2.1 Introduction

OpenEye Scientific Software'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 coordinateless. 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 from the output from tautomers. We recommend that in preparation of small-molecules for study, charge-state and tautomer enumeration be performed before conformer generation.

				QuacPac Quality Atomic Charges, Proton Assignment and Canonicalization