Fragment conformations

Numerical methods. Computer-intensive numerical methods like quantum mechanics, molecular mechanics, or distance geometry [8] do not normally fall into the scope of automatic model builders. However, some model builders have built-in fast geometry optimization procedures or make use of distance geometry in order to generate fragment conformations. 

At the same time, five-membered cycles are formed in the low-molecular copper(II) — glycilglycine system [44], Thus a knowledge of the local chelating fragment conformation allows us to predict PCMU with a specified size of the metallocycles. 

One common query to the CSD (Table 2) involves the classification of fragment conformations - a recognition of the different 3-D shapes that are exhibited by a given 2-D chemical substructure. Here the number of geometrical parameters required to define the 3-D conformation is normally >2. For example, 15 distances or six torsion angles provide suitable descriptors for cyclohexane, and we must resort to multivariate statistical methods to analyse the appropriate G-matrix. Two techniques may be selected within GSTAT principal component analysis and cluster analysis. 

A template contains some knowledge on the fragment conformation, i.e., symbolic description of the conformation, strain energy, flexibility, and coordinates. If no exact expression of a specific unit can be found in the library, similar templates are searched on several levels of generalization. If, for example, no template for a heterocycle can be found, the corresponding carbocycle is taken. The templates are obtained either from moleculai mechanics or X-ray crystallography. 

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