Table 2. Side chain repacking results for seven scaffolds.

PDB	Hydrogen bonds			Binding energy (Proda energy units)
	Native	Minimal	Complex	Native	Minimal	Complex
1c2t	13	5 (38%)	13 (100%)	-68.48	38.07	-69.30
1dqx	19	3 (16%)	17 (89%)	-52.35	30.67	-54.10
1h2j	13	3 (23%)	10 (77%)	-37.72	144.61	-40.15
1jcl	11	4 (36%)	11 (100%)	-30.33	35.20	-28.01
1ney	14	8 (57%)	11 (79%)	-42.98	-18.93	-39.10
1oex	9	6 (67%)	9 (100%)	-57.80	-18.28	-53.86
3vgc	9	8 (89%)	9 (100%)	-30.31	31.77	-30.45
Total	88	37 (42%)	80 (91%)	-	-	-

The columns “Native”, “Minimal”, and “Complex” shows results calculated by TS in the crystal structures, matched TS based on the complex active site model and the minimal active site model, respectively.