An improved experimental databank of transferable multipolar atom models – ELMAM2. Construction details and applications

Abstract

ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.

The active site of hen egg-white lysozyme: flexibility and chemical bonding

“…Instead, useful information about the redistribution of electron density owing to chemical bonding can be obtained from refinements of atomic coordinates and ADPs of structure models incorporating multipole parameters fixed to values from a database of transferable multipole parameters, as is presented here for the ELMAM2 model of HEWL (Jelsch et al, 1998;Dittrich et al, 2008;Dominiak et al, 2009;Domagała et al, 2012).…”

“…Instead, the refinement of multipole models is only meaningful with the multipole parameters fixed to values from a database (Jelsch et al, 1998;Dittrich et al, 2008;Dominiak et al, 2009;Domagała et al, 2012), as performed here for the ELMAM2 model of HEWL. Apparently, this feature has been overlooked in previous electron-density studies on proteins, in which at least part of the multipole parameters have been refined Schmidt et al, 2003Schmidt et al, , 2011Guillot et al, 2008).…”

“…A multipole model was obtained by transfer of multipole parameters from the ELMAM2 database (Domagała et al, 2012) to all protein atoms of the final IAM. Refinements were performed alternatingly of the overall scale factor, the atomic coordinates of ordered non-H atoms with a temperature factor B < 9 Å 2 and the ADPs of these atoms, while all multipole parameters were kept fixed at their database values.…”

“…the C atom in alanine) are nearly the same in all compounds containing this atom (Pichon-Pesme et al, 1995). Based on this principle, several databases of transferable multipole parameters have been developed (PichonPesme et al, 1995(PichonPesme et al, , 2004Volkov et al, 2004;Dittrich et al, 2006;Zarychta et al, 2007;Dominiak et al, 2007Dominiak et al, , 2009Domagała et al, 2012). They offer the possibility of constructing a multipole model of any molecule without the need to refine parameters beyond those of the IAM, i.e.…”

Transferable aspherical atom model refinement of protein and DNA structures against ultra-high-resolution X-ray data

“…This model is called a transferable aspherical atom model (TAAM). The aspherical atom databanks that have currently been developed are ELMAM2 (Domagała et al, 2012), UBDB2011 (Jarzembska & Dominiak, 2012) and the Invariom databank (Dittrich et al, 2013). The performance of all available databanks has previously been tested (Bąk et al, 2011), and refinement against X-ray data using either the IAM or TAAM can be performed, e.g.…”