Fig. 8. RMSD distributions for the three protonation state groups from simulations of the ketoamide-bound structure (PDB entry 6Y2G). (A–C) RMSD of (A) protein, (B) active site, and (C) inhibitor for Group 1. (D–F) RMSD of (D) protein, (E) active site, and (F) inhibitor for Group 2. (G–I) RMSD of (G) protein, (H) active site, and (I) inhibitor for Group 3.
