Table IV.

The scores of the lowest-energy conformation and the heavy-atom RMSD against the crystal structure, showing results of the three water treatments for the five test cases

Complex	Water treatmenta	Lowest energy (kcal/mol)	RMSD versus crystal (Å)
	Designed	−65.88	0.54
1DF7	Explicit	−64.65	0.41
	Omitted	−57.23	0.46
	Designed	−52.11	0.71
1JIO	Explicit	−51.44	0.46
	Omitted	−44.87	0.75
	Designed	−33.22	0.46
1KI8	Explicit	−37.71	0.33
	Omitted	−30.58	0.45
	Designed	−41.92	0.42
1NNC	Explicit	−38.36	0.55
	Omitted	−31.32	0.92
	Designed	−54.41	0.25
1VZQ	Explicit	−59.41	0.31
	Omitted	−43.92	0.27

^aIn the explicit case, all the water molecules from the crystal structure were retained. In the omitted case, all the water molecules from the crystal structure were deleted. In the designed case, all the water molecules were deleted, but the water placement design was performed on the ensemble of ligand poses.