Fig. 3.
Molecular dynamics simulation data analysis for O6K-Mpro, 8-Mpro, and 9-Mpro complexes. (A), (B), (C), and (D) show the RMSD, RoG, SASA, and H-bonds for the O6K-Mpro (blue), 8-Mpro (orange), and 9-Mpro (gray) complexes versus the simulation time in ns. (E) shows the per-residue RMSF from the two chains A (upper) and B (lower) of Mpro in the Apo form (red), O6K-Mpro complex (blue), 8-Mpro complex (orange), and 9-Mpro complex (gray). Active dyads and high fluctuating regions are marked on the curves as illustrated in the text. (F) The ligands RMSD (Å) versus the simulation time (ns) for the dynamics of O6K-Mpro (blue), 8-Mpro (orange), and 9-Mpro (gray) complexes.