Table-1.
The calculated binding energy, hydrogen bonds and contacting receptor residues of co-crystal ligand N3 and top-five natural compounds with SARS-CoV-2 Main Protease (PDB ID: 6LU7) using YASARA structure.
| Compounds Name | Binding energy [kcal/mol] | Hydrogen bonds | Contacting receptor residues |
|---|---|---|---|
| N3 | 7.55 | 8 | Thr24, Thr25, Thr26, Leu27, His41, Val42, Thr45, Ser46, Met49, Tyr54, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, His172, Asp187, Arg188, Gln189 |
| Theaflavin | 10.04 | 4 | His41, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192 |
| Ginkgetin | 9.64 | 4 | Leu27, His41, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, His172, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192 |
| Hesperadin | 8.47 | 4 | Thr24, Thr25, Thr26, Leu27, His41, Met49, Asn142, Gly143, Cys145, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Gln192 |
| Withanolide-D | 8.37 | 1 | Thr25, Thr26, Leu27, His41, Ser46, Met49, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Pro168, Arg188, Gln189, Thr190, Ala191, Gln192 |
| Psoralidin | 8.35 | 4 | His41, Met49, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, His172, Asp187, Arg188, Gln189, Gln192 |