Table 3.
Molecular docking score, interactions, and bond length of the native and docked complex of Mpro (6LU7) with N3 peptide in the two different docking strategies
| Name of the compound | 2D structure | Discovery studio | AutoDock Vina | |||||
|---|---|---|---|---|---|---|---|---|
| LibDock | Binding energy (kcal/mol) | H-bonds | Bond length (Ȧ) | Docking score (kcal/mol) | H-bonds | Bond length (Ȧ) | ||
| N3 peptide |
|
80.84 | − 13.20 | Leu50 ← π–π | 5.15 | − 4.8 | Ser46: HG → O8 | 2.02 |
| Gly143: → π–π | 2.56 | Met49 → π | 4.98 | |||||
| Cys145: SG → π–π | 2.54 | Phe140: O ← H89 | 2.76 | |||||
| His164: O ← H59 | 2.62 | His163: HE2 → H88 | 1.79 | |||||
| His164: O → H55 | 2.52 | Met165 ← C26 | 5.03 | |||||
| Met165 ← C18 | 5.29 | Met165: HA → O24 | 2.44 | |||||
| Met165 ← C26 | 4.10 | Met165: SD → π | 4.49 | |||||
| Glu166: OE1 ← H88 | 3.01 | Glu166: OE2 → H89 | 2.43 | |||||
| Glu166: OE1 ← H87 | 2.47 | Glu166: OE2 ← H89 | 2.78 | |||||
| Leu167 ← C26 | 5.29 | Glu166: HN → O24 | 2.02 | |||||
| Pro168: HA → O39 | 2.67 | Pro168 → π | 5.39 | |||||
| Gln189: OE1 ← H60 | 2.41 | His172: HD2 → O3 | 2.82 | |||||
| Gln189: HE21 → O43 | 3.02 | Gln189: OE1 ← H68 | 2.50 | |||||
| Gln189: OE1 → H69 | 2.32 | |||||||
→ ← H-bond donor and acceptor