Mogul is a library of information available from CCDC about molecular geometries, based on bond-length and valence-angle measurements taken from the Cambridge Structural Database (CSD). Mogul can be used to find out whether a newly determined or partially refined structure from CRYSTALS has any geometrical features that are unusual or even suspect. This is useful both for highlighting possible errors in the refinement and in determining average bond-length and valence-angle values, with standard deviations, for use in restrained refinement.
There are two main ways of using Mogul. First, it can be called by CRYSTALS as a background job. In this mode, the CRYSTALS query structure is transferred transparently into Mogul, which will then:
* Take each bond length or valence angle in turn.
* Automatically find CSD structures containing similar bonds or angles.
It does this by automatically generating and searching for a search substructure, as you might do manually if you were using the CCDC ConQuest program.
* Determine summary statistics of the CSD distributions – means, medians, standard deviations, upper and lower quartiles, and minima and maxima.
* Transfer this summary information back to CRYSTALS.
In this mode, you need not see the Mogul user interface at all.
Alternatively, the query structure can be loaded into the Mogul graphical user interface so that particular bonds or angles can be selected with the mouse and searches run for them. In this mode, it is possible to view a histogram of the bond-length or valence-angle distribution and inspect the CSD structures contributing to the histogram.
In order for Mogul searches to run correctly, it is essential that queries are set up properly. A Mogul query will typically consist of a single molecule, a pair of molecules or ions, or perhaps a larger assembly of molecules or ions. It is critical to:
* Ensure that either complete molecules or ions are specified, or at least as much of the molecule or ion as is required to completely define the chemical environments of the bond and angle fragments of interest.
* Use the correct conventions for bond types.
Detailled information is available in this document from CCDC.