Table 3. Average Structural Parameters (last 20 ns of 100 ns simulations) for the A-RNA Duplex 1QC0′ (r(GCACCGUUGG)) Obtained Using the ff99bsc0 Force Field with Various χ Corrections (values with ff99 force field in italics)a.
| parameter | X-ray | no χ correction | χYIL | χOL-DFT | χOL |
|---|---|---|---|---|---|
| χ/deg | 197.1 ± 4.4 | 203.1 ± 9.2 | 196.0 | 197.4 | 199.1 |
| 209.4 ± 12.7 | 194.0 | 196.3 | 196.7 | ||
| P/deg | 17.7 ± 6.0 | 19.3 ± 13.5 | 15.4 | 19.2 | 17.4 |
| 27.5 ± 16.9 | 13.4 | 17.5 | 17.1 | ||
| minor groove width/Å | 15.4 ± 0.1 | 15.3 ± 0.6 | 15.2 | 15.3 | 15.3 |
| 15.0 ± 0.6 | 14.9 | 15.1 | 14.8 | ||
| major groove width /Å | 14.7 ± 1.5 | 15.9 ± 2.9 | 19.0 | 17.5 | 17.9 |
| 18.9 ± 3.2 | 22.1 | 19.8 | 22.3 | ||
| slide/Å | –1.70 ± 0.25 | –1.69 ± 0.50 | –2.07 | –1.94 | –1.90 |
| -1.89 ± 0.57 | -2.35 | -2.11 | -2.30 | ||
| roll/deg | 8.1 ± 4.1 | 9.7 ± 6.1 | 4.6 | 7.1 | 6.7 |
| 8.5 ± 6.2 | 3.0 | 6.4 | 4.0 | ||
| propeller/deg | –12.5 ± 4.5 | –13.7 ± 8.5 | –6.3 | –10.7 | –9.7 |
| -12.5 ± 8.7 | -4.3 | -9.8 | -7.4 | ||
| X-displ./Å | –4.45 ± 1.18 | –4.85 ± 1.60 | –5.01 | –5.07 | –4.95 |
| -5.35 ± 2.18 | -5.50 | -5.49 | -5.91 | ||
| inclination/deg | 15.2 ± 8.3 | 18.0 ± 11.0 | 8.8 | 13.4 | 12.7 |
| 16.3 ± 11.7 | 5.5 | 12.2 | 8.0 | ||
| helical twist/deg | 32.3 ± 3.6 | 31.7 ± 4.1 | 29.7 | 30.5 | 30.4 |
| 31.1 ± 4.9 | 28.6 | 29.8 | 28.6 | ||
| rmsd/Å | 1.04 | 1.21 | 1.06 | 1.07 | |
| 1.36 | 1.85 | 1.43 | 1.90 |
a
Standard deviations are shown for the unmodified force fields for orientation, and they are very similar for the other force fields. RMSD is mass weighted for all atoms.