The three-body fragment molecular orbital method for accurate calculations of large systems

Abstract The approximations used in the context of the fragment molecular orbital method were critically revised, the origin of the approximation error determined and an improvement proposed. The three-body method which has been so far very expensive, was reformulated to be used with the approximations, and its efficacy both in terms of accuracy and computational timings carefully established on a set of representative systems. Timings and accuracy are reported for the two and three-body methods, including their application to two proteins 1L2Y and 1IO5 (PDB codes) and (H2O)1024 (at the RHF/6-31G∗ level).

[1]  Hiroaki Tokiwa,et al.  Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis , 2006 .

[2]  Kazuo Kitaura,et al.  On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory , 2004 .

[3]  Kazuo Kitaura,et al.  Coupled-cluster theory based upon the fragment molecular-orbital method. , 2005, The Journal of chemical physics.

[4]  Hui Li,et al.  The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO) , 2006, J. Comput. Chem..

[5]  Kaori Fukuzawa,et al.  A configuration analysis for fragment interaction , 2005 .

[6]  Fumitoshi Sato,et al.  Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory , 2001 .

[7]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[8]  Kazuo Kitaura,et al.  Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[9]  Takeshi Ishikawa,et al.  Fragment molecular orbital calculations on large scale systems containing heavy metal atom , 2006 .

[10]  Mark S. Gordon,et al.  Solvent Effects on the SN2 Reaction: Application of the Density Functional Theory-Based Effective Fragment Potential Method , 2005 .

[11]  Kaori Fukuzawa,et al.  Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .

[12]  Kazuo Kitaura,et al.  All electron quantum chemical calculation of the entire enzyme system confirms a collective catalytic device in the chorismate mutase reaction. , 2006, The journal of physical chemistry. B.

[13]  K. Kitaura,et al.  Multilayer formulation of the fragment molecular orbital method (FMO). , 2005, The journal of physical chemistry. A.

[14]  Yuto Komeiji,et al.  Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein , 2005, Comput. Biol. Chem..

[15]  Kazuo Kitaura,et al.  The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[16]  Vladimir B. Sulimov,et al.  Semiempirical calculations of binding enthalpy for protein-ligand complexes , 2004 .

[17]  Hiroshi Kashiwagi,et al.  All‐electron density functional calculation on insulin with quasi‐canonical localized orbitals , 2005, J. Comput. Chem..

[18]  Yuji Mochizuki,et al.  Configuration interaction singles method with multilayer fragment molecular orbital scheme , 2005 .

[19]  Kazuo Kitaura,et al.  Multiconfiguration self-consistent-field theory based upon the fragment molecular orbital method. , 2005, The Journal of chemical physics.