2 OH3 NZ1 CE2 NZ1 OH3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 NZ1 ga_26 CD1 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CE1 NZ1 OH1 ga_26 CE1 NZ1 OH2 ga_26 OH1 NZ1 OH2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 CE2 ga_26 CE1 CZ2 OH3 ga_26 CE2 CZ2 OH3 ga_26 CZ2 OH3 HH3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 NZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 OH3 gi_1 NZ1 CE1 OH1 OH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ2 OH3 HH3 gd_2 CD1 CE1 NZ1 OH1 gd_4 ; 3-nitrotyrosine (0) [ YNB ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.10000 4 ; to add up to 0 net charge NZ1 NR 0.62000 4 ; to add up to 0 net charge OH1 O -0.36000 4 ; from the phosphate group of nucleotides (e.g. ATP) OH2 O -0.36000 4 ; from the phosphate group of nucleotides (e.g. ATP) CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C 0.15000 6 OH3 OA -0.54800 6 HH3 H 0.39800 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 NZ1 gb_11 NZ1 OH1 gb_5 NZ1 OH2 gb_5 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 OH3 gb_12 OH3 HH3 gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE2 CG NZ1 CG CZ2 CD1 HD2 CD1 CE2 CD1 OH3 HD1 CD2 HD1 NZ1 HD1 CZ2 CD2 CE1 CD2 OH3 HD2 HE2 HD2 CZ2 CE1 HE2 HE2 OH3 NZ1 CE2 NZ1 OH3 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 NZ1 ga_26 CD1 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CE1 NZ1 OH1 ga_26 CE1 NZ1 OH2 ga_26 OH1 NZ1 OH2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 CE2 ga_26 CE1 CZ2 OH3 ga_26 CE2 CZ2 OH3 ga_26 CZ2 OH3 HH3 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 NZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 OH3 gi_1 NZ1 CE1 OH1 OH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ2 OH3 HH3 gd_2 CD1 CE1 NZ1 OH1 gd_4 ; 6-nitrotryptophan [ WNI ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C -0.14000 2 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C 0.00000 2 NE1 NR -0.05000 2 HE1 H 0.19000 2 CE2 C 0.00000 2 CE3 C -0.10000 3 HE3 HC 0.10000 3 CZ2 C -0.10000 4 HZ2 HC 0.10000 4 CZ3 C -0.10000 5 HZ3 HC 0.10000 5 CH2 C 0.10000 6 ; to add up to 0 net charge NT NR 0.62000 6 ; to add up to 0 net charge OI1 O -0.36000 6 ; from the phosphate group of nucleotides (e.g. ATP) OI2 O -0.36000 6 ; from the phosphate group of nucleotides (e.g. ATP) C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_9 CG CD2 gb_15 CD1 HD1 gb_3 CD1 NE1 gb_9 CD2 CE2 gb_15 CD2 CE3 gb_15 NE1 HE1 gb_2 NE1 CE2 gb_9 CE2 CZ2 gb_15 CE3 HE3 gb_3 CE3 CZ3 gb_15 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 CH2 NT gb_11 NT OI1 gb_5 NT OI2 gb_5 [ exclusions ] ; ai aj CB HD1 CB NE1 CB CE2 CB CE3 CG HE1 CG HE3 CG CZ2 CG CZ3 CD1 CE3 CD1 CZ2 HD1 CD2 HD1 HE1 HD1 CE2 CD2 HE1 CD2 HZ2 CD2 HZ3 CD2 CH2 NE1 CE3 NE1 HZ2 NE1 CH2 HE1 CZ2 CE2 HE3 CE2 CZ3 CE2 NT CE3 CZ2 CE3 NT HE3 HZ3 HE3 CH2 CZ2 HZ3 HZ2 CZ3 HZ2 NT HZ3 NT [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_36 CB CG CD2 ga_36 CD1 CG CD2 ga_6 CG CD1 HD1 ga_35 HD1 CD1 NE1 ga_35 CG CD1 NE1 ga_6 CG CD2 CE2 ga_6 CD1 NE1 CE2 ga_6 CD1 NE1 HE1 ga_35 HE1 NE1 CE2 ga_35 NE1 CE2 CD2 ga_6 CG CD2 CE3 ga_38 NE1 CE2 CZ2 ga_38 CD2 CE2 CZ2 ga_26 CE2 CD2 CE3 ga_26 CD2 CE3 HE3 ga_24 HE3 CE3 CZ3 ga_24 CD2 CE3 CZ3 ga_26 CE2 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE2 CZ2 CH2 ga_26 CE3 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE3 CZ3 CH2 ga_26 CZ2 CH2 CZ3 ga_26 CZ2 CH2 NT ga_26 CZ3 CH2 NT ga_26 CH2 NT OI1 ga_26 CH2 NT OI2 ga_26 OI1 NT OI2 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 NE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 NE1 CE2 gi_1 CG CD2 CE2 NE1 gi_1 CD1 NE1 CE2 CD2 gi_1 CD1 CG NE1 HD1 gi_1 NE1 CD1 CE2 HE1 gi_1 CD2 CE2 CE3 CG gi_1 CE2 CD2 CZ2 NE1 gi_1 CE3 CD2 CE2 CZ2 gi_1 CD2 CE2 CZ2 CH2 gi_1 CE2 CD2 CE3 CZ3 gi_1 CE2 CZ2 CH2 CZ3 gi_1 CD2 CE3 CZ3 CH2 gi_1 CE3 CZ3 CH2 CZ2 gi_1 CE3 CD2 CZ3 HE3 gi_1 CZ2 CE2 CH2 HZ2 gi_1 CZ3 CE3 CH2 HZ3 gi_1 CH2 CZ2 CZ3 NT gi_1 NT OI1 OI2 CH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CZ2 CH2 NT OI1 gd_4 ; kynurenine [ WKY ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.38000 