Table 3.

RNA L-J parameters

Parameter	Protonated Methyl Ribose	Deprotonated Methyl Ribose	Phosphorane Methyl Ribose	2′,3′-cyclic Methyl Ribose
Rmin/2O2′	1.77	1.75	1.76	1.77
∊ O2′	−0.1521	−0.3236	−0.2378	−0.1521

L-J parameters for the deprotonated ribose phosphate were fit to the water binding coordination distance (1.713 Å) and the water binding coordination energy (18.4 kcal/mol) with TIP3P water (See Table 4 as well). L-J parameters for axial phosphorane oxygens (bond order ≈ 0.5) were determined by averaging between the protonated (bond order ≈ 0.0) and 2′,3′-cyclic (bond order ≈ 1.0) structures.