Table 4.

Geometry fitting results of deprotonated ribose phosphate

Bond (Å)	Protonated DFT	Deprotonated DFT	Relative Difference	Protonated CHARMM	Adjusted CHARMM*
O2′-C2′	1.43	1.33	−0.10	1.43	1.33 (0.00)
O2′-C2′-H2′	109.6	115.8	6.2	109.9	116.1 (0.0)
O2′-C2′-C1′	110.2	112.7	2.5	114.0	116.5 (0.0)
O2′-C2′-C3′	109.8	116.4	6.6	112.2	118.8 (0.0)

	Coordination Distance		Coordination Energy
Reaction	DFT	CHARMM*	DFT	CHARMM*
ribose MeP− + H2O → ribose MeP−:H2O (kcal/mol)	1.71	1.70 (0.00)	−18.4	−18.4 (0.0)

Where ribose MeP⁻ stands for the deprotonated ribose methyl phosphate. Final fitting for the Adjusted CHARMM* residue was performed within the RNA sequence active site taken from the “early intermediate” hammerhead ribozyme x-ray crystal structure.¹⁰