A combination of classical molecular dynamics (MD) simulation and ab initio fragment molecular orbital (FMO) calculation was applied to a complex formed between the main protease of the new coronavirus and the inhibitor N3 to calculate interactions within the complex while incorporating structural fluctuations mimicking physiological conditions. Namely, a statistical evaluation of interaction energies between N3 and amino acid residues was performed by processing a thousand of structure samples. It was found that relative importance of each residue is altered by the structural fluctuation. The MD-FMO combination should be promising to simulate protein related systems in a more realistic way.

将经典分子动力学（MD）模拟和从头片段分子轨道（FMO）计算相结合，应用于新型冠状病毒主要蛋白酶与抑制剂N3形成的复合物，以计算复合物内的相互作用，同时结合模拟生理学的结构波动条件。即，通过处理一千个结构样本，对 N3 和氨基酸残基之间的相互作用能进行统计评估。发现每个残基的相对重要性会因结构波动而改变。MD-FMO 组合应该有望以更现实的方式模拟蛋白质相关系统。