QM/MM optimized coordinates for various structural intermediates of NmHR

The initial geometries used for the calculations were taken from the crystallographic structures at various time intervals. The protonation states of the protein residues were determined by the program tleap from the AMBER software package. All the geometries were optimized using the hybrid quantum mechanics/molecular mechanics (QM/MM) method. The QM part consists of retinal and lysine (Lys235) sidechain forming the retinal protonated Schiff base along with chloride ion and nearby polar and charged residues (Asn98, Thr102 and Asp231). The hydrogen link atom (HLA) scheme was used to place the QM/MM boundary in between the Cδ and Cε atoms of the Lys235 sidechain, whereas all other residues were capped at the corresponding bond between Cα and Cβ. In total, there are 80 atoms in the QM region including the capping atoms. The QM part was described using the BP86 functional in conjunction with the cc-pVDZ basis set and the def2/J auxiliary basis set for the resolution of identity. The remaining proteins were treated with the Amber ff14SB force field. The TIP3P model was used to describe the water molecules. The QM/MM optimizations were performed by using the Orca 4.0 program interfaced with ChemShell software package.