. Author manuscript; available in PMC: 2008 Sep 29.

Published in final edited form as: J Chem Phys. 2007 Oct 21;127(15):155101. doi: 10.1063/1.2771171

Table 3.

Comparison	Pearson Unsquared Correlation Coefficient			Regression Slope			Regression Intercept (kcal/mol)

VDW^a (all \| + \| −)^b	0.90	0.92	0.96	0.85	1.00	0.90	−0.3	−2.0	2.5
VDW ⊕^a (all \| + \| −)	0.97	0.96	0.99	0.94	1.05	0.94	−0.2	−1.1	1.1
OPT^a (all \| + \| −)	0.94	0.96	0.98	0.80	0.87	0.85	−0.1	−1.3	1.9
OPT ⊕^a (all \| + \| −)	0.99	0.99	0.99	0.90	0.92	0.89	0.0	−0.3	0.5

Implicit solvent energies are defined by Eq. 8 in the text. “VDW” refers to solute definition by Lennard-Jones radii taken from the AMBER ff99 forcefield. “OPT” refers to solute definition by a set of optimized radii [54]. A molecular surface definition and 1.4 Å solvent probe were used for all implicit-solvent calculations.

Comparisons were made between all atoms in the protein, as well as between positively or negatively charged atoms specifically. Results in table sub-cells are listed in this order.

A ⊕ symbol refers to implicit solvent energies corrected by adding the energy of each atomic partial charge in the solvent reaction field created by the uncharged protein in SPC/E solvent (see Eq. 10). Figure 7 shows three of these four sets of implicit solvent per-atom energies plotted against per-atom energies obtained with explicit SPC/E water.