Nakata Hiroya, Fedorov Dmitri G, Nagata Takeshi, Kitaura Kazuo, Nakamura Shinichiro
Department of Biomolecular Engineering, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
Research Cluster for Innovation, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
J Chem Theory Comput. 2015 Jul 14;11(7):3053-64. doi: 10.1021/acs.jctc.5b00277.
The fully analytic first and second derivatives of the energy in the frozen domain formulation of the fragment molecular orbital (FMO) were developed and applied to locate transition states and determine vibrational contributions to free energies. The development is focused on the frozen domain with dimers (FDD) model. The intrinsic reaction coordinate method was interfaced with FMO. Simulations of IR and Raman spectra were enabled using FMO/FDD by developing the calculation of intensities. The accuracy is evaluated for S(N)2 reactions in explicit solvent, and for the free binding energies of a protein-ligand complex of the Trp cage protein (PDB: 1L2Y ). FMO/FDD is applied to study the keto-enol tautomeric reaction of phosphoglycolohydroxamic acid and the triosephosphate isomerase (PDB: 7TIM ), and the role of amino acid residue fragments in the reaction is discussed.
在片段分子轨道（FMO）的冻结域公式中，开发了能量的全解析一阶和二阶导数，并将其应用于定位过渡态以及确定对自由能的振动贡献。该开发工作聚焦于二聚体冻结域（FDD）模型。将内禀反应坐标方法与FMO相结合。通过开发强度计算，利用FMO/FDD实现了红外和拉曼光谱的模拟。评估了在明确溶剂中S(N)2反应的准确性，以及色氨酸笼蛋白（PDB：1L2Y）的蛋白质-配体复合物的自由结合能。FMO/FDD被应用于研究磷酸甘氨酰羟肟酸的酮-烯醇互变异构反应和磷酸丙糖异构酶（PDB：7TIM），并讨论了氨基酸残基片段在反应中的作用。
