Table 6.

Geometry fitting results for ribose phosphorane parameterization

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