Analyzing Interactions with the Fragment Molecular Orbital Method

Dmitri G Fedorov

doi:10.1007/978-1-0716-0282-9_4

Analyzing Interactions with the Fragment Molecular Orbital Method

Methods Mol Biol. 2020:2114:49-73. doi: 10.1007/978-1-0716-0282-9_4.

Author

Dmitri G Fedorov¹

Affiliation

¹ Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan. d.g.fedorov@aist.go.jp.

PMID: 32016886
DOI: 10.1007/978-1-0716-0282-9_4

Abstract

Basic concepts in the analysis of binding using the fragment molecular orbital method are discussed at length: polarization, desolvation, and interaction. The components in the pair interaction energy decomposition analysis are introduced, and the analysis is illustrated for a water dimer and a protein-ligand complex.

Keywords: Binding; Charge transfer; Desolvation; Dispersion; Energy decomposition analysis; FMO; Interaction; PIEDA; Polarization; Protein–ligand complex; Solvent screening; Water dimer.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Drug Discovery / methods*
Ligands
Proteins / chemistry
Quantum Theory

Substances

Ligands
Proteins