ArticlePloS one2012
The effective fragment molecular orbital method for fragments connected by covalent bonds.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.The Journal of chemical physics · 2025Article
- Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database.Journal of chemical theory and computation · 2020Article
- Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method.PloS one · 2014Article
- Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.PloS one · 2013Article
- FragIt: a tool to prepare input files for fragment based quantum chemical calculations.PloS one · 2012Article
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Authors and funding
3 authors.
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Abstract
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.
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