. Author manuscript; available in PMC: 2018 Feb 27.

Published in final edited form as: J Chem Theory Comput. 2017 May 26;13(6):2501–2510. doi: 10.1021/acs.jctc.7b00204

Table 2.

Alchemical Free Energy Changes (kcal/mol) Between Benzene and p-Xylene Binding with T4 Lysozyme Calculated Using Pairwise GSLD with Corrections from PMFs.

χ^*	ΔG(χ^*)	–β⁻¹lnP(χ^*\|λ = 0)	–β⁻¹lnP(χ^*\|λ = 1)	ΔG	ΔΔG
trans (χ^* = −180°)	−8.40 ± 0.46	−0.47 ± 0.01	0.4 ± 0.03	−9.27 ± 0.50	0.27 ± 0.56
gauche (χ^* = −60°)	−10.60 ± 0.36	1.14 ± 0.03	−0.45 ± 0.01	−9.01 ± 0.40	0.43 ± 0.46

The alchemical free energy change ΔG in water is −9.44 ± 0.06 kcal/mol and the experimental relative binding free energy ΔΔG is 0.52 ± 0.22 kcal/mol.