Table 5.

Free energy results in kcal/mol obtained by applying DDM to the SSBP/GSBP/CHARMM27 model.^54,54,^a

	ΔA(FEP)charge	ΔA(FEP)LJ-attractive	ΔA(FEP)LJ-repulsive	ΔAR	$\mathrm{\Delta }{A}_{\tau }^0$	Total
Solvent	21.7.±0.1	25.5±0.4	−27.0±0.2			20.2±0.3
Protein	27.1.±0.4	42.7± 0.3	− 21.6±0.7	2.2.±0.2	−5.0	45.4±0.4
Δ, solv –prot	−5.4±0.2	−17.2±0.3	−5.4±0.4	−2.2±0.2	5.0	−25.2±0.5

^aThe elimination of the biotin-environment interactions was obtained by free energy perturbation (FEP) in three steps, treating first the electrostatic interactions, then the attractive and repulsive LJ interactions. ΔA_R and $\mathrm{\Delta }{A}_{\tau }^0$ and ΔA⁰ =−25.2±0.5 kcal/mol are defined in eqs 10 and 11. For each environment the results are averages of five FEP runs started from different ligand or protein-ligand structures.