TABLE III.

Computed ΔG^L→H values (in kcal/mol) for a fully unrestrained blocked serine in solution from the staged transformation approach using different combinations of confined reference structures (i.e., X₀, ${\mathbf{X}}_0^{\prime }$).^a

	${\mathbf{X}}_0^{\prime }$ sample 1	${\mathbf{X}}_0^{\prime }$ sample 2	${\mathbf{X}}_0^{\prime }$ sample 3	${\mathbf{X}}_0^{\prime }$ sample 4	${\mathbf{X}}_0^{\prime }$ sample 5
$\mathrm{\Delta }{G}_0^{L\to H}$	−18 550.6 ± 0.3	−18 551.9 ± 0.2	−18 553.9 ± 0.3	−18 556.3 ± 0.5	−18 550.2 ± 0.2
X0 sample 1	4.5/−18 546.1b	5.0/−18 546.8	9.6/−18 544.3	11.1/−18 545.2	11.1/−18 539.0
X0 sample 2	2.4/−18 548.2	2.9/−18 548.9	7.6/−18 546.3	9.0/−18 547.3	9.1/−18 541.1
X0 sample 3	3.9/−18 546.7	4.5/−18 547.4	9.1/−18 544.8	10.6/−185 45.7	10.6/−18 539.6
X0 sample 4	3.1/−18 547.5	3.7/−18 548.2	8.3/−18 545.7	9.7/−18 546.5	9.8/−18 540.4
X0 sample 5	3.0/−18 547.6	3.5/−18 548.3	8.2/−18 545.8	9.6/−18 546.7	9.6/−18 540.5
Avg.c	−18 545.4 ± 2.9	(−18 546.7 ± 1.2)

^aSee text for the discussion of the selection of the confined structures. The first row lists the values of $\mathrm{\Delta }{G}_0^{L\to H}$, which depends only on the choices of R₀′, as discussed in Sec. II D 2, we introduced an intermediate level of model (M) that uses the CHARMM36 force field, except that the partial charges are replaced by DFTB3/3OB Mulliken charges computed for a single snapshot in solution; thus, $\mathrm{\Delta }{G}_0^{L\to H}=\mathrm{\Delta }{G}_0^{L\to M}+\mathrm{\Delta }{G}_0^{M\to H}$, where the L/M conversion is done with multi-λ TI due to the low computational cost, and M/H conversion is done with 1-λ FEP due to the favorable distribution overlap illustrated in Fig. 8. For other entries, the value before the slash is $\mathrm{\Delta }{G}_{\mathrm{\Lambda }}^L$, and the value after the slash is $\mathrm{\Delta }{G}^{L\to H}=\mathrm{\Delta }{G}_0^{L\to H}+\mathrm{\Delta }{G}_{\mathrm{\Lambda }}^L$.

^bFor this specific combination, the confined structures (X₀, ${\mathbf{X}}_0^{\prime }$) are close to the minima on the L/H free energy surface based on the 2D projection [see Figs. 10(c) and 10(d)].

^cThe average ΔG^L→H value is reported as the “Stage” entry in Table I; values with parentheses are the results without including data from R₀′ sample 5 [see Fig. 10(d)], which leads to consistently different values (see text).