Fig. 3. Processes before deacylation with the minimal active site assembly.

a–c Initial structure of CI with a the LG in the catalytic site, b the water molecule (HW) near the catalytic site, and c HW now moved into the catalytic site (hydrogen bond formed with Nε of His408 is shown in green dotted line). d–f Corresponding PMFs calculated along reaction coordinates d₃, d₄, and θ, respectively. d₃ denotes the distance between the C of CI and C in LG. d₄ denotes the distance between the HW O atom and the yellow sphere, i.e., the center of mass (COM) of C in CI and Nε in His408. θ denotes the bond angle in HW. There are a total 45 atoms in the QM area for the angle-change calculation, and the charge is −1. Data are presented as mean values ± the standard error inferred from three independent runs. Source data for d–f are provided as a Source Data file.