Molecular models for hinge-like complexes from PSI, PSII, and bacterial RC were extracted from crystal structures of Synechococcus elongatus (PDB entry 1JB0), Thermococcus vulcanus (PDB entry 3WU2), and Rhodobacter sphaeroides (PDB entry 1M3X), respectively. In case of protein binding pockets, we included all residues within a distance of 4 Å from atoms of a [Cof• • • His] complex into the model. If at least one atom of a nearby residue appeared within this radius, the entire residue was included into the model. The Reduce program was used to add missing hydrogen atoms to photosynthetic co-factors, whereas CHARMM22 topology files were applied for amino acids. Cut peptide bonds were saturated with neutral capping groups -C(O)CH 3 and -NH 2 , where the initial interatomic bond distances were set to average values found in small organic molecules as reported in Ref. . In cases of overlapping capping groups, the missing amino acid residue was added to the model instead.