I'm not 100% sure about this particular case, but I suspect this is a
limitation of InChI.  For example, the InChI representation of zwitterionic
phenylalanine (negative COO-, positive NH3+) and "neutral" phenylalanine
(neutral COOH, neutral NH2) is exactly the same.  This is by design.  See
https://chemistry.stackexchange.com/questions/34563/pubchem-inchi-smiles-and-uniqueness
for some possibly useful additional discussion.

The InChI FAQ at http://www.inchi-trust.org/technical-faq/#13.2 says:

This is exemplified below by standard InChIKeys as well as standard InChI
> strings for neutral, zwitterionic, anionic and cationic states of glycine
> (note that neutral and zwitterionic states do not differ in the total
> number of protons so they have the same standard InChI/InChIKey):


Is this the same as or at least similar to the issue you are encountering?

Curt

On Thu, Sep 14, 2017 at 11:09 AM, Jason Biggs <jasondbi...@gmail.com> wrote:

> Okay, all three of these smiles strings resolve to the same inchi,
>
> "O=[N+](C1=NC2=CC=CC=C2N=C1)[N-](=O)C1=NC2=CC=CC=C2N=C1"
> "C1=CC=C2C(=C1)N=CC(=N2)N(=N(=O)C3=NC4=CC=CC=C4N=C3)=O"
> "[O-][N+](c1cnc2ccccc2n1)=[N+]([O-])c3cnc4ccccc4n3"
>
> even though to me they seem like different structures due to the specified
> charges.  Is this a limitation of inchi, or do I need to rethink my ideas
> of what makes two chemical structures the same?
>
>
>
>
>
> Jason Biggs
>
>
> On Thu, Sep 14, 2017 at 12:38 PM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> InChI is an identifier and not a representation, you should not read
>> InChIs... but we are beyond hope there so...
>>
>> The InChI string is correct and is the same if you roundtrip your
>> preferred one with charge separated bonds and the 5 valent one.
>>
>> All toolkits will use the InChI library to read/write InChIs and it
>> generates the representation with 5v nitrogens, cactus is either applying
>> normalisation after reading or in this case (since it's the name resolved)
>> doing a identifier lookup from an original SMILES used to generate this
>> InChI:
>>
>> echo 'InChI=1S/C16H10N6O2/c23-21(15-9-17-11-5-1-3-7-13(11)19-15)
>>> 22(24)16-10-18-12-6-2-4-8-14(12)20-16/h1-10H' | inchi -STDIO
>>> -inChi2Struct -OutputSDF | obabel -imol -osmi
>>
>> c1ccc2c(c1)ncc(n2)N(=N(=O)c1cnc2ccccc2n1)=O Structure #1
>>
>> SDF also attached without going though Open Babel.
>>
>> - John
>>
>>
>>
>
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