2 OD1 O -0.38000 2 CD2 C 0.00000 3 CE1 C 0.00000 3 NZ1 NT -0.83000 4 ; from ARGN HZ11 H 0.41500 4 ; from ARGN HZ12 H 0.41500 4 ; from ARGN CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C -0.10000 6 HZ2 HC 0.10000 6 CZ3 C -0.10000 7 HZ3 HC 0.10000 7 CH C -0.10000 8 HH HC 0.10000 8 C C 0.380 9 O O -0.380 9 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG CD2 gb_22 CD2 CE1 gb_15 CD2 CE2 gb_15 CE1 NZ1 gb_8 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ3 gb_15 NZ1 HZ11 gb_2 NZ1 HZ12 gb_2 CZ2 HZ2 gb_3 CZ2 CH gb_15 CZ3 HZ3 gb_3 CZ3 CH gb_15 CH HH gb_3 [ exclusions ] ; ai aj CB CE1 CB CE2 CG NZ1 CG HE2 CG CZ2 CG CZ3 CD2 HZ11 CD2 HZ12 CD2 HZ2 CD2 HZ3 CD2 CH CE1 HE2 CE1 CZ3 CE1 HH CE2 CZ2 CE2 HH HE2 HZ3 HE2 CH NZ1 CE2 NZ1 HZ2 NZ1 CH HZ11 CZ2 HZ12 CZ2 CZ2 HZ3 HZ2 CZ3 HZ2 HH HZ3 HH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_26 CB CG CD2 ga_26 OD1 CG CD2 ga_26 CG CD2 CE1 ga_26 CG CD2 CE2 ga_26 CE1 CD2 CE2 ga_26 CD2 CE1 NZ1 ga_26 CD2 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ3 ga_24 CD2 CE2 CZ3 ga_26 CE1 NZ1 HZ11 ga_22 CE1 NZ1 HZ12 ga_22 HZ11 NZ1 HZ12 ga_23 CE1 CZ2 HZ2 ga_24 HZ2 CZ2 CH ga_24 CE1 CZ2 CH ga_26 CE2 CZ3 HZ3 ga_24 HZ3 CZ3 CH ga_24 CE2 CZ3 CH ga_26 CZ2 CH HH ga_24 CZ3 CH HH ga_24 CZ2 CH CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD2 OD1 CB gi_1 CD2 CE1 CE2 CG gi_1 CE2 CD2 CE1 CZ2 gi_1 CE1 CD2 CE2 CZ3 gi_1 CD2 CE1 CZ2 CH gi_1 CD2 CE2 CZ3 CH gi_1 CE1 CZ2 CH CZ3 gi_1 CE2 CZ3 CH CZ2 gi_1 CE1 CD2 CZ2 NZ1 gi_1 CE2 CD2 CZ3 HE2 gi_1 NZ1 HZ11 HZ12 CE1 gi_1 CZ2 CH CE1 HZ2 gi_1 CZ3 CH CE2 HZ3 gi_1 CH CZ2 CZ3 HH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CB CG CD2 CE1 gd_1 CD2 CE1 NZ1 HZ11 gd_4 ; 3-hydroxykynurenine [ WKH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.38000 2 OD1 O -0.38000 2 CD2 C 0.00000 3 CE1 C 0.00000 3 NZ1 NT -0.83000 4 ; from ARGN HZ11 H 0.41500 4 ; from ARGN HZ12 H 0.41500 4 ; from ARGN CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C 0.15000 6 ; from the hydroxyl group of TYR OH1 OA -0.54800 6 ; from the hydroxyl group of TYR HH1 H 0.39800 6 ; from the hydroxyl group of TYR CZ3 C -0.10000 7 HZ3 HC 0.10000 7 CH2 C -0.10000 8 HH2 HC 0.10000 8 C C 0.380 9 O O -0.380 9 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG CD2 gb_22 CD2 CE1 gb_15 CD2 CE2 gb_15 CE1 NZ1 gb_8 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ3 gb_15 NZ1 HZ11 gb_2 NZ1 HZ12 gb_2 CZ2 OH1 gb_12 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 OH1 HH1 gb_1 CH2 HH2 gb_3 [ exclusions ] ; ai aj CB CE1 CB CE2 CG HE2 CG NZ1 CG CZ2 CG CZ3 CD2 HZ11 CD2 HZ12 CD2 HZ3 CD2 OH1 CD2 CH2 CE1 HE2 CE1 CZ3 CE1 HH1 CE1 HH2 CE2 CZ2 CE2 HH2 HE2 HZ3 HE2 CH2 NZ1 CE2 NZ1 OH1 NZ1 HH1 NZ1 CH2 HZ11 CZ2 HZ11 OH1 HZ12 CZ2 HZ12 OH1 CZ2 HZ3 HZ3 HH2 OH1 CZ3 OH1 HH2 HH1 CH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_26 CB CG CD2 ga_26 OD1 CG CD2 ga_26 CG CD2 CE1 ga_26 CG CD2 CE2 ga_26 CE1 CD2 CE2 ga_26 CD2 CE1 NZ1 ga_26 CD2 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ3 ga_24 CD2 CE2 CZ3 ga_26 CE1 NZ1 HZ11 ga_22 CE1 NZ1 HZ12 ga_22 HZ11 NZ1 HZ12 ga_23 CE1 CZ2 OH1 ga_26 CE1 CZ2 CH2 ga_26 OH1 CZ2 CH2 ga_26 CE2 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE2 CZ3 CH2 ga_26 CZ2 OH1 HH1 ga_11 CZ2 CH2 HH2 ga_24 CZ3 CH2 HH2 ga_24 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD2 OD1 CB gi_1 CD2 CE1 CE2 CG gi_1 CE2 CD2 CE1 CZ2 gi_1 CE1 CD2 CE2 CZ3 gi_1 CD2 CE1 CZ2 CH2 gi_1 CD2 CE2 CZ3 CH2 gi_1 CE1 CZ2 CH2 CZ3 gi_1 CE2 CZ3 CH2 CZ2 gi_1 CE1 CD2 CZ2 NZ1 gi_1 CE2 CD2 CZ3 HE2 gi_1 NZ1 HZ11 HZ12 CE1 gi_1 CZ2 CH2 CE1 OH1 gi_1 CZ3 CH2 CE2 HZ3 gi_1 CH2 CZ2 CZ3 HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CB CG CD2 CE1 gd_1 CD2 CE1 NZ1 HZ11 gd_4 CE1 CZ2 OH1 HH1 gd_2 ; formyl-kynurenine [ WKF ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.38000 2 OD1 O -0.38000 2 CD2 C 0.00000 3 CE1 C 0.00000 3 NZ1 N -0.28000 4 ; from the peptide bond HZ1 H 0.28000 4 ; from the peptide bond CH1 C 0.28000 5 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 HH1 HC 0.10000 5 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 