Table 1. PDB IDs of Protein–Ligand Complexes Used in the RBFE Calculations for the Ligand Transformations.

protein	ligand	PDB ID
thrombin	B5	2ZFF(41)
	B1a	2ZDV(41)
scytalone	C 3d	5STDa(40)
dehydratase	C 5d	3STD(39)
factor Xa	IID	2BQ7(42)
	IIE	2BQW(42)
BACE1	C4j	4DJW(43)
	C4b	4DJV(43)
BTK	S8	4ZLZ(44)
	S11	4Z3V(44)

^aIndicates the PDB ID of the complex containing a closely related ligand.