Figure 4.

Analysis of MD simulations of MMP−13 complexed with various ligands occupying S1′-site: (A) Structures of ligands used for MD simulations; a–f are scaffolds of ligands, and the complete 2−D structures of ligands are present in Table S4.; (B) A data plot of pIC₅₀ vs. binding affinities calculated from MM/GBSA; (C) RMSD of MD simulations of MMP−13 complexed with C99, C100, C101, and C102; (D) The offset π−π stacking interactions of benzene and fluorobenzene obtained from QM calculations; (E) The F252 energy decomposition analyses of MMP−13 complexed with C99−C110 via MM/GBSA calculations; (F) The shift of C103 (green) in the S1′−site due to additional H−bond interactions.