Table 1.

Binding free energies.

Ligand	Deep-LDA	Exp
G1	−6.31 ± 0.06	−5.24
G2	−6.19 ± 0.08	−5.04
G3	−6.27 ± 0.07	−5.94
G4	−2.51 ± 0.07	−2.38
G5	−3.91 ± 0.09	−3.90
G6	−4.97 ± 0.07	−4.52

We show the mean binding free energy ΔG (kcal mol⁻¹) for every ligand and the corresponding experimental value. We calculate ΔG as a weighted block average over the simulations with all Deep-LDA CVs (see the Supplementary Methods for further details).