OpenEye’s Tautomers program is used for canonicalizing and/or enumerating the tautomeric forms of a small molecule. Canonicalization converts any of the tautomeric forms of a given molecule into a single unique representation. This is useful for database registration where alternate representations of tautomeric compounds often leads to duplicate entries in a database.
Some effort is made by the Tautomers program to direct the canonical representation to be a physiologically preferred form. However, there are no guarantees the tautomer selected is indeed the lowest energy and, indeed, solvent effects, etc., preclude there being a single best form of a tautomer. Fortunately, this is not necessary for database work.
Tautomers is not a conformer generation program and will not create coordinates for molecules that are read in with no coordinates. When used on molecules with three-dimensional coordinates, Tautomers attempts to place hydrogens in a reasonable manner. However, Tautomers does not modify the heavy-atom coordinates of the molecule. In cases where the change in tautomer-state dictates a change in conformation, one will need to use a conformer-generation tool (such as OMEGA) to generate reasonable conformations for the output from Tautomers. We recommend that in the preparation of small-molecules for study, charge-state and tautomer enumeration be performed before conformer generation.