IQA QM/MM test dataset

Published: 5 November 2021| Version 1 | DOI: 10.17632/f69z2gbgdp.1
Contributor:
Dimas Suarez

Description

The interacting quantum atoms (IQA) method decomposes the total quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kind of covalent and non-covalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artefacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by the IQA energy decomposition.

Files

Steps to reproduce

The modular version of the PROMOLDEN code together with a set of auxiliary BASH and Octave scripts that required for performing QM/MM IQA calculations are available upon request.

Categories

Computational Chemistry Application, Hybrid QM/MM, Computational Molecular Modeling, Quantum Chemistry

License