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. Author manuscript; available in PMC: 2009 Oct 14.
Published in final edited form as: J Am Chem Soc. 2008 Feb 12;130(9):2817–2831. doi: 10.1021/ja0771033

Table 2.

Inhibition data for the congeneric ligand pairs binding to factor Xa. Our predicted activity differences from the trained 3-parameter and 5-parameter displaced-solvent functionals and MM-GBSA method. When a ligand was taken from a solved crystal structure, the ligand was designated “(pdb id):(ligand residue name)”; and when the ligand was built from congeneric series data, the ligand was designated “(first author of the reporting publication):(molecule number in the reporting publication)”.

Initial Ligand Final Ligand ΔΔGexp
(kcal/mol)		 ΔΔG3p
(kcal/mol)		 ΔΔG5p
(kcal/mol)		 ΔΔGab initio
(kcal/mol)		 ΔΔGMM-GBSA
(kcal/mol)		 Ref.
1MQ5:XLC 1MQ6:XLD −2.94 −2.85 −2.54 −2.97 −4.22 Adler02
1NFU:RRP 1NFY:RTR −1.56 −2.56 −2.98 −3.23 −0.47 Maignan03
1NFX:RDR 1NFW:RRR −0.59 1.35 0.94 0.21 2.01 Maignan03
Matter:25 Matter:28 −0.62 −0.61 −0.62 −2.17 −0.48 Matter05
Matter:25 2BMG:I1H −1.05 −1.31 −1.31 −3.52 −3.8 Matter05
Matter:28 2BMG:I1H −0.43 −0.70 −0.69 −1.35 −3.32 Matter05
Mueller:3 Mueller:2 −0.90 −2.05 −2.34 −4.53 −8.35 Mueller02
Haginoya:56 Haginoya:57 −0.59 −1.15 −1.12 −0.23 1.41 Haginoya04
Haginoya:60 Haginoya:56 −0.19 0.00 0.00 0.08 0.81 Haginoya04
Haginoya:56 1V3X:D76 −0.54 −1.15 −1.12 −0.31 −5.04 Haginoya04
Haginoya:60 Haginoya:57 −0.79 −1.15 −1.12 −0.15 2.22 Haginoya04
1V3X:D76 Haginoya:57 −0.05 0.00 0.00 0.08 6.45 Haginoya04
Haginoya:60 1V3X:D76 −0.74 −1.15 −1.12 −0.23 −4.23 Haginoya04
2BQ7:IID 2BQW:IIE −2.01 −1.73 −1.95 −5.42 −8.81 Nazare05
2BQ7:IID 2BOH:IIA −2.01 −1.80 −2.09 −1.98 −6.7 Nazare05
2BQW:IIE 2BOH:IIA 0.00 −0.07 −0.13 3.44 2.11 Nazare05
Quan:11a Quan:43 −0.09 0.04 0.39 0.27 0.3 Quan05
Quan:43 1Z6E:IK8 −0.68 −0.04 −0.45 −0.49 −3.47 Quan05
Quan:11a 1Z6E:IK8 −0.77 0.00 −0.06 −0.22 −3.17 Quan05
1G2L:T87 1G2M:R11 −0.21 0.79 0.20 −0.32 10.1 Nar01
Guertin:5c 1KSN:FXV −0.13 −0.87 −0.78 −0.68 −4.42 Guertin02
2FZZ:4QC 2G00:5QC −1.06 −1.70 −1.68 0.06 0.31 Pinto06
Matter:107 1LQD:CMI −3.93 −2.52 −2.48 −2.84 −15.71 Matter02
Matter:108 Matter:46 −3.09 −2.52 −2.48 −2.78 −11.49 Matter02
1F0R:815 1F0S:PR2 −0.12 0.09 0.14 −1.06 −3.53 Maignan00
Young:33 2J4I:GSJ −0.82 0.00 0.00 0.36 −7.53 Young06
Young:32 2J4I:GSJ −4.93 −4.87 −4.83 −5.31 −15.25 Young06
Young:38 2J4I:GSJ −6.26 −4.87 −4.83 −5.67 −7.27 Young06
Young:32 Young:33 −4.11 −4.87 −4.83 −5.67 −7.72 Young06
Young:38 Young:33 −5.44 −4.87 −4.83 −6.03 0.26 Young06
Young:38 Young:32 −1.33 0.00 0.00 −0.36 7.98 Young06