Journal Article10.1016/S0009-2614(01)01416-6
Fragment molecular orbital method: use of approximate electrostatic potential
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Kaori Fukuzawa,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +6 more
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TL;DR: The fragment molecular orbital (FMO) method as discussed by the authors has been proposed to reproduce ab initio total energies and geometries of molecules in good accuracy, but the most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation.
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About: This article is published in Chemical Physics Letters. The article was published on 17 Jan 2002. The article focuses on the topics: Fragment molecular orbital & Ab initio.
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Citations
Full Electron Calculation Beyond 20,000 Atoms: Ground Electronic State of Photosynthetic Proteins
Tsutomu Ikegami,Toyokazu Ishida,Dmitri G. Fedorov,Kazuo Kitaura,Yuichi Inadomi,Hiroaki Umeda,Mitsuo Yokokawa,Satoshi Sekiguchi +7 more
- 12 Nov 2005
TL;DR: A full electron calculation for the photosynthetic reaction center of Rhodopseudomonas viridis was performed by using the fragment molecular orbital (FMO) method on a massive cluster computer.
Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches
Tomohiro Sato,Katsuhiko Sekimata,Naoki Sakai,Hisami Watanabe,Chiemi Mishima-Tsumagari,Tomonori Taguri,Takehisa Matsumoto,Yoshifumi Fujii,Noriko Handa,Akiko Tanaka,Mikako Shirouzu,Shigeyuki Yokoyama,Yoshinobu Hashizume,Kohei Miyazono,Hiroo Koyama,Teruki Honma +15 more
- 12 May 2020
TL;DR: The detailed procedure of the in silico approach employed to identify the initial bis-heteroaryl pyrazole-based ALK2 (R206H) inhibitor RK-59638 and the analysis of the ALK1 (R 206H) RK -59638 complex structure to guide the synthetic optimization of the chemical series, obtaining RK+71807 showing improved potency and metabolic stability, were described.
15
Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method.
TL;DR: The developed FMO-MECP method can help to clarify the role of nonadiabatic spin-dependent processes in complex systems and can be used for designing mutations aimed at controlling these processes in metalloproteins, including spin- dependent catalysis and electron transfer.
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Efficient Geometry Optimization of Large Molecular Systems in Solution Using the Fragment Molecular Orbital Method.
Hiroya Nakata,Dmitri G. Fedorov +1 more
TL;DR: The analytic gradient is derived for the frozen domain formulation of the fragment molecular orbital (FMO) method combined with the polarizable continuum model and applied to a geometry optimization of the K-Ras protein-ligand complex using two domain definitions, and the optimized structures are consistent with experiment.
15
Examination of numerical accuracy on fragment-DFT calculations with integral values of total electron density functions
TL;DR: In this paper, the total accuracy of numerical integrations employed in those calculations was examined by the total number of electrons in the molecules, and it was shown that the numerical integral of the total density function under the fragment approximation works as an indicator for the numerically total accuracy on the F-DFT implementation.
15
References
Fragment molecular orbital method: an approximate computational method for large molecules
TL;DR: In this paper, an approximate molecular orbital (MO) method was proposed to calculate the total energy of a molecule by assigning the electrons of the molecules to fragments and calculating the MOs of fragments and fragment pairs.
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Fragment molecular orbital method: application to polypeptides
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +5 more
TL;DR: In this article, the fragment molecular orbital method (FMO) was applied to the model peptides of (Gly)n and (Ala)n (n=5-20), [Met5]enkephalin (YGGFM), and the synthetic designed peptide ALPHA-1 (acetyl-ELLKKLLEELKG) and the calculated total energies compare well with those from the conventional ab initio MO method.
358
Fragment molecular orbital method: analytical energy gradients
TL;DR: In this article, the fragment molecular orbital (FMO) method with the analytical energy gradient at the HF level of theory has been incorporated into the G aussian 94 (G94) package.
210
Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
TL;DR: The 0.75 Å crystal structure of a racemic mixture of the 12‐residue designed peptide “Alpha‐1” (Acetyl‐ELLKKLLEELKG) is reported, the L‐enantiomer of which is described in the accompanying paper.
Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Christian Jelsch,Martha M. Teeter,Victor S. Lamzin,Virginie Pichon-Pesme,Robert H. Blessing,Claude Lecomte +5 more
TL;DR: The charge density distribution of a protein has been refined experimentally and the resulting electron density maps of redistributed valence electrons compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide.