Table 2.

Relative free energy differences in kcal/mol as calculated from molecular dynamics simulations.^a

	Lipid A	Lipid IVa	DA193
ΔGbindb	−1.3 ± 0.4	−2.4 ± 0.4	−3.0 ± 0.4
ΔGpose (A>B)c	1.6 ± 0.3	2.2 ± 0.4	−0.1 ± 0.4

^aError estimates are calculated from block averages.

^bFree energy of binding as estimated by the LIE method: ΔG_bind = αΔ<V_vdw> + βΔ<V_el>, where <V_vdw> and <V_el> are the average ligand-surrounding van der Waals and electrostatic interaction energies, Δindicates the difference between the ligand-bound and unbound simulations; α = 0.18 and β = 0.09, using exponential averages of different poses.⁴⁸ The free energy of binding is logarithmically dependent on the dissociation constant K_d: ΔG_bind=  RTlnK_d, where R is the gas-constant and T is the absolute temperature.

^cRelative free energy difference between poses A and B, calculated using the LIE model.³³