Fig. 3.

The equilibrium structure of the SARS-CoV-2 Mpro + inhibitor in the rPBC box was used as the initial conformation of the FPL calculation. In particular, pulling force versus displacement of nirmatrelvir over unbinding pathways (A), in which four colors imply the various trajectories; The SARS-CoV-2 Mpro + inhibitor in dPBC box was relaxed over MD simulations, in which all-atom RMSD of the complex SARS-CoV-2 Mpro + nirmatrelvir over 4 MD trajectories (B); (C) Superposition between experimental (gray) and SMD-initial (green) structures of SARS-CoV-2 Mpro + nirmatrelvir; (D) Superposition between experimental (gray) and MD-refined (blue) structures of SARS-CoV-2 Mpro + nirmatrelvir. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)