Table 6.
Bond (Å) | DFT | CHARMM* |
---|---|---|
C2-O2 | 1.361 | 1.361 (0.00) |
P-O2 | 1.99 | 1.99 (0.00) |
P-O3 | 1.79 | 1.79 (0.00) |
P-O5 | 1.84 | 1.84 (0.00) |
P-OR/S | 1.53 | 1.53 (0.00) |
O2-O5 | 3.78 | 3.79 (0.01) |
Angle (°) | DFT | CHARMM* |
---|---|---|
C1-C2-O2 | 113.5 | 113.7 (0.2) |
C3-C2-O2 | 105.9 | 105.9 (0.0) |
C2-O2-P | 109.3 | 109.3 (0.0) |
C3-O3-P | 117.5 | 117.5 (0.0) |
O2-P-O5 | 163.5 | 164.0 (0.5) |
OR-P-OS | 129.1 | 129.1 (0.0) |
O3-P-OR/S | 115.3 | 115.3 (0.0) |
O2-P-OR/S | 91.4 | 91.4 (0.0) |
O5-P-OR/S | 95.4 | 95.3 (0.1) |
O2-P-O3 | 81.0 | 81.0 (0.0) |
O3-P-O5 | 83.3 | 83.3 (0.0) |
Final fitting for the Adjusted CHARMM* residue was performed within the RNA sequence active site taken from the “late intermediate” hammerhead ribozyme x-ray crystal structure.74