CSD - Molecular Geometry Analysis Panel
Display an analysis of ligand molecular geometries in terms of known geometries derived from the Cambridge Structural Database (CSD). The deviations of the molecular geometries from those found in the database are plotted in a "bubble plot" to give a visual indication of possible inaccuracies in the geometries.
To open this panel: click the Tasks button and browse to Structure Analysis → CSD Analysis.
- Using
- Features
- Additional Resources
Using the CSD - Molecular Geometry Analysis Panel
The results returned from the query give the z-scores for the deviation of bond lengths and bond angles from the mean values in the CSD, and the local density of torsions in the CSD for the torsional angle. (Local density is the percentage of observed values within 10 degrees (by default) of the query value.) The analysis of torsions does not take into account much of the environment of the torsion, so for example, if there are bulky substituents the value might be marked as a poor match to the database, but in fact be quite reasonable. The main point is to provide a way of quickly identifying problems in structures and examining them to see if they are indeed problems. Another possible source of discrepancies might occur if the environment of the ligand is very different from that in the crystal, so that environmental differences have a significant effect on the geometry.
CSD - Molecular Geometry Analysis Panel Features
- Query ligand text
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The text to the right of this label gives the title of the ligand entry.
- Ligand navigation buttons
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Use these buttons to step through the ligands. Clicking the right arrow displays data for the next ligand in the tabs and includes the ligand in the Workspace; clicking the left arrow displays the previous ligand.
- Bubble plots
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The results for each geometric parameter are plotted in separate tabs. The plots take the form of "bubbles": circles whose size reflects the value of the z-score or distance value. The circles are colored green, yellow, or red according to whether the value is considered good, marginal, or poor. If you click on the label of one of the parameters, a histogram is displayed showing the distribution of values in the CSD, with the current value draw as a red vertical line. The histogram for torsions ignores the sign of the torsion, and shows torsion values from 0° to 180°.
- Highlight atoms option
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With this option selected, when you click on the label of one of the geometric parameters, the atoms corresponding to the geometric parameter are marked in the Workspace.