OI O -0.38000 5 ; from the carbonyl group (of e.g. GLN) CE2 C -0.10000 6 HE2 HC 0.10000 6 CZ2 C -0.10000 7 HZ2 HC 0.10000 7 CZ3 C -0.10000 8 HZ3 HC 0.10000 8 CH2 C -0.10000 9 HH2 HC 0.10000 9 C C 0.380 10 O O -0.380 10 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG OD1 gb_4 CG CD2 gb_22 CD2 CE1 gb_15 CD2 CE2 gb_15 CE1 NZ1 gb_8 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ3 gb_15 NZ1 HZ1 gb_2 NZ1 CH1 gb_9 CZ2 HZ2 gb_3 CZ2 CH2 gb_15 CZ3 HZ3 gb_3 CZ3 CH2 gb_15 CH1 HH1 gb_3 CH1 OI gb_4 CH2 HH2 gb_3 [ exclusions ] ; ai aj CB CE1 CB CE2 CG NZ1 CG HE2 CG CZ2 CG CZ3 CD2 HZ1 CD2 HZ2 CD2 HZ3 CD2 CH2 CE1 HE2 CE1 CZ3 CE1 HH2 CE2 CZ2 CE2 HH2 HE2 HZ3 HE2 CH2 NZ1 CE2 NZ1 HZ2 NZ1 CH2 HZ1 CZ2 CZ2 HZ3 HZ2 CZ3 HZ2 HH2 HZ3 HH2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG OD1 ga_26 CB CG CD2 ga_26 OD1 CG CD2 ga_26 CG CD2 CE1 ga_26 CG CD2 CE2 ga_26 CE1 CD2 CE2 ga_26 CD2 CE1 NZ1 ga_26 CD2 CE1 CZ2 ga_26 NZ1 CE1 CZ2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ3 ga_24 CD2 CE2 CZ3 ga_26 CE1 NZ1 HZ1 ga_17 HZ1 NZ1 CH1 ga_31 CE1 NZ1 CH1 ga_30 CE1 CZ2 HZ2 ga_24 HZ2 CZ2 CH2 ga_24 CE1 CZ2 CH2 ga_26 CE2 CZ3 HZ3 ga_24 HZ3 CZ3 CH2 ga_24 CE2 CZ3 CH2 ga_26 NZ1 CH1 HH1 ga_18 HH1 CH1 OI ga_29 NZ1 CH1 OI ga_32 CZ2 CH2 HH2 ga_24 CZ3 CH2 HH2 ga_24 CZ2 CH2 CZ3 ga_26 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD2 OD1 CB gi_1 CD2 CE1 CE2 CG gi_1 CE2 CD2 CE1 CZ2 gi_1 CE1 CD2 CE2 CZ3 gi_1 CD2 CE1 CZ2 CH2 gi_1 CD2 CE2 CZ3 CH2 gi_1 CE1 CZ2 CH2 CZ3 gi_1 CE2 CZ3 CH2 CZ2 gi_1 CE1 CD2 CZ2 NZ1 gi_1 CE2 CD2 CZ3 HE2 gi_1 NZ1 CH1 CE1 HZ1 gi_1 CZ2 CH2 CE1 HZ2 gi_1 CZ3 CH2 CE2 HZ3 gi_1 CH1 OI NZ1 HH1 gi_1 CH2 CZ2 CZ3 HH2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD2 gd_20 CB CG CD2 CE1 gd_1 CD2 CE1 NZ1 CH1 gd_4 CE1 NZ1 CH1 OI gd_4 ; chlorotyrosine [ YCH ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG C 0.00000 1 CD1 C -0.10000 2 HD1 HC 0.10000 2 CD2 C -0.10000 3 HD2 HC 0.10000 3 CE1 C 0.08700 4 ; from CHCL3 CLZ1 CL -0.08700 4 ; from CHCL3 CE2 C -0.10000 5 HE2 HC 0.10000 5 CZ2 C 0.15000 6 OH OA -0.54800 6 HH H 0.39800 6 C C 0.380 7 O O -0.380 7 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD1 gb_15 CG CD2 gb_15 CD1 HD1 gb_3 CD1 CE1 gb_15 CD2 HD2 gb_3 CD2 CE2 gb_15 CE1 CLZ1 gb_37 CE1 CZ2 gb_15 CE2 HE2 gb_3 CE2 CZ2 gb_15 CZ2 OH gb_12 OH HH gb_1 [ exclusions ] ; ai aj CB HD1 CB HD2 CB CE1 CB CE2 CG HE2 CG CLZ1 CG CZ2 CD1 HD2 CD1 CE2 CD1 OH HD1 CD2 HD1 CLZ1 HD1 CZ2 CD2 CE1 CD2 OH HD2 HE2 HD2 CZ2 CE1 HE2 HE2 OH CLZ1 CE2 CLZ1 OH [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD1 ga_26 CB CG CD2 ga_26 CD1 CG CD2 ga_26 CG CD1 HD1 ga_24 HD1 CD1 CE1 ga_24 CG CD1 CE1 ga_26 CG CD2 HD2 ga_24 HD2 CD2 CE2 ga_24 CG CD2 CE2 ga_26 CD1 CE1 CLZ1 ga_26 CD1 CE1 CZ2 ga_26 CLZ1 CE1 CZ2 ga_26 CD2 CE2 HE2 ga_24 HE2 CE2 CZ2 ga_24 CD2 CE2 CZ2 ga_26 CE1 CZ2 CE2 ga_26 CE1 CZ2 OH ga_26 CE2 CZ2 OH ga_26 CZ2 OH HH ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CG CD1 CD2 CB gi_1 CD2 CG CD1 CE1 gi_1 CD1 CG CD2 CE2 gi_1 CG CD1 CE1 CZ2 gi_1 CG CD2 CE2 CZ2 gi_1 CD1 CE1 CZ2 CE2 gi_1 CD2 CE2 CZ2 CE1 gi_1 CD1 CG CE1 HD1 gi_1 CD2 CG CE2 HD2 gi_1 CE1 CZ2 CD1 CLZ1 gi_1 CE2 CZ2 CD2 HE2 gi_1 CZ2 CE1 CE2 OH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD1 gd_20 CE1 CZ2 OH HH gd_2 ; homocitrulline [ KAM ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 2 NZ N -0.28000 3 ; from the peptide bond HZ H 0.28000 3 ; from the peptide bond CH C 0.38000 4 ; from ASN/GLN OI1 O -0.38000 4 ; from ASN/GLN NI2 NT -0.83000 5 ; from ASN/GLN HI21 H 0.41500 5 ; from ASN/GLN HI22 H 0.41500 5 ; from ASN/GLN C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH gb_9 CH OI1 gb_4 CH NI2 gb_8 NI2 HI21 gb_2 NI2 HI22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_17 CE NZ CH ga_30 HZ NZ CH ga_31 NZ CH OI1 ga_29 NZ CH NI2 ga_21 OI1 CH NI2 ga_29 CH NI2 HI21 ga_22 CH NI2 HI22 ga_22 HI21 NI2 HI22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CH CE HZ gi_1 CH NI2 OI1 NZ gi_1 NI2 HI21 HI22 CH gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_19 CE NZ CH NI2 gd_4 NZ CH NI2 HI21 gd_4 ; carboxylysine (-1) [ KCA ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ N -0.28000 4 ; from the peptide bond HZ H 0.28000 4 ; from the peptide bond CH C 0.27000 5 ; from the carboxyl group (of e.g. GLU) OI1 OM -0.63500 5 ; from the carboxyl group (of e.g. GLU) OI2 OM -0.63500 5 ; from the carboxyl group (of e.g. GLU) C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH gb_9 CH OI1 gb_5 CH OI2 gb_5 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_17 CE NZ CH ga_30 HZ NZ CH ga_31 NZ CH OI1 ga_21 NZ CH OI2 ga_21 OI1 CH OI2 ga_37 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CH CE HZ gi_1 CH NZ OI1 OI2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_19 CE NZ CH OI1 gd_4 ; carboxylysine (0) [ KCN ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 CG CH2 0.00000 2 CD CH2 0.00000 2 CE CH2 0.00000 3 NZ N -0.28000 4 ; from the peptide bond HZ H 0.28000 4 ; from the peptide bond CH C 0.53000 5 ; from the carboxyl group (of e.g. GLUH) OI1 O -0.38000 5 ; from the carboxyl group (of e.g. GLUH) OI2 OA -0.54800 5 ; from the carboxyl group (of e.g. GLUH) HI2 H 0.39800 5 ; from the carboxyl group (of e.g. GLUH) C C 0.380 6 O O -0.380 6 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 CE NZ gb_20 NZ HZ gb_2 NZ CH gb_9 CH OI1 gb_4 CH OI2 gb_12 OI2 HI2 gb_1 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 CD CE NZ ga_14 CE NZ HZ ga_17 CE NZ CH ga_30 HZ NZ CH ga_31 NZ CH OI1 ga_30 NZ CH OI2 ga_20 OI1 CH OI2 ga_30 CH OI2 HI2 ga_11 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 NZ CH HZ CE gi_1 CH NZ OI1 OI2 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 CG CD CE NZ gd_17 CD CE NZ CH gd_19 CE NZ CH OI2 gd_4 NZ CH OI2 HI2 gd_3 ; S-carbamoyl-cysteine [ CAM ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 SG S 0.00000 1 CD C 0.38000 2 ; from ASN/GLN OE1 O -0.38000 2 ; from ASN/GLN NE2 NT -0.83000 3 ; from ASN/GLN HE21 H 0.41500 3 ; from ASN/GLN HE22 H 0.41500 3 ; from ASN/GLN C C 0.380 4 O O -0.380 4 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB SG gb_30 SG CD gb_30 CD OE1 gb_4 CD NE2 gb_8 NE2 HE21 gb_2 NE2 HE22 gb_2 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB SG ga_15 CB SG CD ga_3 SG CD OE1 ga_29 SG CD NE2 ga_18 OE1 CD NE2 ga_32 CD NE2 HE21 ga_22 CD NE2 HE22 ga_22 HE21 NE2 HE22 ga_23 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 CD NE2 OE1 SG gi_1 NE2 CD HE21 HE22 gi_1 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB SG gd_17 CA CB SG CD gd_13 CB SG CD NE2 gd_20 SG CD NE2 HE21 gd_4 ; norleucine [ LNO ] [ atoms ] N N -0.28000 0 H H 0.28000 0 CA CH1 0.00000 1 CB CH2 0.00000 1 ; from aliphatic carbon atoms CG CH2 0.00000 1 ; from aliphatic carbon atoms CD CH2 0.00000 2 ; from aliphatic carbon atoms CE CH3 0.00000 2 ; from aliphatic carbon atoms C C 0.380 3 O O -0.380 3 [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 C +N gb_9 CA CB gb_26 CB CG gb_26 CG CD gb_26 CD CE gb_26 [ angles ] ; ai aj ak gromos type -C N H ga_31 H N CA ga_17 -C N CA ga_30 N CA C ga_12 CA C +N ga_18 CA C O ga_29 O C +N ga_32 N CA CB ga_12 C CA CB ga_12 CA CB CG ga_14 CB CG CD ga_14 CG CD CE ga_14 [ impropers ] ; ai aj ak al gromos type N -C CA H gi_1 C CA +N O gi_1 CA N C CB gi_2 [ dihedrals ] ; ai aj ak al gromos type -CA -C N CA gd_4 -C N CA C gd_19 N CA C +N gd_20 N CA CB CG gd_17 CA CB CG CD gd_17 CB CG CD CE gd_17 ; pyruvic acid (N-terminal modification) [ PYA ] [ atoms ] CA C 0.380 0 ; from the carbonyl group (of e.g. GLN) OB2 O -0.380 0 ; from the carbonyl group (of e.g. GLN) CB1 CH3 0.00000 1 ; from aliphatic carbon atoms C C 0.380 2 O O -0.380 2 [ bonds ] CA C gb_22 ; shorter bond type to account for double bond effect CA OB2 gb_4 C O gb_4 C +N gb_9 CA CB1 gb_26 [ angles ] ; ai aj ak gromos type CA C +N ga_18 CA C O ga_29 O C +N ga_32 C CA CB1 ga_26 C CA OB2 ga_26 OB2 CA CB1 ga_26 [ impropers ] ; ai aj ak al gromos type C CA +N O gi_1 CA OB2 C CB1 gi_1 [ dihedrals ] ; ai aj ak al gromos type CB1 CA C +N gd_4 ; aminoacids.n.tdb file (N-terminal parameters) ; N-methyl-AA (0) [ 1NM ] [ replace ] N NT 14.0067 -0.83 ; from NZ of LYS CA CH1 13.019 