Figure 4
From: Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
(A) RMSD of rubraxanthone binding at Mpro and Mpro/substrate complex allosteric sites and corresponding RMSD clustering on last 400 ns trajectories. (B) MM/GBSA per-residue decomposition free energy (\(\Delta {\text{G }}_{{{\text{bind}}}}^{{{\text{residue}}}}\)) for rubraxanthone binding in top two Mpro and Mpro/substrate complex clusters (A-1 and -2 and S-1 and -2, respectively). Residues responsible for ligand binding with \(\Delta {\text{G }}_{{{\text{bind}}}}^{{{\text{residue}}}}\) ≤ − 1 kcal/mol and/or hydrogen bonding are depicted in right figure panel.
