Fig. 5.

(A) The bridging water molecule (W382D) that connects between the ligand Nδ site of P_D2 and the keto O site of Chl_D1. H-bonds and ligand interactions are indicated by dotted lines. The donor to acceptor orientations of the H-bonds are indicated by blue solid arrows. The Qy transition dipole is indicated by the dotted blue arrow (see SI Appendix, Fig. S1 for the orientations of the Qx and Qy transition dipoles). (B) Distribution of HOMO (pink and cyan spaces) at the Chl_D1 moiety, which were obtained based on QM/MM/PCM (r = 3.0) with the CAM-B3LYP functional (μ = 0.14). The QM region was defined as Chl_D1, the ligand (W424D), second sphere ligand (W1003A), and bridging (W382D) water molecules, and the side chains of D1-Met172 and D1-Phe180 in van der Waals contact with Chl_D1, and the ligand (or ligand-associated) side chains of D1-Thr179 and D2-His197.