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 1 H1 N CA C H 1.008 0.410 ; derived from terminal hydrogen atoms of LYS 1 4 CN1 N CA C CH3 15.035 0.210 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N CN1 gb_20 [ angles ] CN1 N H1 ga_10 CA N H1 ga_10 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-methyl-glycine (0) [ GLY-1NM ] [ replace ] N NT 14.0067 -0.83 ; from NZ of LYS CA CH2 14.027 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 1 H1 N CA C H 1.008 0.410 ; derived from terminal hydrogen atoms of LYS 1 4 CN1 N CA C CH3 15.035 0.210 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N CN1 gb_20 [ angles ] CN1 N H1 ga_10 CA N H1 ga_10 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-methyl-proline (0) [ PRO-1NM ] [ replace ] N NT 14.0067 -0.63 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CA CH1 13.019 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CD CH2 14.027 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 4 CN1 N CA C CH3 15.035 0.210 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ bonds ] N CN1 gb_20 [ angles ] CA N CN1 ga_12 CD N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-methyl-AA (+1) [ 1NM+ ] [ replace ] N NL 14.0067 0.104 ; to add up to +1 net charge CA CH1 13.019 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 2 4 H N CA C H 1.008 0.248 1 1 CN1 N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N H2 gb_2 N CN1 gb_20 [ angles ] H1 N H2 ga_9 H2 N CN1 ga_10 CN1 N H1 ga_10 CA N H1 ga_10 CA N H2 ga_10 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-methyl-glycine (+1) [ GLY-1NM+ ] [ replace ] N NL 14.0067 0.104 ; to add up to +1 net charge CA CH2 14.027 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 2 4 H N CA C H 1.008 0.248 1 1 CN1 N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N H2 gb_2 N CN1 gb_20 [ angles ] H1 N H2 ga_9 H2 N CN1 ga_10 CN1 N H1 ga_10 CA N H1 ga_10 CA N H2 ga_10 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-methyl-proline (+1) [ PRO-1NM+ ] [ replace ] N NL 14.0067 0.152 ; to add up to +1 net charge CA CH1 13.019 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CD CH2 14.027 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 4 H N CA C H 1.008 0.248 1 1 CN1 N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ bonds ] N H gb_2 N CN1 gb_20 [ angles ] H N CD ga_10 CD N CN1 ga_12 CN1 N H ga_10 CA N H ga_10 CA N CD ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N-dimethyl-AA (0) [ 2NM ] [ replace ] N NT 14.0067 -0.63 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CA CH1 13.019 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 2 4 CN N CA C CH3 15.035 0.210 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N CN1 gb_20 N CN2 gb_20 [ angles ] CN1 N CN2 ga_12 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N-dimethyl-glycine (0) [ GLY-2NM ] [ replace ] N NT 14.0067 -0.63 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CA CH2 14.027 0.210 0 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 2 4 CN N CA C CH3 15.035 0.210 ; from trimethylamine reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N CN1 gb_20 N CN2 gb_20 [ angles ] CN1 N CN2 ga_12 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N-dimethyl-AA (+1) [ 2NM+ ] [ replace ] N NL 14.0067 0.152 ; to add up to +1 net charge CA CH1 13.019 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 1 H1 N CA C H 1.008 0.248 2 4 CN N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N CN1 gb_20 N CN2 gb_20 [ angles ] CN1 N H1 ga_10 CN1 N CN2 ga_12 CN2 N H1 ga_10 CA N H1 ga_10 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N-dimethyl-glycine (+1) [ GLY-2NM+ ] [ replace ] N NL 14.0067 0.152 ; to add up to +1 net charge CA CH2 14.027 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 1 1 H1 N CA C H 1.008 0.248 2 4 CN N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N H1 gb_2 N CN1 gb_20 N CN2 gb_20 [ angles ] CN1 N H1 ga_10 CN1 N CN2 ga_12 CN2 N H1 ga_10 CA N H1 ga_10 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N-dimethyl-proline (+1) [ PRO-2NM+ ] [ replace ] N NL 14.0067 0.200 ; to add up to +1 net charge CA CH1 13.019 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 CD CH2 14.027 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 2 4 CN N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ bonds ] N CN1 gb_20 N CN2 gb_20 [ angles ] CN1 N CD ga_12 CN1 N CN2 ga_12 CN2 N CD ga_12 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N,N-trimethyl-AA (+1) [ 3NM+ ] [ replace ] N NL 14.0067 0.200 ; to add up to +1 net charge CA CH1 13.019 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 3 4 CN N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N CN1 gb_20 N CN2 gb_20 N CN3 gb_20 [ angles ] CN1 N CN3 ga_12 CN1 N CN2 ga_12 CN2 N CN3 ga_12 CA N CN3 ga_12 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N,N,N-trimethyl-glycine (+1) [ GLY-3NM+ ] [ replace ] N NL 14.0067 0.200 ; to add up to +1 net charge CA CH2 14.027 0.200 0 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ add ] 3 4 CN N CA C CH3 15.035 0.200 ; derived by analogy to methyl groups of amines reported by Oostenbrink et al. DOI: 10.1002/cphc.200400542 [ delete ] H [ bonds ] N CN1 gb_20 N CN2 gb_20 N CN3 gb_20 [ angles ] CN1 N CN3 ga_12 CN1 N CN2 ga_12 CN2 N CN3 ga_12 CA N CN3 ga_12 CA N CN2 ga_12 CA N CN1 ga_12 [ dihedrals ] CN1 N CA C gd_14 ; N-acetyl-AA [ NAC ] [ add ] 1 2 H N C CA H 1.008 0.2800 ; from the peptide bond 1 1 CN1 N C CA C 12.011 0.2800 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 1 2 ON2 N CA C O 15.9994 -0.3800 ; from the carbonyl group (of e.g. GLU) 1 2 CN2 N C CA CH3 15.035 0.1000 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 [ bonds ] N H gb_2 N CN1 gb_9 CN1 ON2 gb_4 CN1 CN2 gb_26 [ angles ] CA N H ga_17 CN1 N H ga_31 CN1 N CA ga_30 N CN1 ON2 ga_32 N CN1 CN2 ga_18 CN2 CN1 ON2 ga_29 [ impropers ] N CN1 CA H gi_1 CN1 CN2 N ON2 gi_1 [ dihedrals ] CN2 CN1 N CA gd_4 CN1 N CA C gd_19 ; N-acetyl-proline [ PRO-NAC ] [ add ] 1 1 CN1 N C CA C 12.011 0.3800 ; from the carbonyl group (of e.g. GLU) 1 2 ON2 N CA C O 15.9994 -0.2800 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 1 2 CN2 N C CA CH3 15.035 0.1000 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 [ bonds ] N CN1 gb_9 CN1 ON2 gb_4 CN1 CN2 gb_26 [ angles ] CN1 N CD ga_30 CN1 N CA ga_30 N CN1 ON2 ga_32 N CN1 CN2 ga_18 CN2 CN1 ON2 ga_29 [ impropers ] N CN1 CA CD gi_1 CN1 CN2 N ON2 gi_1 [ dihedrals ] CN2 CN1 N CA gd_4 CN1 N CA C gd_19 ; pyroglutamic acid [ PGA-NH ] [ replace ] N N 14.0067 -0.28 [ add ] 1 1 H N CA CD H 1.008 0.28 [ bonds ] N H gb_2 [ angles ] CA N H ga_30 CD N H ga_30 [ impropers ] N CA CD H gi_1 [ dihedrals ] CD N CA C gd_19 ; N-formylmethionine [ MET-FOR ] [ add ] 1 2 H N C CA H 1.008 0.28 ; from the peptide bond 1 1 CN1 N C CA C 12.011 0.2800 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 1 2 ON2 N CA C O 15.9994 -0.3800 ; from the carbonyl group (of e.g. GLU) 1 2 HN1 N C CA H 1.008 0.1 ; by analogy to the aldehyde group reported by Dolenc et al. DOI: 10.1093/nar/gki195 [ bonds ] N H gb_2 N CN1 gb_9 CN1 ON2 gb_4 CN1 HN1 gb_3 [ angles ] CA N H ga_17 CA N CN1 ga_30 H N CN1 ga_31 N CN1 ON2 ga_32 N CN1 HN1 ga_18 ON2 CN1 HN1 ga_29 [ impropers ] N CN1 CA H gi_1 CN1 N ON2 HN1 gi_1 [ dihedrals ] ON2 CN1 N CA gd_4 CN1 N CA C gd_19 ; aminoacids.c.tdb file (C-terminal parameters) ; AA-amide [ AMD ] [ add ] 1 2 NC1 C CA N NT 14.00670 -0.8300 ; from ASN/GLN 1 1 HC11 C O N H 1.008 0.4150 ; from ASN/GLN 1 1 HC12 C N O H 1.008 0.4150 ; from ASN/GLN [ bonds ] C NC1 gb_8 NC1 HC11 gb_2 NC1 HC12 gb_2 [ angles ] O C NC1 ga_32 CA C O ga_29 CA C NC1 ga_18 C NC1 HC11 ga_22 C NC1 HC12 ga_22 HC11 NC1 HC12 ga_23 [ impropers ] C CA O NC1 gi_1 NC1 C HC11 HC12 gi_1 [ dihedrals ] N CA C NC1 gd_20 CA C NC1 HC11 gd_4 ; AA-methyl ester [ CME ] [ replace ] C C 12.011 0.56 ; from the carbonyl group (of e.g. GLU) with the partial charge increased by 0.18 - see the comment of CC2 atom O OA 15.9994 -0.36 ; from the ring oxygen atom of nucleotides (e.g. ATP) [ add ] 1 2 OC1 C CA N O 15.9994 -0.38 ; from the carbonyl group (of e.g. GLU) 1 2 CC2 O C CA CH3 15.035 0.18 ; 0.36 charge divided between CG and CE to add up to 0 net charge, similar to methyl groups of other methylation residues and also used in other building blocks (e.g. TMP) [ bonds ] C O gb_12 C OC1 gb_4 O CC2 gb_17 [ angles ] O C OC1 ga_32 C O CC2 ga_11 CA C O ga_18 CA C OC1 ga_29 [ dihedrals ] N CA C O gd_20 CA C O CC2 gd_3 [ impropers ] C CA OC1 O gi_1 ; aminoacids.hdb file (hydrogen databese) ; phosphoserine (-1) S1P 2 1 1 H N -C CA 1 2 HE3 OE3 PD OG ; phosphoserine (-2) S2P 1 1 1 H N -C CA ; phosphothreonine (-1) T1P 2 1 1 H N -C CA 1 2 HE3 OE3 PD OG1 ; phosphothreonine (-2) T2P 1 1 1 H N -C CA ; phosphotyrosine (-1) Y1P 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 2 HI3 OI3 PT OH ; phosphotyrosine (-2) Y2P 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ ; phosphoaspartate (-1) D1P 2 1 1 H N -C CA 1 2 HZ3 OZ3 PE OD2 ; phosphoaspartate (-2) D2P 1 1 1 H N -C CA ; phospholysine (-1) K1P 3 1 1 H N -C CA 1 1 HZ NZ PH CE 1 2 HI3 OI3 PH NZ ; phospholysine (-2) K2P 2 1 1 H N -C CA 1 1 HZ NZ PH CE ; phosphoarginine (0) R0P 5 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE 1 1 HH2 NH2 PT CZ 1 2 HI3 OI3 PT NH2 ; phosphoarginine (-1) R1P 4 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE 1 1 HH2 NH2 PT CZ ; 1-phosphohistidine (-1) H11 2 1 1 H N -C CA 1 2 HH3 OH3 PZ NE2 ; 1-phosphohistidine (-2) H12 1 1 1 H N -C CA ; 3-phosphohistidine (-1) H31 2 1 1 H N -C CA 1 2 HZ3 OZ3 PE3 ND1 ; 3-phosphohistidine (-2) H32 1 1 1 H N -C CA ; N6-methyllysine (0) KMN 2 1 1 H N -C CA 1 2 HZ NZ CE CD ; N6-methyllysine (+1) KMC 2 1 1 H N -C CA 2 4 HZ NZ CE CD ; N6,N6-dimethyllysine (0) K2M 1 1 1 H N -C CA ; N6,N6-dimethyllysine (+1) K2C 2 1 1 H N -C CA 1 2 HZ NZ CE CD ; N6,N6,N6-trimethyllysine K3C 1 1 1 H N -C CA ; omega-N-methylarginine (0) RMN 3 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH2 NH2 CZ NE ; omega-N-methylarginine (+1) RMC 4 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE 1 1 HH2 NH2 CT CZ ; symmetric-dimethylarginine (0) RSM 3 1 1 H N -C CA 1 1 HE NE CD CZ 1 1 HH2 NH2 CT2 CZ ; symmetric-dimethylarginine (+1) RMS 4 1 1 H N -C CA 1 1 HE NE CD CZ 1 1 HH1 NH1 CT1 CZ 1 1 HH2 NH2 CT2 CZ ; asymmetric-dimethylarginine (0) RAM 3 1 1 H N -C CA 1 1 HE NE CD CZ 1 2 HH1 NH1 CZ NE ; asymmetric-dimethylarginine (+1) RMA 3 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH1 NH1 CZ NE ; 1-methylhistidine (0) H1M 1 1 1 H N -C CA ; 1-methylhistidine (+1) H1C 2 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 ; 3-methylhistidine (0) H3M 1 1 1 H N -C CA ; 3-methylhistidine (+1) H3C 2 1 1 H N -C CA 1 1 HE2 NE2 CE1 CD2 ; N5-methylglutamine QME 2 1 1 H N -C CA 1 1 HE2 NE2 CZ CD ; N4-methylasparagine NME 2 1 1 H N -C CA 1 1 HD2 ND2 CE CG ; glutamate methyl ester EME 1 1 1 H N -C CA ; aspartate methyl ester DMA 1 1 1 H N -C CA ; S-methylcysteine CYM 1 1 1 H N -C CA ; N6-acetyllysine KAC 2 1 1 H N -C CA 1 1 HZ NZ CE CH ; 3-hydroxyproline (R) PH3 1 1 2 HG1 OG1 CB CA ; 3-hydroxyproline (S) P3H 1 1 2 HG1 OG1 CB CA ; 4-hydroxyproline (S) HY2 1 1 2 HD1 OD1 CG CB ; 3,4-dihydroxyproline PHH 2 1 2 HG1 OG1 CB CA 1 2 HD1 OD1 CG2 CB ; 5-hydroxylysine (0,R) KH5 3 1 1 H N -C CA 1 2 HE1 OE1 CD CB 2 4 HZ NZ CE2 CD ; 5-hydroxylysine (0,S) K5H 3 1 1 H N -C CA 1 2 HE1 OE1 CD CB 2 4 HZ NZ CE2 CD ; 5-hydroxylysine (+1,R) KPH 3 1 1 H N -C CA 1 2 HE1 OE1 CD CB 3 4 HZ NZ CE2 CD ; 5-hydroxylysine (+1,S) KHP 3 1 1 H N -C CA 1 2 HE1 OE1 CD CB 3 4 HZ NZ CE2 CD ; 3,4-dihydroxyphenylalanine HTY 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 2 HZ1 OZ1 CE1 CD1 1 1 HE2 CE2 CD2 CZ2 1 2 HH OH CZ2 CE1 ; 7-hydroxytryptophan W7H 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH3 1 1 HH3 CH3 CZ3 CZ2 1 2 HH2 OH2 CZ2 CE2 ; 3-hydroxyaspartate (-1,R) DH3 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA ; 3-hydroxyaspartate (-1,S) D3H 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA ; 3-hydroxyaspartate (0,R) DN3 3 1 1 H N -C CA 1 2 HG1 OG1 CB CA 1 2 HD2 OD2 CG2 CB ; 3-hydroxyaspartate (0,S) D3N 3 1 1 H N -C CA 1 2 HG1 OG1 CB CA 1 2 HD2 OD2 CG2 CB ; 3-hydroxyasparagine (R) N3H 3 1 1 H