Table 29.
Geometry RMSD, in Å, of Protein Structures Optimized with the Fixed-Chares (OPLS-AA) Force Field and the Presented Polarizable Force Field from PDB Geometries.
| No H atoms |
Backbone only |
|||
|---|---|---|---|---|
| Molecule | OPLS | PFF | OPLS | PFF |
| 155c | 2.22 | 2.37 | 1.86 | 2.07 |
| 1bp2 | 1.93 | 1.90 | 1.53 | 1.55 |
| 1cc5 | 1.92 | 2.22 | 1.65 | 1.91 |
| 1crn | 2.00 | 1.83 | 1.60 | 1.63 |
| 1ctf | 2.26 | 2.18 | 1.76 | 1.65 |
| 1fdx | 2.67 | 2.43 | 2.33 | 1.94 |
| 1fx1 | 2.46 | 2.21 | 1.71 | 1.47 |
| 1gcn | 4.14 | 3.77 | 2.88 | 2.00 |
| 1gcr | 1.53 | 1.54 | 1.07 | 1.11 |
| 1paz | 1.73 | 1.71 | 0.96 | 1.04 |
| 1pcy | 1.78 | 1.77 | 1.05 | 1.05 |
| 1pgx | 4.10 | 4.02 | 2.43 | 2.15 |
| 1ppt | 2.20 | 1.90 | 1.07 | 1.70 |
| 1r69 | 1.68 | 1.70 | 1.12 | 1.13 |
| 1rnt | 2.32 | 2.30 | 1.27 | 1.30 |
| 1sn3 | 2.56 | 2.28 | 1.52 | 1.17 |
| 1ubq | 2.08 | 1.97 | 1.35 | 1.16 |
| 2cdv | 3.41 | 3.53 | 2.25 | 2.37 |
| 2fxb | 2.32 | 2.01 | 1.87 | 1.61 |
| 2gn5 | 2.57 | 2.53 | 2.10 | 2.06 |
| 2lzm | 1.65 | 1.81 | 1.21 | 1.37 |
| 2ovo | 1.74 | 1.76 | 1.53 | 1.55 |
| 2prk | 1.26 | 1.33 | 1.03 | 1.10 |
| 2rn2 | 1.92 | 1.54 | 1.34 | 1.09 |
| 2sns | 2.09 | 2.27 | 1.37 | 1.53 |
| 2ssi | 1.93 | 1.89 | 1.49 | 1.48 |
| 351c | 1.64 | 1.77 | 1.20 | 1.38 |
| 3adk | 1.65 | 1.62 | 1.26 | 1.28 |
| 3c2c | 2.11 | 2.02 | 1.29 | 1.16 |
| 3fxc | 3.66 | 3.92 | 2.67 | 3.11 |
| 3icb | 2.24 | 1.82 | 1.90 | 1.47 |
| 3wrp | 1.93 | 1.98 | 1.30 | 1.28 |
| 4fdl | 2.51 | 2.48 | 1.82 | 1.76 |
| 4fin | 2.89 | 2.50 | 2.20 | 1.79 |
| 4fxn | 2.25 | 1.91 | 1.38 | 1.07 |
| 4pti | 2.41 | 2.30 | 1.66 | 1.58 |
| 5cpv | 1.97 | 1.97 | 1.11 | 1.29 |
| 5fin | 3.83 | 2.87 | 3.32 | 2.40 |
| 7rxn | 1.73 | 1.74 | 1.26 | 1.31 |
| Average | 2.29 | 2.20 | 1.66 | 1.57 |