Table 2.
Different bonding interactions in 3CLpro and PLpro-ligand complex after 0, 25, 50, 75, and 100 ns of molecular dynamics simulation.
| Complex | Residue | Interaction type | Distance(Å) |
|---|---|---|---|
| 3CLpro-Ligand (0 ns) | Glu166 | Hydrogen bond | 2.37 |
| Arg188 | Hydrogen bond | 2.76 | |
| Gln189 | Hydrogen bond | 3.03 | |
| Met49 | Hydrogen bond | 3.77 | |
| His41 | Hydrogen bond | 2.37 | |
| Cys145 | Pi-Alkyl | 5.26 | |
| Met165 | Pi-Donor | 4.64 | |
| Asn142 | Pi-Sigma | 3.42 | |
| 3CLpro-Ligand (25 ns) | Arg188 | Hydrogen bond | 2.28 |
| Glu166 | Hydrogen bond | 1.94 | |
| Met49 | Pi-Sulfur | 5.56 | |
| Met165 | Pi-Alkyl | 4.95 | |
| Cys145 | Pi-Alkyl | 4.65 | |
| 3CLpro-Ligand (50 ns) | Glu166 | Hydrogen bond | 1.58 |
| His163 | Hydrogen bond | 2.73 | |
| His41 | Pi-Pi-T shape | 4.68 | |
| Met165 | Pi-Alkyl | 4.67 | |
| Cys145 | Pi-Alkyl | 5.3 | |
| Met49 | Pi-Alkyl | 5.29 | |
| 3CLpro-Ligand (75 ns) | His41 | Hydrogen bond | 2.72 |
| Arg188 | Hydrogen bond | 2.75 | |
| Met49 | Hydrogen bond | 2.98 | |
| Glu166 | Hydrogen bond | 2.37 | |
| Asn142 | Hydrogen bond | 2.51 | |
| Met165 | Pi-Alkyl | 4.63 | |
| Cys145 | Pi-Alkyl | 5.26 | |
| 3CLpro-Ligand (100 ns) | Glu166 | Hydrogen bond | 1.86 |
| Phe140 | Hydrogen bond | 3.01 | |
| His172 | Hydrogen bond | 1.86 | |
| Leu141 | Hydrogen bond | 2.73 | |
| His41 | Hydrogen bond | 2.75 | |
| Asn142 | Amide-Pi stacked | 3.83 | |
| Met49 | Pi-Alkyl | 5.44 | |
| PLpro-Ligand (0 ns) | Asp164 | Hydrogen bond | 1.99 |
| Arg166 | Hydrogen bond | 3.19 | |
| Glu167 | Hydrogen bond | 2.95 | |
| Tyr264 | Hydrogen bond | 2.29 | |
| Tyr273 | Hydrogen bond | 2.2 | |
| Pro247 | Pi-Alkyl | 5.33 | |
| Pro248 | Pi-Alkyl | 4.26 | |
| PLpro-Ligand (25 ns) | Arg166 | Hydrogen bond | 2.34 |
| Glu167 | Hydrogen bond | 2.95 | |
| Tyr264 | Hydrogen bond | 2.29 | |
| Asp164 | Hydrogen bond | 1.98 | |
| Tyr273 | Hydrogen bond | 2.19 | |
| Asn267 | Hydrogen bond | 2.67 | |
| Tyr268 | Hydrogen bond | 2.81 | |
| Pro247 | Alkyl | 4.26 | |
| Pro248 | Pi-Alkyl | 4.96 | |
| PLpro-Ligand (50 ns) | Arg166 | Hydrogen bond | 2.23 |
| Gln269 | Hydrogen bond | 2.5 | |
| Asp164 | Hydrogen bond | 1.58 | |
| Tyr273 | Hydrogen bond | 2.44 | |
| Asn267 | Hydrogen bond | 2.66 | |
| Tyr264 | Hydrogen bond | 4.35 | |
| Tyr268 | Pi-Pi Stacked | 5.93 | |
| Pro248 | Alkyl | 5.05 | |
| PLpro-Ligand (75 ns) | Glu167 | Hydrogen bond | 1.79 |
| Asp164 | Hydrogen bond | 1.94 | |
| Arg166 | Hydrogen bond | 3.98 | |
| Tyr268 | Pi-Pi Stacked | 4.6 | |
| Pro247 | Pi-Alkyl | 5.31 | |
| Pro248 | Pi-Alkyl | 5.06 | |
| PLpro-Ligand (100 ns) | Glu167 | Hydrogen bond | 1.79 |
| Asp164 | Hydrogen bond | 1.66 | |
| Arg166 | Electrostatic | 3.98 | |
| Tyr268 | Pi-Pi Stacked | 2.68 | |
| Pro247 | Pi-Alkyl | 5.31 | |
| Pro248 | Pi-Alky | 5.06 |