Figure 4.

Joint distribution of the dihedral angles along the ethyl and isobutyl groups of compounds (A) 1d and (B) 1e, as well as the root-mean-square deviations of the substrate (RMSD), during 30 ns molecular dynamics simulations of each compound in complex with wild-type AMDase in preparation for subsequent EVB simulations. In the case of the dihedral angles, the C1–C2–C3–C4 and C1–C2–C3–H1 atoms of the ethyl group and of isobutyl group of 1d and 1e, respectively, were chosen for analysis in each case (see Figure S2). Snapshots were taken every 100 ps of the 30 ns simulations, and thus this analysis was performed on 9000 discrete data points per plot.