Table 1.

Calculated and experimental relative binding free energies for 20 compound pairs based on adenine. 2D structures of the compounds are shown in Fig. 1C.

Ligand pair (A → B)		cmpd A		cmpd B		ΔΔGbind (kcal/mol)
		R1	R2	R1	R2	Experimentala	Calculatedb
1 → 2	pocket A	—	—	H	CH3	<−1.6	−3.9 ± 0.2
3 → 4		Br	CH3	Br	H	2.0 ± 0.3	2.4 ± 0.0
5 → 3		Br	CH3CH2	Br	CH3	0.5 ± 0.3	−1.2 ± 0.0
6 → 5		Br	HOCH2CH2	Br	CH3CH2	−1.5 ± 0.2	−2.5 ± 0.1
7 → 5		Br	CH3CH2CH2	Br	CH3CH2	−1.1 ± 0.2	−0.5 ± 0.1
8 → 5		Br	(CH3)2CHCH2	Br	CH3CH2	−2.9 ± 0.3	−2.3 ± 0.1
9 → 2		H	CH3CH2	H	CH3	0.7 ± 0.2	0.2 ± 0.0
10 → 9		H	HOCH2CH2	H	CH3CH2	−1.0 ± 0.2	−1.4 ± 0.1
11→ 9		H	(CH3)2CHCH2	H	CH3CH2	<−2.3	−3.2 ± 0.0
12 → 13		H	HOCH2CH2CH2	H	CH3CH2CH2	0.5 ± 0.2	0.6 ± 0.4
3 →2	Pocket B	Br	CH3	H	CH3	2.4 ± 0.2	2.3 ± 0.2
5 → 9		Br	CH3CH2	H	CH3CH2	2.2 ± 0.3	1.5 ± 0.0
14 → 15		Br	cC5H9	H	cC5H9	0.0 ± 0.3	−2.2 ± 0.2
16 → 17		Br	CH2CHCH2CH2	H	CH2CHCH2CH2	1.0 ± 0.2	0.3 ± 0.2
18 → 9		CH3	CH3CH2	H	CH3CH2	1.4 ± 0.2	1.4 ± 0.0
19 → 9		furyl	CH3CH2	H	CH3CH2	3.8 ± 0.2	5.4 ± 0.2
20 → 9		OH	CH3CH2	H	CH3CH2	0.4 ± 0.2	0.1 ± 0.1
21 → 18		CH3O	CH3CH2	CH3	CH3CH2	1.3 ± 0.1	2.7 ± 0.1
22 → 21		CH3CH2O	CH3CH2	CH3O	CH3CH2	−0.3 ± 0.2	−0.4 ± 0.0
23 → 21		(CH3)2CHO	CH3CH2	CH3O	CH3CH2	<−4.9/−0.8c	0.0 ± 0.1

^aUncertainties are calculated as the standard error of the mean based on the maximal and minimal affinities values obtained from the 95% confidence intervals of the experimentally determined K_i values. Experimental K_i values can be found in Supplementary Table 1.

^bAverage relative binding free energy from three independent trajectories with uncertainties estimated as the standard error of the mean.

^cK_i value from reference 23/Remeasured K_i value in this work (Supplementary Table 1).