FMODB: The World’s First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method

• DOI: 10.1021/acs.jcim.0c01062
• Publication Date: 2021-01-29T13:29:05Z
• Authors: Daisuke Takaya; Chiduru Watanabe; Shunpei Nagase; Kikuko Kamisaka; Yoshio Okiyama; Hirotomo Moriwaki; Hitomi Yuki; Tomohiro Sato; Noriyuki Kurita; Yoichiro Yagi; Tatsuya Takagi; Norihito Kawashita; Kenichiro Takaba; Tomonaga Ozawa; Midori Takimoto-K...; Shigenori Tanaka; Kaori Fukuzawa; Teruki Honma
• Keywords: Fragment molecular orbital

We developed the world's first web-based public database for storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in contains relevant background information on how was compiled as well total energy each system interfragment interaction (IFIE) pair decomposition analysis (PIEDA) values. Currently, more than 13 600 sets, a comprehensive search function implemented at front-end. The procedure selecting target proteins, preprocessing experimental structures, construction database, details front-end were described. Then, we demonstrated use FMODB by comparing IFIE value distributions hydrogen bond, ion-pair, XH/π obtained method to those mechanics approach. From comparison, statistical provided standard reference values three types that will be useful determining whether given is relatively strong or weak compared contained within FMODB. In final part, demonstrate examine contribution halogen atoms binding affinity human cathepsin L its inhibitors. found electrostatic term derived PIEDA greatly correlated with affinities containing inhibitors, indicating importance QM quantitative interactions. Thus, conducting analyses drug discovery, recognition studies structural biology, other involving quantum mechanics-based