Table-2.
The calculated binding energy, hydrogen bonds and contacting receptor residues of co-crystal ligand K36 and top-five natural compounds with SARS-CoV-2 Omicron variant (PDB ID: 7TOB) using YASARA structure.
| Compounds Name | Binding energy [kcal/mol] | Hydrogen bonds | Contacting receptor residues |
|---|---|---|---|
| K36 | 7.80 | 8 | Thr25, Thr26, Leu27, His41, Met49, Pro52, Tyr54, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, His172, Asp187, Arg188, Gln189, Thr190 |
| Theaflavin | 8.51 | 4 | Thr25, Leu27, His41, Met49, Phe140, Leu141, Asn142, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191 |
| Ginkgetin | 7.80 | 2 | Thr26, His41, Met49, Phe140, Leu141, Asn142, Ser144, His164, Met165, Glu166, Leu167, Arg188, Gln189, Thr190, Ala191 |
| Hesperadin | 7.27 | 3 | Thr24, Thr25, Thr26, Leu27, His41, Met49, Asn142, Gly143, Cys145, His164, Met165, Glu166, Leu167, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192 |
| Withanolide_D | 6.89 | 2 | Thr25, Thr26, Leu27, His41, Ser46, Met49, Ser144, Cys145, His164, Met165, Glu166, Pro168, Arg188, Gln189, Thr190, Ala191, Gln192 |
| Psoralidin | 6.26 | 3 | Thr25, His41, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Leu167, His172, Asp187, Arg188, Gln189 |