TABLE 2.

Free energy of binding, H-bonds, and surface matching coefficients for the inhibitors MBX2319, NMP, PAβN, and D13-9001, the substrate MIN, all bound to wild-type AcrB, and the substrate DOX bound to the F610A variant of AcrB

Compound	Calculated binding free energy								H-bond interactions and surface matchingb
	ΔGb (kcal/mol)a			Contribution to ΔGsolv (%)
				DPc		G-loop	Interface	Cleft
	ΔGb	ΔGsolv	TΔSconf	Total	Trapf				H-bonds	SMTotd	SMLd
MBX2319	−12.5 ± 6.6	−37.7 ± 2.8	−25.2 ± 3.8	31	21 (68)	0	2	4	0 (0)	0.77 (0.77)	0.87 (0.87)
NMP	−10.6 ± 7.9	−26.9 ± 3.9	−16.3 ± 4.0	26	18 (69)	4	1	0	0 (0)	0.82 (0.61)	0.91 (0.67)
PAβN	−13.4 ± 10.8	−40.8 ± 5.8	−27.4 ± 5.0	32	17 (53)	2	0	0	5.4 (0)	0.71 (0.44)	0.81 (0.63)
D13-9001	−18.2 ± 12.3	−48.8 ± 4.8	−30.6 ± 7.5	49	30 (61)	1	1	1	5.9 (0)	0.74 (0.71)	0.88 (0.91)
MIN	−7.2 ± 7.7	−29.3 ± 4.7	−22.1 ± 3.0	41	12 (29)	0	0	0	0 (1.2)	0.65 (0.62)	0.82 (0.85)
DOXF610A	NCe	−30.0 ± 4.5	NC	54	28 (52)	3 (NC)	1 (NC)	0	1.1 (NC)	0.71 (NC)	0.84 (NC)

^aThe total free energy of binding (ΔG_b) is the sum of the contribution calculated with the MM/GBSA method (ΔG_solv) and of the conformational entropy of the solute (TΔS_conf). The contributions to ΔG_b from residues belonging to selected regions are also reported. In the case of the hydrophobic trap, embedded in the DP, the weight of the contribution from the trap relative to the whole pocket is reported in parentheses.

^bCalculated on the conformation of the complex with the lower RMSD from the average extracted from the unbiased MD simulations. SM_Tot and SM_L refer to the total and lipophilic surface matching coefficients, respectively. See the supplemental material for further details.

^cThe residues within the various regions are listed in Fig. 1.

^dValues in parentheses are those for the starting structures.

^eNC, not calculated.

^fValues in parentheses are the percentages of the binding energy contributed by the hydrophobic trap in relation to that contributed by the entire DP.