A knowledge-based library of molecular geometry derived from the Cambridge Structural Database (CSD)


Mogul provides precise information on preferred molecular geometries by enabling access to millions of chemically classified bond lengths, valence angles, acyclic torsion angles, and ring conformations derived from the CSD.

Mogul enables you to rapidly validate the complete geometry of a given query structure and identify any unusual features without the need to construct complex search queries, or carry out detailed data analyses.

Mogul is becoming an essential tool enabling crystallographers to generate ligand restraint dictionaries. Interfaces to Mogul are available in CCP4's Coot, Grade from Global Phasing, and eLBOW from Phenix. Mogul is also used routinely to check the conformations of both computationally and experimentally generated models, and will form an integral part of the PDB's ligand validation pipeline for newly deposited structures. Medicinal Chemists rely on Mogul not only to validate ligand geometries, but also to aid design decisions.

Mogul provides:

  • The ability to load query molecules in a variety of formats (MOL2, CIF, PDB, RES), or sketch a 2D structure.
  • Easy selection of geometric features of interest and the ability to perform a “one click” validation of all bonds, angles, torsions and ring conformations in the query molecule.
  • Automatic generation of search substructures. The chemical environment around the feature of interest is encoded ensuring that search results are highly relevant to the query structure. Mogul also has the ability to find structurally related fragments if insufficient hits are found.
  • Rapid retrieval of geometric data. Results are displayed as a histogram calculated from matching entries in the CSD. Full descriptive statistics and figures of merit are provided allowing easy identification of unusual geometries. 
  • A simple text-based instructions file interface that allows Mogul to be run in batch mode from the command line and enables easy integration with client applications.


Mogul Image

Mogul Image

Identification of strained ligand geometry in aminotransferase structure 1ajs. The Mogul torsional distribution for the C-O-P-O dihedral in similar chemical environments is shown. The query torsion value is shown in red.