. Author manuscript; available in PMC: 2021 Apr 14.

Published in final edited form as: J Chem Theory Comput. 2020 Mar 9;16(4):2803–2813. doi: 10.1021/acs.jctc.9b01119

Table 3.

Absolute Binding Free Energy Components for EPI-G4 Complex Calculated Using the Simple PMF Approach and AlchemPMF

Component	Simple PMF	AlchemPMF
−w(r*)	−42.55 ± 4.92	−10.69 ± 0.82
$Δ G_{r e s t r}^{b u l k}$	9.79	9.79
$- Δ G_{(θ, ϕ, Θ, Φ, Ψ)}^{b o u n d}$	−2.57 ± 0.20	−2.57 ± 0.20
$- Δ G_{b o u n d - b u l k}^{v i b r}$	0.77 ± 0.004	0.04 ± 0.06
$- Δ G_{d e c o u p l e}^{b o u n d} - Δ G_{r e c o u p l e}^{b u l k}$	0	−11.59 ± 0.10
$Δ G_{b i n d}^{°}$ ^a	−34.61 ± 4.88	−15.03 ± 0.74
$Δ G_{b i n d}^{°} (e x p t)$ ^b	−10.7	−10.7

$Δ G_{b i n d}^{°}$ was obtained using the last 10 ns trajectory segment in each of the umbrella sampling windows.

Determined from fluorescence measurements.²⁸