{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:15:38Z","timestamp":1760058938600,"version":"build-2065373602"},"reference-count":78,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T00:00:00Z","timestamp":1746489600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>SARS-CoV-2 remains a severe threat to worldwide public health, particularly as the virus continues to evolve and diversify into variants of concern (VOCs). Among these VOCs, Omicron variants exhibit unique phenotypic traits, such as immune evasion, transmissibility, and severity, due to numerous spike protein mutations and the rapid subvariant evolution. These Omicron subvariants have more than 15 mutations in the receptor-binding domain (RBD), a region of the SARS-CoV-2 spike protein that is important for recognition and binding with the angiotensin-converting enzyme 2 (ACE2) human receptor. To address the impact of these high numbers of Omicron mutations on the binding process, we have developed a novel method to precisely quantify amino acid interactions via the amino acid\u2013amino acid bond pair (AABP). We applied this concept to investigate the interface interactions of the RBD\u2013ACE2 complex in four Omicron Variants (BA.1, BA.2, BA.5, and XBB.1.16) with its Wild Type counterpart. Based on the AABP analysis, we have identified all the sites that are affected by mutation and have provided evidence that unmutated sites are also impacted by mutation. We have calculated that the binding between RBD and ACE2 is strongest in OV BA.1, followed by OV BA.2, WT, OV BA.5, and OV XBB.1.16. We also present the partial charge values for all 311 residues across these five models. Our analysis provides a detailed understanding of changes caused by mutation in each Omicron interface complex.<\/jats:p>","DOI":"10.3390\/molecules30092061","type":"journal-article","created":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T09:08:56Z","timestamp":1746522536000},"page":"2061","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid\u2013Amino Acid Bond Pair Concept"],"prefix":"10.3390","volume":"30","author":[{"given":"Puja","family":"Adhikari","sequence":"first","affiliation":[{"name":"Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6252-3999","authenticated-orcid":false,"given":"Bahaa","family":"Jawad","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA"},{"name":"College of Applied Sciences, University of Technology, Baghdad 10066, Iraq"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7738-8822","authenticated-orcid":false,"given":"Wai-Yim","family":"Ching","sequence":"additional","affiliation":[{"name":"Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Lostao, A., Lim, K., Pallar\u00e9s, M.C., Ptak, A., and Marcuello, C. 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