Comparison of 3D Structures

one needs to compare different 3D structures or conformations of a molecule. That is done internally by the 3D stmcture generation program to weed out too similar conformations of fragments. Another aspect is the need of the computational chemist to compare different generated or experimental structures. A well-established measure is the so-called root mean square (RMS) value of all atom-atom distances between two 3D structures. The RMS value needed here is a minimum value achieved by superimposing the two 3D structures optimally. Before calculating the RMS, the sum of interatomic distances is minimized by optimizing the superimposition in 3D. [Pg.174]

The RMS value is only a rough measure for the similarity of two conformations. It is summarized over all atoms under consideration. That means that a local drastic deviation between two conformations can be hidden in an overall good fit. Reversely, a deviation in one part of the molecule can hide a perfect fit of another part. However, the RMS is very useful for obtaining a quick, robust measure of conformational similarity. A few recommendations can help to a better understanding [Pg.174]

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