Table 2. Protein-ligand distances.
| Distance | Unrestrained | Restrained | Free1 | Free2 | Free3 | Free4 |
|---|---|---|---|---|---|---|
| EPI-N1/TRP143-O | 6.2 ± 1.7 | 4.5 ± 0.9 | 4.7 ± 1.0 | 4.4 ± 0.9 | 5.1 ± 1.5 | 4.5 ± 0.9 |
| EPI-N1/TYR189-OH | 6.5 ± 2.4 | 5.3 ± 1.1 | 5.9 ± 1.4 | 4.9 ± 0.5 | 6.2 ± 2.1 | 5.3 ± 1.1 |
| EPI-N2/TYR87-OH | 6.2 ± 1.3 | 5.9 ± 2.0 | 6.0 ± 1.3 | 5.9 ± 1.2 | 6.6 ± 1.8 | 5.9 ± 2.0 |
| EPI-CL/LEU103-N | 8.9 ± 5.2 | 4.2 ± 0.8 | 4.1 ± 0.8 | 4.3 ± 0.8 | 5.4 ± 2.6 | 5.1 ± 1.2 |
| EPI-CL/LEU113-N | 8.2 ± 3.0 | 5.1 ± 1.2 | 5.3 ± 1.3 | 5.8 ± 1.2 | 6.5 ± 2.1 | 5.6 ± 1.6 |
| EPI-pyrimidine/TRP143-indole | 6.1 ± 1.3 | 5.0 ± 0.7 | 5.1 ± 0.8 | 5.3 ± 0.8 | 5.2 ± 0.9 | 4.9 ± 0.7 |
| EPI-bridge ring/TYR189-ring | 6.3 ± 2.5 | 5.3 ± 1.1 | 5.0 ± 0.7 | 4.9 ± 0.5 | 6.0 ± 2.2 | 5.5 ± 1.7 |
| EPI-bridge ring/TYR182-ring | 5.3 ± 0.7 | 5.2 ± 0.4 | 5.3 ± 0.4 | 5.4 ± 0.4 | 5.8 ± 1.2 | 5.6 ± 0.8 |
Distances (in Å) between epibatidine and selected residues (see Section “C loops conformation and interaction with the agonist epibatidine”). Values averaged along 200ns, using data collected from the five subunits.