Strange formula obtained from a SMILES string

User c9ecc1389b

02-02-2016 10:48:42

Hi


JChem returns a strange formula for some compounds


e.g. (C6H12N2O)1-7C13H22N6O7


InChI=1S/C19H34N8O8/c20-3-1-2-7(21)4-10(30)24-13-14(31)15(35-18(22)33)9(6-28)34-17(13)27-19-25-11-8(29)5-23-16(32)12(11)26-19/h7-9,11-15,17,28-29,31H,1-6,20-21H2,(H2,22,33)(H,23,32)(H,24,30)(H2,25,26,27)/t7-,8+,9+,11+,12-,13+,14-,15-,17+/m0/s1


[H]NCCC[C@H](N)CC(=O)N[C@@H]1[C@H](O)[C@@H](OC(N)=O)[C@@H](CO)O[C@H]1\N=C1\N[C@]2([H])[C@H](O)CNC(=O)[C@@]2([H])N1


 


Do you know what it means?


Is it visible somehow in the InChI or SMILES returned by JChem?


 


Regards

ChemAxon abe887c64e

03-02-2016 08:30:49

Hi Sébastien,


This formula really seems to be strange, so we would like to clarify some conditions.


Which version of JChem are you using ? Did you use the JChem API to calculate Formula ? If yes, could you paste the relevant code particle?


Thank you,


Krisztina

User c9ecc1389b

03-02-2016 09:27:53

Hi


 


we get those formula from the JChem API version 6.2.0 but we also get them from command line with the evaluate program and the attached mol file.


evaluate -e "formula" ChEBI_26789.mol

ChemAxon abe887c64e

03-02-2016 10:32:46

Hi Sébastien,


The molfile you sent contains a repeating unit (a part of the structure is repeated by 1-7 times), this repetition property is displayed in the formula: (C6H12N2O)1-7C13H22N6O7. So this formula is correct.


If you convert this molfile to smiles or inchi, the repetition is lost, because smiles and inchi formats do not support the repeating units. The formula calculated from the smiles or inchi format files is : C19H34N8O8.


We recommend to use ChemAxon Extended Smiles format (cxsmiles), this format also supports repeating units.


[H]NCCC[C@H](N)CC(=O)N[C@@H]1[C@H](O)[C@@H](OC(N)=O)[C@@H](CO)O[C@H]1\N=C1\N[C@]2([H])[C@H](O)CNC(=O)[C@@]2([H])N1 |Sg:n:8,7,9,5,6,1,2,4,3:1-7:ht|


Best regards,


Krisztina


 


 

User c9ecc1389b

03-02-2016 12:11:48

Thanks Krisztina


 


I didn't know this syntax other than for example n-7 that means n monomers minus 7 monomers and not from n to 7 monomers for me.


 


We will try the Extended Smiles format.


Thanks for your explanation.


 


Sébastien