In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target
Fig 2
A score that uses a Morse potential (Eq 3) was implemented for scoring the flexibility of the ligand inside the pocket using MD simulations. The input variable is the standard deviation of the RMSD of the ligand’s atomic positions around the binding site. Ligands that show large RMSD variations are considered very flexible -with dissociation tendencies (i.e., unstable)- and their behavior is penalized (right of vertical black dashed arrow). Ligands with small RMSD fluctuations are considered rigid leading to a conformational penalization (left of black vertical dashed arrow). The Morse potential was implemented with a force constant k = 1 kcal/mol.nm2, a depth of the well of ω = 1 kcal/mol, and the minimum is localized at r0 = 0.242 Å.