The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development.

中文翻译：

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SARS-CoV-2 刺突蛋白受体结合域的分子内和分子间原子级相互作用：对 ACE2 受体结合的影响。

COVID-19 大流行给人类健康带来了前所未有的社会和经济破坏，对人类健康构成了严重威胁。SARS-CoV-2 病毒中的刺突 (S) 糖蛋白对于了解病毒解剖结构至关重要，因为它启动了与人体细胞中 ACE2 受体的早期接触。S 蛋白 A 链中的亚基 S1 具有四个结构域：受体结合域 (RBD)、n 端域 (NTD) 和两个子域 (SD1、SD2)。我们使用密度泛函理论报告了 RBD 的分子内和分子间结合机制的详细信息，包括电子结构、原子间键合和部分电荷分布。我们确定了五个强氢键并分析了它们在结合中的作用。