Table 6.

Comparison of free energy terms^¶ with different selections of the anchoring atoms.

Ligand	#§	$\mathrm{\Delta }{G}_{\text{int}}^{\text{site}}+\mathrm{\Delta }\mathrm{\Delta }{G}_{\text{t},\text{r}}$
benzene	C1	−5.4 ± 0.3
	C2	−5.3 ± 0.4
	C3	−5.9 ± 0.2
indole	C1	−9.0 ± 0.1
	C2	−8.5 ± 0.1
	C3	−8.8 ± 0.2
n-butylbenzene	C1	−8.4 ± 0.2
	C2	−9.5 ± 0.2
	C3	−8.2 ± 0.3
SB3	C1	−24.0 ± 0.5
	C2	−23.6 ± 1.4
	C3	−25.7 ± 1.0
SBX	C1	−22.7 ± 0.7
	C2	−22.3 ± 0.8
	C3	−23.0 ± 1.1
FK5	C1	−50.6 ± 0.8
	C2	−49.2 ± 1.0
	C3	−49.4 ± 1.5

^¶Units of free energies are kcal/mol. The errors of all the free energy values are standard deviation of the last five cycles of FEP/MD, each started with the last snapshot of previous cycle and random velocities.

^§C1, C2, and C3 represent independent FEP/MD simulations for each ligand.