Table 6.
Main hydrogen bond interactions formed by RdRp with remdesivir and polyphenols along with the corresponding average distance and percentage of occupancy determined using the trajectories of production simulations.
| Acceptor | Donor | Avg. Distance (Å) | Occupancy (%) |
|---|---|---|---|
| RdRp/Remdesivir | |||
| Asp760@OD2 | Lig@O7 | 2.66 | 19.46 |
| Asp761@OD1 | Lig@O7 | 2.65 | 17.70 |
| Asp761@OD2 | Lig@O6 | 2.63 | 16.86 |
| Asp760@OD2 | Lig@O6 | 2.65 | 16.65 |
| Lig@O6 | Ser759@OG | 2.80 | 11.63 |
| Asp760@OD1 | Lig@O7 | 2.66 | 10.59 |
| RdRp/EGCG | |||
| Asp618@OD1 | Lig@O5 | 2.61 | 30.13 |
| Asp618@OD1 | Lig@O6 | 2.61 | 29.28 |
| Asp618@OD2 | Lig@O5 | 2.61 | 18.25 |
| Asp618@OD2 | Lig@O6 | 2.61 | 17.38 |
| Asp760@OD1 | Lig@O5 | 2.63 | 16.09 |
| Tyr455@OH | Lig@O11 | 2.83 | 10.97 |
| RdRp/TF3 | |||
| Asp761@OD1 | Lig@O11 | 2.61 | 69.84 |
| Glu811@O | Lig@O10 | 2.76 | 58.43 |
| Thr556@O | Lig@O3 | 2.72 | 56.95 |
| Lig@O14 | Arg836@NH2 | 2.83 | 52.66 |
| Lig@O14 | Arg836@NE | 2.86 | 48.70 |
| Asp761@OD2 | Lig@O20 | 2.62 | 44.51 |
| RdRp/TF2b | |||
| Pro832@O | Lig@O8 | 2.77 | 26.31 |
| Lig@O11 | Tyr877@OH | 2.75 | 24.39 |
| Glu811@OE1 | Lig@O7 | 2.65 | 22.45 |
| Glu811@OE2 | Lig@O7 | 2.65 | 18.89 |
| Asp833@OD2 | Lig@O8 | 2.65 | 12.01 |
| Asn874@OD1 | Lig@O11 | 2.68 | 8.58 |
| RdRp/TF2a | |||
| Asp618@OD1 | Lig@O10 | 2.59 | 38.68 |
| Asp618@OD1 | Lig@O11 | 2.62 | 38.38 |
| Asp760@O | Lig@O11 | 2.70 | 20.83 |
| Asp618@OD2 | Lig@O11 | 2.62 | 16.59 |
| Asp618@OD2 | Lig@O10 | 2.58 | 16.49 |
| Asp618@OD1 | Lig@O15 | 2.67 | 16.37 |