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How to Perform FMO Calculation in Drug Discovery

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Recent Advances of the Fragment Molecular Orbital Method

Abstract

In order to apply the fragment molecular orbital (FMO) method to practical drug discovery research, what procedure should be used? This chapter summarizes the preliminary knowledge necessary for applying the FMO method to the field of drug discovery. First, as a pretreatment of calculation, preparation of structure, fragmentation, and selection of the theoretical method are explained. Then, as to how to evaluate the binding properties of ligand from the obtained results of the FMO calculation, the evaluation method using binding free energy, interaction energy, and its energy components will be explained. Further, various physical quantities obtained from the FMO calculation such as charge distribution, electrostatic potential, and electron density distribution are introduced. Then, how to interpret these values will be explained.

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Acknowledgments

The authors would like to thank Prof. Yuji Mochizuki and Prof. Shigenori Tanaka for ongoing discussions on FMO. A part of this research was done in activities of the FMO drug design consortium (FMODD). PIEDA analysis was carried out by using MIZUHO/BioStation Viewer. This research was partially supported by Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP20am0101113. C.W. acknowledges the JST PRESTO Grant Number JPMJPR18GD, Japan.

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Authors and Affiliations

  1. School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo, 142-8501, Japan

    Kaori Fukuzawa

  2. Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan

    Kaori Fukuzawa

  3. RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

    Chiduru Watanabe

  4. JST, PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan

    Chiduru Watanabe

  5. Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Kanagawa, Japan

    Yoshio Okiyama & Tatsuya Nakano

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  1. Kaori Fukuzawa
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  2. Chiduru Watanabe
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  3. Yoshio Okiyama
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  4. Tatsuya Nakano
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Correspondence to Kaori Fukuzawa .

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Editors and Affiliations

  1. Department of Chemistry, Faculty of Science, Rikkyo University, Tokyo, Japan

    Yuji Mochizuki

  2. Graduate School of System Informatics, Kobe University, Kobe, Japan

    Shigenori Tanaka

  3. School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan

    Kaori Fukuzawa

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Fukuzawa, K., Watanabe, C., Okiyama, Y., Nakano, T. (2021). How to Perform FMO Calculation in Drug Discovery. In: Mochizuki, Y., Tanaka, S., Fukuzawa, K. (eds) Recent Advances of the Fragment Molecular Orbital Method. Springer, Singapore. https://doi.org/10.1007/978-981-15-9235-5_7

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