dearomatization

Karen Karapetyan

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Apr 3, 2013, 5:37:21 PM4/3/13

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Please investigate why this molecule doesn't get dearomatized both when loading from molfile below and smiles: Nc1ncnc2c(nnc12)[C@@H]1O[C@@H](COP(O)(O)=O)[C@H](O)[C@H]1O

------------------

-INDIGO-04031317332D

23 25 0 0 1 0 0 0 0 0999 V2000

-4.4944 -2.9073 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

-2.8944 -2.9073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-2.0944 -4.2930 0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0

-0.4944 -4.2930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.3056 -2.9073 0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0

-0.4944 -1.5217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.2944 0.9405 0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0

-2.5889 0.0000 0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0

-2.0944 -1.5217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

1.5217 0.4944 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0

2.8161 -0.4460 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

4.1105 0.4944 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

5.6322 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.9649 -1.5650 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

7.4866 -2.0595 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0

8.6756 -0.9889 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

7.8192 -3.6245 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

9.0083 -2.5539 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

3.6161 2.0161 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0

4.5566 3.3105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

2.0161 2.0161 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

1.0757 3.3105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

1 2 1 0 0 0 0

2 3 4 0 0 0 0

3 4 4 0 0 0 0

4 5 4 0 0 0 0

5 6 4 0 0 0 0

6 7 4 0 0 0 0

7 8 4 0 0 0 0

8 9 4 0 0 0 0

9 10 4 0 0 0 0

10 2 4 0 0 0 0

10 6 4 0 0 0 0

11 7 1 1 0 0 0

11 12 1 0 0 0 0

12 13 1 0 0 0 0

13 14 1 6 0 0 0

14 15 1 0 0 0 0

15 16 1 0 0 0 0

16 17 1 0 0 0 0

16 18 1 0 0 0 0

16 19 2 0 0 0 0

13 20 1 0 0 0 0

20 21 1 1 0 0 0

20 22 1 0 0 0 0

22 11 1 0 0 0 0

22 23 1 6 0 0 0

M END

-------------------

Mikhail Rybalkin

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Apr 4, 2013, 6:43:35 AM4/4/13

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Hi Ken,

In both cases the reason is that for the loaded structure Indigo think that all Nitrogens has zero Hydrogens. But cases are different:

1. For loading from SMILES it seems that there is an old code that treats undefined hydrogens in SMILES loading procedure and I have to check why is it so: if it is a bug or not.

2. For loading from Molfile the reason is that it is explicitly marked that there are 0 hydrogens for each Nitrogen. This number + 1 is in the 4th integer column in Molfile:

-1.2944 0.9405 0.0000 N 0 0 0 1 0 0 0 0 0 0 0 0

This highlighted "1" means that here are zero hydrogens for this atom.

You have to place 0 there if you want to leave them undefined. I have attached such Molfile.

I think you loaded it from SMILES, Indigo by mistake set the number of hydrogens to 0 and then you saved it into Molfile. Right?

Best regards,

Mikhail

indsp-127_noh.mol

Mikhail Rybalkin

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Apr 19, 2013, 4:29:09 PM4/19/13

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Hi Ken,

I fixed our bug in the SMILES loaded that set invalid number of hydrogens in such cases. Now everything should work find in the version Indigo 1.1.10. Thank you for the bug report!