PubChem3D: Conformer generation

Table 2 The average root-mean-square distance (RMSD), the average Shape-Tanimoto (ST), the average number of conformers per chemical structure, and the count of the 100-k limit cases for conformer models for all 25,972 3-D reference structures

Energy Window^a					5/5					5/15		10/10	10/15	15/15
Conformer FF^b		Full			NoEstat			Trunc		Trunc		NoEstat	NoEstat	NoEstat
Fragment FF^b	Full	NoEstat	Trunc	Full	NoEstat	Trunc	Full	NoEstat	Trunc	Full	Trunc	Trunc	Trunc	Trunc
Sampling rate = 20
RMSD	0.69	0.69	0.71	0.48	0.48	0.48	0.467	0.467	0.462	0.41	0.41	0.42	0.40	0.42
ST	0.89	0.89	0.89	0.93	0.93	0.93	0.93	0.93	0.93	0.95	0.95	0.94	0.943	0.94
# Conformers	698	698	645	2827	2,814	2,870	5,369	5,352	5,852	12,957	13,012	10,794	13,118	10,794
# 100-k Limit cases	23	18	36	94	93	118	216	211	239	2,203	2,209	1,842	2,198	1,842
Sampling rate = 50
RMSD	0.69	0.69	0.71	0.48	0.48	0.48	0.466	0.467	0.462	0.41	0.41	0.42	0.40	0.42
ST	0.89	0.89	0.89	0.93	0.93	0.93	0.93	0.93	0.93	0.95	0.95	0.94	0.946	0.94
# Conformers	696	697	646	2,834	2,818	2,875	5,377	5,358	5,857	12,981	13,025	10,796	13,124	10,796
# 100-k Limit cases	21	18	36	96	96	119	217	211	239	2,203	2,210	1,841	2,196	1,841

^aThe first and second numbers indicate the energy windows used for model building and torsion search, respectively.
^bFull = the 94s variant of the Merck molecular force field (MMFF94s); NoEstat = MMFF94s without coulombic interaction terms; Trunc = MMFF94s without coulombic and van der Waals attractive terms.

ISSN: 1758-2946