Table 5.
CHelpG charge fitting for ribose phosphorane
| Atom | q*D | qD | q’D | qTS | q’TS | δq | q*TS |
|---|---|---|---|---|---|---|---|
| C1′ | −0.12 | 0.31 | −0.19 | 0.21 | −0.09 | 0.10 | −0.02 |
| H1′ | 0.09 | −0.12 | 0.09 | −0.10 | 0.09 | 0.00 | 0.09 |
| H1″ | 0.09 | −0.20 | 0.09 | −0.02 | 0.09 | 0.00 | 0.09 |
| C2′ | 0.23 | 0.70 | 0.30 | 0.42 | 0.17 | −0.13 | 0.10 |
| H2″ | 0.09 | −0.31 | 0.09 | −0.16 | 0.09 | 0.00 | 0.09 |
| O2′ | −0.91 | −0.97 | −0.97 | −0.74 | −0.74 | 0.23 | −0.68 |
| C3′ | 0.18 | 0.65 | 0.37 | 0.54 | 0.29 | −0.08 | 0.10 |
| H3′ | 0.09 | −0.19 | 0.09 | −0.16 | 0.09 | 0.00 | 0.09 |
| O3′ | −0.63 | −0.63 | −0.63 | −0.62 | −0.62 | 0.01 | −0.62 |
| P | 1.64 | 1.37 | 1.37 | 1.54 | 1.54 | 0.17 | 1.81 |
| O1P | −0.84 | −0.84 | −0.83 | −0.88 | −0.90 | −0.08 | −0.92 |
| O2P | −0.84 | −0.81 | −0.83 | −0.92 | −0.90 | −0.08 | −0.92 |
| O3P | −0.65 | −0.58 | −0.58 | −0.68 | −0.68 | −0.10 | −0.75 |
| C3T | −0.23 | 0.36 | −0.16 | 0.54 | −0.21 | −0.05 | −0.28 |
| H3T1 | 0.09 | −0.08 | 0.09 | −0.14 | 0.09 | 0.00 | 0.09 |
| H3T2 | 0.09 | −0.08 | 0.09 | −0.16 | 0.09 | 0.00 | 0.09 |
| H3T3 | 0.09 | −0.09 | 0.09 | −0.18 | 0.09 | 0.00 | 0.09 |
| C4′ | −0.11 | 0.14 | −0.12 | 0.02 | −0.14 | −0.02 | −0.13 |
| H4′ | 0.09 | −0.07 | 0.09 | −0.04 | 0.09 | 0.00 | 0.09 |
| H4″ | 0.09 | −0.01 | 0.09 | 0.02 | 0.09 | 0.00 | 0.09 |
| O4′ | −0.53 | −0.55 | −0.55 | −0.53 | −0.53 | 0.02 | −0.51 |
CHelpG adjusted charges for determining ribose phosphorane partial atomic charges. New charges were created by taking the adjusted CHelpG charge difference δq between the ribose MeP− charges calculated in Table 2 and the ribose phosphorane. qTS are the ribose phosphorane CHelpG charges, q’TS are the adjusted CHelpG charges and q*TS are the final CHARMM* charges. See Eqn. 3 and 4 of text for further details.