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WIREs Comput Mol Sci
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The fragment molecular orbital method: theoretical development, implementation in GAMESS , and applications

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The physical picture of the fragment molecular orbital (FMO) method is described on the basis of a many‐body expansion with terms describing the polarization of isolated fragments, charge transfer (CT), and exchange‐repulsion (EX) between them. Aspects of fragmentation are discussed in detail and FMO development in GAMESS‐US is summarized. Recent progress in method development and applications is reviewed, with a focus on studies of protein–ligand binding, excited states, and spectra of large molecular systems. WIREs Comput Mol Sci 2017, 7:e1322. doi: 10.1002/wcms.1322

Illustration of the junction rule. (a) Molecular clusters (n = 1), (b) chains, two fragments are connected (n = 2), and (c) surfaces, three fragments form a junction (n = 3). The fragments forming a junction are numbered.
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Interaction and binding energies in the complex of Trp‐cage (PDB: 1L2Y) with its ligand, p‐PhCOO.
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Cyclic water trimer (H2O)3 calculated with HF/6‐31G**. (a) Dipole moments on isolated (FMO0) and fully polarized (FMO1) water molecules are shown as blue and red arrows, respectively, centered on oxygens. (b) Isosurface of the total electron density ρ FMO0(r) of isolated molecules, with the cutoff of 0.05. (c) Change in the electron density ρ(r) due to polarization (Δρ 1(r) = ρ FMO1(r) − ρ FMO0(r)), with the cutoff of ±0.001. (d) Change in the electronic density ρ(r) due to two‐body CT and EX (Δρ 2(r) = ρ FMO2(r) − ρ FMO1(r)), with the cutoff of ±0.001. (d) Change in the electronic density ρ(r) due to three‐body CT and EX (Δρ 3(r) = ρ FMO3(r) − ρ FMO2(r)) , with the cutoff of ±0.0001. Red and blue surfaces show regions where the density change is positive and negative, respectively. Hydrogen bonds are shown as green, dashed lines.
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Structure and Mechanism > Computational Biochemistry and Biophysics
Molecular and Statistical Mechanics > Molecular Interactions
Electronic Structure Theory > Ab Initio Electronic Structure Methods

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