Figure 7
From: Promising SARS-CoV-2 main protease inhibitor ligand-binding modes evaluated using LB-PaCS-MD/FMO
(A) RMSD, Rg, hydrogen bonding, and dcom of rubraxanthone active-site binding plotted as functions of simulation time. Ligand distribution and top three clusters (P3, P5, and P7), as determined from FMO-based RMSD clustering, are shown above and below plots, respectively. (B) MM/GBSA-calculated binding free energy (\(\Delta {\text{G}} _{{{\text{bind}}}}^{{\text{MM/GBSA}}}\)) and energy components for rubraxanthone binding in P3, P5, and P7 clusters are represented by black circles and bar graphs, respectively.