N -C CA 1 2 HG1 OG1 CB CA 2 3 HD2 ND2 CG2 CB ; 3-hydroxyasparagine (S) NH3 3 1 1 H N -C CA 1 2 HG1 OG1 CB CA 2 3 HD2 ND2 CG2 CB ; 4-carboxyglutamate (-2) ECA 1 1 1 H N -C CA ; 4-carboxyglutamate (-1) ECN 2 1 1 H N -C CA 1 2 HE2 OE2 CD1 CG ; sulfotyrosine YSU 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ ; dehydroalanine SDH 1 1 1 H N -C CA ; 2,3-didehydrobutyrine TDH 1 1 1 H N -C CA ; 6-bromotryptophan WBR 6 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 1 HZ2 CZ2 CE2 CH2 ; S-nitrosocysteine CSN 1 1 1 H N -C CA ; citrulline RCI 3 1 1 H N -C CA 1 1 HE NE CD CZ 2 3 HH2 NH2 CZ NE ; allysine (aminoadipic semialdehyde) KAL 2 1 1 H N -C CA 1 1 HE CE OZ CD ; N-acetylglucosamine (N4-linked to ASN) NNG 6 1 1 H N -C CA 1 1 HD2 ND2 CG C1 1 1 HN2 N2 C7 C2 1 2 HO3 O3 C3 C2 1 2 HO4 O4 C4 C3 1 2 HO6 O6 C6 C5 ; 2,3-dihydroxyphenylalanine F23 6 1 1 H N -C CA 1 2 HE3 OE3 CD1 CG 1 1 HD2 CD2 CG CE2 1 2 HZ1 OZ1 CE1 CD1 1 1 HE2 CE2 CD2 CZ2 1 1 HZ2 CZ2 CE1 CE2 ; 2-hydroxyphenylalanine F2H 6 1 1 H N -C CA 1 2 HE3 OE3 CD1 CG 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 ; 3-hydroxyphenylalanine F3H 6 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 2 HZ1 OZ1 CE1 CD1 1 1 HE2 CE2 CD2 CZ2 1 1 HZ2 CZ2 CE1 CE2 ; 6-hydroxytryptophan W6H 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 2 HI OI CH2 CZ2 1 1 HZ2 CZ2 CE2 CH2 ; 5-hydroxytryptophan W5H 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 2 HH3 OH3 CZ3 CE2 1 1 HH2 CH2 CZ3 CZ2 1 1 HZ2 CZ2 CE2 CH2 ; 4-hydroxytryptophan W4H 7 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 2 HZ4 OZ4 CE3 CD2 1 1 HZ3 CZ3 CE3 CH2 1 1 HH2 CH2 CZ3 CZ2 1 1 HZ2 CZ2 CE2 CH2 ; 2-hydroxytryptophan W2H 7 1 1 H N -C CA 1 2 HE4 OE4 CD1 CG 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 1 HH2 CH2 CZ3 CZ2 1 1 HZ2 CZ2 CE2 CH2 ; 3-hydroxyleucine (R) L3H 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA ; 3-hydroxyleucine (S) LH3 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA ; 4-hydroxyleucine L4H 2 1 1 H N -C CA 1 2 HD3 OD3 CG CB ; 5-hydroxyleucine (R) L5H 2 1 1 H N -C CA 1 2 HE OE CD2 CG ; 5-hydroxyleucine (S) LH5 2 1 1 H N -C CA 1 2 HE OE CD2 CG ; 3-hyroxyvaline V3H 2 1 1 H N -C CA 1 2 HG3 OG3 CB CA ; cysteine sulfenic acid CYH 2 1 1 H N -C CA 1 2 HD OD SG CB ; 5-hydroxyproline (R) PH5 1 1 2 HE OE CD CG ; 5-hydroxyproline (S) P5H 1 1 2 HE OE CD CG ; glutamic semialdehyde GSA 2 1 1 H N -C CA 1 1 HD CD OE CG ; 2-amino-3-ketobutyric acid TOX 1 1 1 H N -C CA ; 2-oxo-histidine H2X 3 1 1 H N -C CA 1 1 HD1 ND1 CG CE1 1 1 HE2 NE2 CE1 CD2 ; methionine sulfoxide (R) MSX 1 1 1 H N -C CA ; methionine sulfoxide (S) MXS 1 1 1 H N -C CA ; methionine sulfone MES 1 1 1 H N -C CA ; cysteine sulfinic acid CSA 1 1 1 H N -C CA ; cysteic acid CSE 1 1 1 H N -C CA ; 3-nitrotyrosine (-1) YNI 4 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE2 CE2 CD2 CZ2 ; 3-nitrotyrosine (0) YNN 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE2 CE2 CD2 CZ2 1 2 HH3 OH3 CZ2 CE1 ; 3-nitrotyrosine (0) YNB 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE2 CE2 CD2 CZ2 1 2 HH3 OH3 CZ2 CE1 ; 6-nitrotryptophan WNI 6 1 1 H N -C CA 1 1 HD1 CD1 CG NE1 1 1 HE1 NE1 CD1 CE2 1 1 HE3 CE3 CD2 CZ3 1 1 HZ3 CZ3 CE3 CH2 1 1 HZ2 CZ2 CE2 CH2 ; kynurenine WKY 6 1 1 H N -C CA 1 1 HE2 CE2 CD2 CZ3 2 3 HZ1 NZ1 CE1 CD2 1 1 HZ2 CZ2 CE1 CH 1 1 HZ3 CZ3 CE2 CH 1 1 HH CH CZ2 CZ3 ; 3-hydroxykynurenine WKH 6 1 1 H N -C CA 1 1 HE2 CE2 CD2 CZ3 2 3 HZ1 NZ1 CE1 CD2 1 1 HZ3 CZ3 CE2 CH2 1 2 HH1 OH1 CZ2 CE1 1 1 HH2 CH2 CZ2 CZ3 ; formyl-kynurenine WKF 7 1 1 H N -C CA 1 1 HE2 CE2 CD2 CZ3 1 1 HZ1 NZ1 CE1 CH1 1 1 HZ2 CZ2 CE1 CH2 1 1 HZ3 CZ3 CE2 CH2 1 1 HH1 CH1 NZ1 OI 1 1 HH2 CH2 CZ2 CZ3 ; chlorotyrosine YCH 5 1 1 H N -C CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE2 CE2 CD2 CZ2 1 2 HH OH CZ2 CE1 ; homocitrulline KAM 3 1 1 H N -C CA 1 1 HZ NZ CH CE 2 4 HI2 NI2 CH NZ ; carboxylysine (-1) KCA 2 1 1 H N -C CA 1 1 HZ NZ CH CE ; carboxylysine (0) KCN 3 1 1 H N -C CA 1 1 HZ NZ CH CE 1 2 HI2 OI2 CH NZ ; S-carbamoyl-cysteine CAM 2 1 1 H N -C CA 2 3 HE2 NE2 CD SG ; norleucine LNO 1 1 1 H N -C CA