. Author manuscript; available in PMC: 2017 May 10.

Published in final edited form as: J Chem Theory Comput. 2016 Apr 26;12(5):2459–2470. doi: 10.1021/acs.jctc.6b00134

Table 2.

Binding free energy of T4L/L99A/p-xylene starting from trans and gauche conformations from BEDAM-REMD simulations with and without flattening of VAL111 side chain torsion

Starting Conformation	Method	$Δ G_{B i n d i n g}^{*}$
Trans	REMD_{no–flattening}	−2.55 ± 0.21
Trans	REMD_flattening	−3.07 ± 0.17
Gauche	REMD_{no–flattening}	−3.02 ± 0.22
Gauche	REMD_flattening	−3.21 ± 0.29

in kcal/mol and experimental binding affinity data (−4.67 kcal/mol) for the T4L system from Mobley’s paper (ref.²⁶) (also reported by Jiang et. al in ref.²⁹).