TY - JOUR
T1 - FMODB
T2 - The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method
AU - Takaya, Daisuke
AU - Watanabe, Chiduru
AU - Nagase, Shunpei
AU - Kamisaka, Kikuko
AU - Okiyama, Yoshio
AU - Moriwaki, Hirotomo
AU - Yuki, Hitomi
AU - Sato, Tomohiro
AU - Kurita, Noriyuki
AU - Yagi, Yoichiro
AU - Takagi, Tatsuya
AU - Kawashita, Norihito
AU - Takaba, Kenichiro
AU - Ozawa, Tomonaga
AU - Takimoto-Kamimura, Midori
AU - Tanaka, Shigenori
AU - Fukuzawa, Kaori
AU - Honma, Teruki
N1 - Funding Information:
This research was partially supported by the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from Japan Agency for Medical Research and Development (AMED) under Grant No. JP20am0101113. Finally, D.T. and C.W. acknowledge JSPS KAKENHI Grant No. 18K06619. C.W. acknowledges JST PRESTO Grant No. JPMJPR18GD.
Publisher Copyright:
© 2021 American Chemical Society.
PY - 2021/2/22
Y1 - 2021/2/22
N2 - We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/πinteractions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
AB - We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/πinteractions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
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U2 - 10.1021/acs.jcim.0c01062
DO - 10.1021/acs.jcim.0c01062
M3 - Article
C2 - 33511845
AN - SCOPUS:85100648007
SN - 0095-2338
VL - 61
SP - 777
EP - 794
JO - Journal of Chemical Documentation
JF - Journal of Chemical Documentation
IS - 2
ER -