Table 5. Molecular geometry (Å, °) of N1-substituted cytosine.
N denotes the number of fragments used to determine the parameters. The recommended restraints are printed in bold.
| PDB 1d8g (N = 3) | PDB 3p4j (N = 6) | Parkinson (N = 28) | CSD (N = 147) | QM for C | QM for CG | |
|---|---|---|---|---|---|---|
| N1—C2 | 1.397 (6) | 1.392 (3) | 1.397 (10) | 1.395 (9) | 1.432 | 1.414 |
| C2—N3 | 1.363 (10) | 1.351 (3) | 1.353 (8) | 1.353 (7) | 1.363 | 1.355 |
| N3—C4 | 1.333 (14) | 1.342 (2) | 1.335 (7) | 1.337 (8) | 1.314 | 1.340 |
| C4—C5 | 1.436 (13) | 1.431 (4) | 1.425 (8) | 1.424 (10) | 1.429 | 1.438 |
| C5—C6 | 1.331 (14) | 1.345 (5) | 1.339 (8) | 1.338 (8) | 1.355 | 1.360 |
| C6—N1 | 1.349 (14) | 1.366 (3) | 1.367 (6) | 1.365 (7) | 1.348 | 1.361 |
| C2—O2 | 1.234 (3) | 1.248 (3) | 1.240 (9) | 1.240 (8) | 1.217 | 1.240 |
| C4—N4 | 1.320 (6) | 1.327 (2) | 1.335 (9) | 1.330 (8) | 1.356 | 1.338 |
| C6—N1—C2 | 120.8 (10) | 120.9 (2) | 120.3 (4) | 120.3 (5) | 121.08 | 120.35 |
| N1—C2—N3 | 118.3 (11) | 119.3 (3) | 119.2 (7) | 119.1 (6) | 117.09 | 118.62 |
| C2—N3—C4 | 121.0 (9) | 120.1 (2) | 119.9 (5) | 120.1 (5) | 120.90 | 121.28 |
| N3—C4—C5 | 120.2 (8) | 121.5 (2) | 121.9 (4) | 121.6 (6) | 123.21 | 121.13 |
| C4—C5—C6 | 118.1 (7) | 117.4 (3) | 117.4 (5) | 117.5 (5) | 116.20 | 117.09 |
| C5—C6—N1 | 121.4 (10) | 120.8 (1) | 121.0 (5) | 121.2 (6) | 121.53 | 121.54 |
| O2—C2—N1 | 119.8 (5) | 119.0 (4) | 118.9 (6) | 118.8 (8) | 117.87 | 117.88 |
| O2—C2—N3 | 121.9 (7) | 121.7 (4) | 121.9 (7) | 122.0 (6) | 125.04 | 123.50 |
| N4-C4—C5 | 121.2 (9) | 120.2 (2) | 120.2 (7) | 120.3 (7) | 119.62 | 120.99 |
| N4—C4—N3 | 118.6 (16) | 118.3 (2) | 118.0 (7) | 118.1 (6) | 117.18 | 117.89 |
| RMSD versus 3p4j (d/a) | 0.0069/0.375 | 0.0062/0.381 | 0.0248/1.581 | 0.0117/0.937 | ||
| RMSD versus 1d8g (d/a) | 0.0211/1.325 | 0.0205/1.266 | 0.0285/2.053 | 0.0236/1.373 | ||
| RMSD versus QM for C (d/a) | 0.0166/1.135 | |||||