Table 1. Distances between the oxygen atom of water molecules W1–W5 and key ligand atoms and protein residues after AMMOS2 minimization compared to their X-ray positions in the PDB 1YDS complex.
| Water molecules (W) displacement | Distance, in Å | ||||
|---|---|---|---|---|---|
| X-ray | Case 1 (5 Ws) | Case 1 (12 Ws in 6 Å) | Case 3 (5 Ws) | Case 3 (12 Ws in 6 Å) | |
| W1 - O2 ligand | 3.28 | 4.77 | 4.42 | 4.41 | 4.21 |
| W1 - NZ K72 | 3.51 | 3.28 | 2.75 | 2.81 | 2.76 |
| W2 - NZ K72 | 3.81 | 2.89 | 2.71 | 3.41 | 3.5 |
| W3 - N4΄ ligand | 3.28 | 3.8 | 3.9 | 3.52 | 3.85 |
| W3 - OE1 E127 | 3.85 | 3.0 | 3.75 | 3.12 | 3.27 |
| W4 - O1 ligand | 3.75 | 3.14 | 3.68 | 3.64 | 3.43 |
| W4 - N1΄ ligand | 2.37 | 3.67 | 3.76 | 4.7 | 3.45 |
| W4 - OE2 E127 | 2.89 | 2.82 | 2.81 | 2.81 | 2.81 |
| W5 - O1 ligand | 5.66 | 5.69 | 6.18 | 6.17 | 5.78 |
| W5 - OH Y330 | 2.89 | 2.83 | 2.78 | 2.83 | 2.76 |