Table 3. Calculated Thermodynamic Properties for the Hydration Site Lying within the Alanine Pocketa.
| MD scheme | free (kcal mol-1) | restrained (kcal mol-1) | fixed (kcal mol-1) |
|---|---|---|---|
| occupancy | 0.77 | 0.82 | 0.88 |
| E (pw) | –13.41 | –13.98 | –13.79 |
| E (ww) | –9.11 | –7.99 | –8.61 |
| E (total) | –22.52 | –21.97 | –22.40 |
| ΔE | +1.10 | +1.65 | +1.22 |
| TS (density) | 0.68 | 0.72 | 0.76 |
| TS (pw, trans) | 0.12 | 0.16 | 0.26 |
| TS (pw, orient) | 1.83 | 2.03 | 2.28 |
| TS (pw) | 1.94 | 2.19 | 2.54 |
| TS (ww, trans) | 0.01 | 0.01 | 0.01 |
| TS (ww, orient) | 0.84 | 1.42 | 0.95 |
| TS (ww) | 0.85 | 1.43 | 0.96 |
| TS (total) | 3.47 | 4.34 | 4.26 |
| –TΔS | +0.12 | +0.99 | +0.91 |
| ΔF | +1.22 | +2.64 | +2.13 |
a
Details on the thermodynamic properties for the hydration site lying within the alanine pocket, calculated using the restrained MD scheme. The protein–water terms are denoted pw, and the water–water terms are denoted ww. The translational contributions are denoted trans, and the orientational contributions are denoted orient. E is the interaction energy, and F is the free energy.