IQA QM/MM test dataset

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.

相互作用量子原子（interacting quantum atoms, IQA）方法基于分子中原子的量子理论，将分子系统的总量子力学（quantum mechanical, QM）能量拆解为单中心与双中心（原子）贡献项。将该方法与分子力学（molecular mechanics, MM）、泊松-玻尔兹曼表面积（Poisson-Boltzmann surface-area, PBSA）溶剂化方法相结合后，可自然拓展至混合QM/MM方法学领域，得到可表征各类共价与非共价键相互作用的残基内及残基间能量项。为验证该方法的鲁棒性，研究以锌(II)与镁(II)水团簇为对象，通过改变QM区域的尺寸得到IQA描述符，以此表征金属-水相互作用及QM/MM边界伪影。此外，本研究针对一系列与基质金属蛋白酶（matrix metalloproteinase, MMP-12）结合的同源抑制剂，先对其晶体结构开展QM/MM-PBSA计算，再通过IQA能量分解完成分析。