Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

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Authors

IONESCU Crina-Maria GEIDL Stanislav SVOBODOVÁ VAŘEKOVÁ Radka KOČA Jaroslav

Year of publication 2013
Type Article in Periodical
Magazine / Source Journal of Chemichal Information a Modeling
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://pubs.acs.org/doi/pdf/10.1021/ci400448n
Doi http://dx.doi.org/10.1021/ci400448n
Field Biochemistry
Keywords MOLECULAR ELECTROSTATIC POTENTIALS; PREDICTING PK(A) VALUES; DYNAMICS SIMULATIONS; POPULATION ANALYSIS; ORGANIC-MOLECULES; DIPOLE-MOMENTS; METHOD EEM; BASIS-SET; VALIDATION; SCHEMES
Attached files
Description We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartre-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.
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