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.

本计算所采用的初始几何构型取自不同时间节点下的晶体学结构。蛋白质残基的质子化状态通过AMBER软件包中的tleap程序确定。所有几何构型均采用杂化量子力学/分子力学（QM/MM）方法进行优化。量子力学区域包含视黄醛以及形成视黄醛质子化希夫碱的赖氨酸（Lys235）侧链，同时包含氯离子与邻近的极性、带电残基（Asn98、Thr102及Asp231）。采用氢连接原子（HLA）方案在Lys235侧链的Cδ与Cε原子之间设置QM/MM边界，其余所有残基则在Cα与Cβ之间的对应化学键处封端。量子力学区域总计包含80个原子，其中包括封端原子。量子力学区域采用BP86泛函结合cc-pVDZ基组，以及用于恒等分辨率近似的def2/J辅助基组进行描述。剩余的蛋白质体系采用Amber ff14SB力场进行处理。采用TIP3P模型描述水分子。QM/MM几何优化通过与ChemShell软件包对接的Orca 4.0程序完成。