2.2. Induced Fit Docking

IFD was performed using the module Induced Fit Docking of Maestro v9.1. (Schrodinger, LLC). The entire receptor molecule constrained and minimized with an RMSD cutoff of 0.18 Å, which was selected for generation of the centroid of the residues and the box size was generated automatically. The initial Glide docking for each ligand was carried out. The side chains were trimmed automatically based on the B-factor, with receptor and ligand van der Waals scaling from 0.70 to 0.50, respectively. The number of poses generated was set to be 20. The prime side-chain prediction and minimization were carried out in which residues were refined within 5.0 Å of ligand poses and side chains were optimized. This leads to a ligand structure and conformation that is induced to fit to each pose of the receptor structure. Lastly, Glide XP redocking was carried out into structures within 30.0 kcal/mol of the best structure, and within the top 20 structures overall. The ligand was rigorously docked into the induced-fit receptor structure and the results yielded an IFD score for each output pose.