OMEGA is a tool for generating 3D conformations of molecules. OMEGA provides 2 different methods for conformation generation: torsion driving and distance geometry. The torsion driving method works best on molecules that do NOT contain large, flexible rings, while the distance geometry method works for all molecules but has been designed for molecules that do contain large, flexible rings (macrocycles).

The minimal input into OMEGA is a file of molecules, with all stereocenters defined (see flipper below) in any readable format. The minimal output is a file of molecules with conformations.


The OMEGA distribution comprises 2 applications:


  • Generates conformations for molecules in the input file


  • Removes molecules in the input file that do not conform to a set of physico-chemical properties

  • Molecules should be processed through FILTER before using OMEGA

There are OMEGA command examples elsewhere in this chapter.

Utility Programs

The following utility programs are also included in this distribution:

  • Flipper: Enumerates all (unspecified) stereocenters in input molecules, ensuring that every stereocenter in a molecule is defined. These stereoisomers are then suitable for input to OMEGA.

  • MakeFraglib: Generates 3D fragment geometries for rings and linkers; makes a custom library of these fragments for OMEGA.

  • Oeb2SdConf: Helper utility for users of the MOE tool; converts OMEGA conformers from OEB format into a form usable by MOE.

Conformations from OMEGA can be used as input into several other OpenEye tools, including OEDocking, ROCS, and Freeform.