CrystalEye: what should InChIs reference?

In response to my post on the technical issues of CrystalEye, Egon has asked about InChIs (see Unofficial InChI FAQ):

  1. Egon Willighagen Says:
    November 4th, 2007 at 1:43 pm eRegarding the InChIs: I would prefer one InChI for each moiety, not one InChI for the full structure. Or not only, at least.

Thanks Egon. This is an important and complex area. I’ll try to show some recent examples and make some suggestions. As I go through I am also noticing bugs…
(entry A) 10.1107/S1600536807043048 single molecule per asym unit. No problem:
(entry B) 10.1107/S160053680705338X.

one dication, two picrates and a solvent:
Nick has drawn the dication first, but the others are drawable by scrolling.
There is NO InChI for the complete molecule (I’m not sure if this is deliberate), but there IS an InChI for the dication under “Moities” as there also is for the solvent. (The anions are missing from the moities – this may be a CrystalEye bug or it may be an author problem). InChI for dication:
InChI for solvent (CH3CN):
(Nick: BUG. The picrates are in the complete CML file but they don’t have InChIs and they don’t appear in the pages)
(entry C) 10.1107/S160053680705009X
This structure has disorder, which always complicates the inpterpretation of the chemical structure (note the warning)
The InChI is calculated for the major component.
(Entry D) 10.1107/S1600536807048301 This contains two identical solvate molecules to one of solvent (dioxan). Because the solvent lies on a symmetry element it is recorded as A B(0.5) rather than A2.B though this is probably inconsistent
Note that this is also disordered.
The InChI here represents the compound molecule as A2.B
In summary, therefore, I think we should certainly have InChIs for the moieties (and I think we have, at least in principle). I am less clear how useful it is for the overall crystal structure (as in D). Note that for inorganic structures without discrete moieties there are no InChIs. I am looking for some with discrete moieties.
That’s enough for now. I’ll tackle fragments in the new post or so.

This entry was posted in crystaleye. Bookmark the permalink.

2 Responses to CrystalEye: what should InChIs reference?

  1. Nick D says:

    For some reason CrystalEye failed to find a set of bonds orders and charges for the picrates (as you will have noticed from the Jmol image). When this happens, an InChI won’t be generated for that particular moiety (as obviously the bonds and charges are essential for a correct InChI representation of the structure) nor will one for the crystal structure as a whole (as has happened here).
    If the bond orders and charges are successfully added to all components of the crystal, then an InChI will always be added for each moiety, as well as one for the entire crystal. An example of the CML can be found at
    Note that at the moment we don’t generate InChIs for inorganic structures or polymeric organometallics.

  2. pm286 says:

    (1) Many thanks Nick,
    Yes, I remember now. Maybe we need a note somewhere pointing this out.

Leave a Reply

Your email address will not be published. Required fields are marked *