Taking Water into Account with the Fragment Molecular Orbital Method

Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Abstract

This chapter describes the current status of development of the fragment molecular orbital (FMO) method for analyzing the electronic state and intermolecular interactions of biomolecular systems in solvent. The orbital energies and the inter-fragment interaction energies (IFIEs) for a specific molecular structure can be obtained directly by performing FMO calculations by exposing water molecules and counterions around biomolecular systems. Then, it is necessary to pay attention to the thickness of the water shell surrounding the biomolecules. The single-point calculation for snapshots from MD trajectory does not incorporate the effects of temperature and configurational fluctuation, but the SCIFIE (statistically corrected IFIE) method is proposed as a many-body correlated method that partially compensates for this deficiency. Furthermore, implicit continuous dielectric models have been developed as effective approaches to incorporating the screening effect of the solvent in thermal equilibrium, and we illustrate their usefulness for theoretical evaluation of IFIEs and ligand-binding free energy on the basis of the FMO-PBSA (Poisson–Boltzmann surface area) method and other computational methods.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages105-122
Number of pages18
DOIs
Publication statusPublished - 2020
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume2114
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Dielectric continuum
  • Fragment molecular orbital (FMO) method
  • Hydration shell
  • Inter-fragment interaction energy (IFIE)
  • Ligand binding
  • Poisson–Boltzmann equation
  • Solvent effect
  • Statistically corrected IFIE (SCIFIE)
  • Water molecule

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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