Table 3. Trajectory analysis results for each of [E6+lig]-hx systems during 50 ns of MD.
| Ligand name/ system | RMSD ligand (Å) |
RMSD protein (Å) |
Dis- tance E6-hx (Å) | RMSF of pocket (Å) |
E6 pocket volume (Å3) |
ΔΔHGB (kcal/ mol) | ΔΔHP B (kcal/ mol) |
|---|---|---|---|---|---|---|---|
|
LxxLL motif [E6]-hx |
NA | 3.4 ± 0.3 | 9.6 ±0.7a | 1.0 ± 0.7 | 1,301 ± 54 | 0.0 ± 9.5 | 0.0 ±13.7 |
| Luteolin [E6+luteolin]-hx |
0.8 ±0.1 | 6.1 ± 0.5 | 14.1 ±0.5a | 1.0 ± 0.6 | 1,098 ± 78 | 20.6 ±8.1 | -9.6 ±9.5 |
| Lig1 [E6+Lig1]-hx |
1.3 ±0.5 | 4.2 ± 0.5 | 13.6 ±0.4a | 0.9 ± 0.6 | 1,279 ± 65 | 31.2 ±6.0* | 4.6 ± 7.4 |
| Lig2 [E6+Lig2]-hx |
0.7 ±0.1 | 3.9 ± 0.3 | 13.2 ±0.4a | 1.0 ± 0.5 | 1,360 ±155 | 30.8 ±7.3 | 6.9 ±9.5* |
| Lig3 [E6+Lig3]-hx |
2.0 ±0.5 | 4.5 ± 0.3 | 13.7 ±0.5a | 0.9 ± 0.8 | 1,302 ± 62 | 17.3 ±5.9 | 2.8 ± 8.3 |
* The best results according to the evaluated objective. The highest ΔΔHbind values are highlighted.
a Distance between E6 protein and LxxLL helical motif in [E6+lig]-hx systems.