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.