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Fragment interaction analysis based on local MP2

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Abstract

We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.

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Authors and Affiliations

  1. Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan

    Takeshi Ishikawa, Yuji Mochizuki & Hiroaki Tokiwa

  2. CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

    Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano & Shigenori Tanaka

  3. Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan

    Shinji Amari & Kiyoshi Tanaka

  4. Division of Safety Information on Drug, Food and Chemicals, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan

    Tatsuya Nakano

  5. Graduate School of Science and Technology, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo, 657-8501, Japan

    Shigenori Tanaka

  6. AdvanceSoft Corporation, Center for Collaborative Research, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan

    Kiyoshi Tanaka

Authors
  1. Takeshi Ishikawa
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  2. Yuji Mochizuki
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  3. Shinji Amari
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  4. Tatsuya Nakano
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  5. Hiroaki Tokiwa
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  6. Shigenori Tanaka
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  7. Kiyoshi Tanaka
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Correspondence to Takeshi Ishikawa.

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Ishikawa, T., Mochizuki, Y., Amari, S. et al. Fragment interaction analysis based on local MP2. Theor Chem Account 118, 937–945 (2007). https://doi.org/10.1007/s00214-007-0374-7

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  • DOI: https://doi.org/10.1007/s00214-007-0374-7

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