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Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):639-47. Epub 2006 May 12.

Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials.

Author information

1
Chemistry Department, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA.

Abstract

Intermolecular interaction energies between fragments of glycopeptide antibiotics and small peptide ligands are evaluated using geometries determined by X-ray crystallography and recently developed methods suitable for application to very large molecular complexes. The calculation of the electrostatic contributions is based on charge densities constructed with a databank of transferable aspherical atoms described by nucleus-centered spherical harmonic density functions, and uses the accurate and fast EPMM method. Dispersion, induction and exchange-repulsion contributions are evaluated with atom-atom potentials fitted to intermolecular energies from SAPT (symmetry-adapted perturbation theory) calculations on a large number of molecules. For a number of the complexes, first-principle calculations using density functional theory have been performed for comparison. Results of the new methods agree within reasonable bounds with those from DFT calculations, while being obtained at a fraction (less than 1%) of the computer time. A strong dependence on the geometry of the interaction is found, even when the number of hydrogen bonds between the substrate and antibiotic fragment is the same. While high-resolution X-ray data are required to obtain interaction energies at a quantitative level, the techniques developed have potential for joint X-ray/energy refinement of macromolecular structures.

PMID:
16699191
DOI:
10.1107/S0907444906013072
[Indexed for MEDLINE]

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