Table 3.

Overall effects of the choice of the force field and energy window upon the average RMSD and ST values between the computationally generated conformations and the experimental conformations for the 25,972 3-D reference structures

		Torsion Search Force Fielda
Energy window (kcal/mol)	Fragment Force Fielda	Full		NoEstat		Trunc
		RMSD	ST	RMSD	ST	RMSD	ST
5	Full	0.69	0.89	0.48	0.93	0.47	0.93
	NoEstat	0.69	0.89	0.48	0.93	0.47	0.93
	Trunc	0.71	0.89	0.48	0.93	0.46	0.93
10	Full	0.52	0.92	0.42	0.94	0.42	0.94
	NoEstat	0.52	0.92	0.42	0.94	0.42	0.94
	Trunc	0.52	0.92	0.41	0.94	0.42	0.94
15	Full	0.46	0.93	0.40	0.94	0.40	0.95
	NoEstat	0.46	0.93	0.40	0.94	0.40	0.95
	Trunc	0.46	0.93	0.40	0.94	0.40	0.95

^a Full = the 94s variant of the Merck molecular force field (MMFF94s); NoEstat = MMFF94s without coulombic interaction terms; Trunc = MMFF94s without coulombic and van der Waals interaction terms.