In the mcule database chemical structures can be described in three structure specification levels: conformers, structures and compounds.

Conformers have a fully specified 3D structure including the position of all hydrogens. They are in a fixed tautomeric and protonation state, and they have a known absolute stereo configuration (as reflected in the geometry).

Structures refer to molecular structures representing a fixed tautomeric and protonation state as reflected by the 2D structural formula. They can have a fully defined or a partially or fully unknown/undefined stereo configuration.

Compounds refer to chemical compounds that can be represented by multiple molecular structures, i.e. with multiple tautomeric and protonation forms. Their stereo configuration can be well-defined as well as fully or partially unknown / undefined, similarly to the case of structures.

Chemical structures with different stereo configurations are distinguished at all specification levels. Depending on the stereo configuration type, they represent a single isomer or a set of potential isomers and/or mixtures of isomers. (figure) Their stereo configurations are treated identical if and only if the represented isomers / set of isomers are identical. If the configuration differs, the chemical structures are treated as different database entries.

Compounds can have more symmetries than structures. In compounds neither the number of hydrogens nor the position of some hydrogens are fixed. A compound can represent all realistic tautomeric and protonation states (structures). Therefore those asymmetry centers that are present only in one potential structure (tautomer and protonation state) are not treated as stereogenic at the compound level. Similarly, some cis-trans bonds found a structure might be missing from the corresponding compound.