Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

Several criteria were defined to select a dataset of high-quality X-ray structures from the Cambridge file resulting in 639 molecules. Six currently available programs for automatic 3D structure generation were compared by converting the connectivity tables including appropriate stereodescriptors from this dataset of 639 molecular structures into 3D geometries: CONCORD, ALCOGEN, Chem-X, MOLGEO, COBRA, and CORINA. The geometries produced by the different programs were evaluated in terms of several quality criteria and are discussed in detail. These criteria measure how well the different programs reproduce the X-ray geometries of the 639 input structures. Accordingly, the major strengths and weaknesses of the programs are indicated.

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