The interacting quantum
atoms (IQA) method decomposes the 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. Here, we demonstrate that 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 kinds of covalent and noncovalent bonding interactions.
To test the robustness of this approach, both metal–water interactions
and QM/MM boundary artifacts 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 IQA energy decomposition. Overall, these applications
not only show the advantages of the IQA QM/MM approach but also address
some of the challenges lying ahead for expanding the QM/MM methodology.