Table 3.
Average van der Waals energy (kcal/mol) and rise (Å) in the GpC, CpG, CG/GG, GG/CG, GG/GC, GC/GG steps measured over last 200ns of the simulations. For each structure, the top and bottom rows represent the average van der Waals energy and the rise between the steps in a given helix, respectively. Numbers in black (blue) represent data obtained from OL15 (BSC1) FF calculations
| Structure | GpC | CpG | CG/GG | GG/CG | GG/GC | GC/GG |
|---|---|---|---|---|---|---|
| GGC8BZ, out | –6.99, –7.19 | –5.06, –4.73 | – | – | – | – |
| 3.52, 3.35 | 3.53, 3.81 | – | – | – | – | |
| GGC8ZZ, out | –7.18, –5.46 | –5.07, –5.07 | – | – | – | – |
| 3.45, 3.90 | 3.46, 3.84 | – | – | – | – | |
| GGC8ZZ, in | – | –4.89, –4.66 | – | – | –9.36, –9.29 | –9.35, –9.31 |
| – | 4.31, 4.41 | – | – | 3.16, 3.19 | 3.15, 3.18 | |
| CGG4ZZ, in | –7.84, –8.15 | – | –7.08, –6.38 | –6.56, –6.50 | – | – |
| 3.11, 3.47 | – | 3.49, 2.68 | 3.52, 2.73 | – | – | |
| GGC4ZZ, alt | –6.38, –6.44 | –4.75, –4.75 | – | – | – | – |
| 3.02, 3.72 | 3.37, 2.95 | – | – | – | – | |
| GC6Z-DNA | –7.22,–7.55 | –5.29, –5.54 | – | – | – | – |
| 3.25, 3.29 | 3.70, 3.82 | – | – | – | – |