2.5 Binding free energy
Eventually, a thorough analysis of the binding free energy (∆Gbind) of all selected scaffolds was carried out using Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) protocol by the g-mmpbsa package [15]. MM-PBSA analysis gives a detailed estimation of the binding affinity of protein-ligand interaction. To calculate the total ∆Gbind, the free polar solvation energy, SASA energy, and potential energy (Van der Waals and electrostatic interactions) of each protein-ligand complex were analyzed.