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. Author manuscript; available in PMC: 2010 May 13.
Published in final edited form as: J Comput Chem. 2007 Jan 30;28(2):495–507. doi: 10.1002/jcc.20474

Table 2.

CHelpG charge fitting for deprotonated ribose phosphate

Atom qo qP q’P qD q’D δq q*D
C1′ 0.07 0.19 0.00 0.31 −0.19 −0.19 −0.12
H1′ 0.09 0.03 0.09 −0.12 0.09 0.00 0.09
H1” 0.09 −0.04 0.09 −0.20 0.09 0.00 0.09
C2′ 0.14 0.35 0.21 0.70 0.30 0.09 0.23
H2” 0.09 −0.05 0.09 −0.31 0.09 0.00 0.09
O2′ −0.66 −0.71 −0.72 −0.97 −0.97 −0.25 −0.91
H2 ′ 0.43 0.42 0.43 - - −0.43 -
C3′ 0.01 0.30 0.20 0.65 0.37 0.17 0.18
H3′ 0.09 −0.01 0.09 −0.19 0.09 0.00 0.09
O3′ −0.57 −0.57 −0.57 −0.63 −0.63 −0.06 −0.63
P 1.50 1.23 1.23 1.37 1.37 0.14 1.64
O1P −0.78 −0.77 −0.77 −0.84 −0.83 −0.06 −0.84
O2P −0.78 −0.76 −0.76 −0.81 −0.83 −0.06 −0.84
O3P −0.57 −0.50 −0.50 −0.58 −0.58 −0.08 −0.65
C3T −0.17 0.31 −0.10 0.36 −0.16 −0.06 −0.23
H3T1 0.09 −0.06 0.09 −0.08 0.09 0.00 0.09
H3T2 0.09 −0.05 0.09 −0.08 0.09 0.00 0.09
H3T3 0.09 −0.03 0.09 −0.09 0.09 0.00 0.09
C4′ 0.07 0.27 0.06 0.14 −0.12 −0.18 −0.11
H4′ 0.09 −0.03 0.09 −0.07 0.09 0.00 0.09
H4” 0.09 0.00 0.09 −0.01 0.09 0.00 0.09
O4′ −0.50 −0.52 −0.52 −0.55 −0.55 −0.03 −0.53

Adjusted charges (q’P/q’D) were determined by changing all CHelpG hydrogen charges to be consistent with CHARMM27 by the procedure outlined in Eqn. 3 and 4 of the text. This difference between the CHARMM27 (qo) and CHelpG charges (qP/qD) was then added into the nearest heavy atom charge. Once the adjusted atomic charge differences between the protonated and deprotonated structures were determined (δq), these differences were then added to the standard CHARMM27 charges to correct for deprotonation (q*D).