Hi Maria
I would say that the behaviour of RDKit with your MOL2 file is right.
SMILES notation doesn't have a way to represent the delocalised form of a
carboxylate anion, so the O=C[O-] form is the correct SMILES for this
structure. RDKit does a good job in recognising that it's the anion based
on the fractional charges in the MOL2 file (openBabel would give the
neutral carboxylic acid as output).
Using aromatic atoms/bonds to represent delocalisation generally is not
possible in SMILES. It's also not strictly correct to use aromatic bonds
(type 4) in an SD or MOL file either unless the structure is a query - the
representation of a 'real' molecule in this file format should also be in
the charge-separated rather than delocalised form.
Sorry that this isn't particularly helpful for your case, but it is correct
behaviour.
Best regards,
Chris
On 28 March 2018 at 10:53, Maria Matveyeva <[email protected]> wrote:
> Sorry, i forgot to ask a question: how can i retain the initial form?
> Maria
>
> 2018-03-28 11:46 GMT+02:00 Maria Matveyeva <[email protected]>:
>
>> Hello all,
>> When i read mol2 format from either mol2 file or block, it changes
>> represenation of carboxylic group from tripos aromatic representaiton with
>> -0.5 charges on oxygens to representaion with one single and one double
>> bond (when same representation read from sdf/mol it retains "aromatic"
>> form):
>>
>>
>>
>> from rdkit import Chem
>>
>> mol = Chem.MolFromMol2Block('@<TRIPOS>MOLECULE\n\n7 6
>> 1\nSMALL\nUSER_CHARGES\n@<TRIPOS>ATOM\n1\tC1 83.1235 48.4843
>> -1.9335\tC.3\t\t1\tnoname\t0.0000\n2\tC2 84.4055 49.1718
>> -2.1563\tC.2\t\t1\tnoname\t0.0000\n3\tO1 85.5783 48.5739
>> -1.8454\tO.co2\t1\tnoname -0.5000\n4\tO2 84.4327 50.3304
>> -2.6301\tO.co2\t1\tnoname -0.5000\n5\tH1 82.7117 47.9177
>> 0.7151\tH\t\t1\tnoname\t0.0000\n6\tH2 82.6153 48.8969
>> -1.0496\tH\t\t1\tnoname\t0.0000\n7\tH3 82.4727 48.5910
>> -2.8139\tH\t\t1\tnoname\t0.0000\n@<TRIPOS>BOND\n1\t1\t2\t1\
>> n2\t2\t3\tar\n3\t2\t4\tar\n4\t1\t6\t1\n5\t1\t7\t1\n6\t5\t1\t1\n@
>> <TRIPOS>SUBSTRUCTURE\n1\tnoname\t1\n')
>>
>> Chem.MolToSmiles(mol)
>>
>> 'CC(=O)[O-]'
>>
>> Thanks in advance,
>> Maria
>>
>
>
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