aromotized molecule after passing through tautomer plugin

User 162d60ff7f

14-10-2013 20:45:16

input:

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

-INDIGO-10141315002D

93104 0 0 1 0 0 0 0 0999 V2000

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4.6248 -15.2656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.1959 -15.2721 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

5.4356 -15.4392 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

5.8481 -14.7247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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8.3059 -14.4654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.8163 -13.7960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.9983 -13.8852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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5.9218 -17.0481 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0

6.6752 -17.3845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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11.1435 -15.0675 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

11.1446 -15.8925 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

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6.8460 -18.1917 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

6.2325 -18.7431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

7.6304 -18.4473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.8012 -19.2544 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

8.5856 -19.5101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.7563 -20.3172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

9.1991 -18.9586 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

8.2083 -20.9308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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9.4273 -21.4749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.6204 -21.6440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.3650 -22.4259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

8.9154 -23.0392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

9.7245 -22.8656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

9.9762 -22.0839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3876 -20.8464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

6.9041 -21.5149 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

7.5577 -22.5961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

7.3015 -23.3802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

5.4480 -18.4875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.8345 -19.0389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

5.2772 -17.6803 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

4.0303 -18.8717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

3.6171 -19.5858 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0

4.1686 -20.1994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

4.9225 -19.8644 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

3.9964 -21.0062 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

3.2115 -21.2606 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

-0.8637 -18.6836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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4.6091 -21.5588 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

4.3204 -22.3317 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0

3.5068 -22.4682 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

4.8455 -22.9681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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3.2183 -23.2411 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

2.4068 -23.3744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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2.6395 -24.7826 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

3.4545 -24.6479 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0

3.7475 -23.8738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

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2.3480 -25.5544 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0

1.3035 -24.2766 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0

1.5339 -25.6878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

2.8707 -26.1927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0

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51 53 2 0 0 0 0

26 27 2 0 0 0 0

53 56 1 0 0 0 0

55 54 1 0 0 0 0

54 51 1 0 0 0 0

12 14 2 0 0 0 0

27 28 1 0 0 0 0

55 56 2 0 0 0 0

6 7 2 0 0 0 0

56 57 1 0 0 0 0

28 29 2 0 0 0 0

57 58 2 0 0 0 0

13 15 1 0 0 0 0

58 59 1 0 0 0 0

29 30 1 0 0 0 0

59 60 2 0 0 0 0

60 55 1 0 0 0 0

2 3 2 0 0 0 0

53 61 1 0 0 0 0

30 31 2 0 0 0 0

61 62 1 0 0 0 0

31 26 1 0 0 0 0

57 63 1 0 0 0 0

23 26 1 0 0 0 0

63 64 1 0 0 0 0

15 16 1 0 0 0 0

47 65 1 0 0 0 0

27 32 1 0 0 0 0

65 66 1 0 0 0 0

7 8 1 0 0 0 0

65 67 2 0 0 0 0

66 68 2 0 0 0 0

30 33 1 0 0 0 0

34 35 2 0 0 0 0

15 17 1 1 0 0 0

3 4 1 0 0 0 0

68 69 1 0 0 0 0

69 70 1 0 0 0 0

70 71 2 0 0 0 0

71 66 1 0 0 0 0

13 18 1 1 0 0 0

70 72 1 0 0 0 0

7 9 1 0 0 0 0

72 73 1 6 0 0 0

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18 19 1 0 0 0 0

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77 78 1 1 0 0 0

29 34 1 0 0 0 0

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32 39 2 0 0 0 0

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1 2 1 0 0 0 0

81 93 1 1 0 0 0

M END

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

plugin options used:

TautomerizationPlugin plugin = new TautomerizationPlugin();

plugin.setProtectAllTetrahedralStereoCenters(False);

plugin.setProtectAromaticity(False);

plugin.setProtectDoubleBondStereo(False);

plugin.setProtectEsterGroups=False

plugin.setProtectLabeledTetrahedralStereoCenters(False);

plugin.setExcludeAntiAromaticCompounds(False);

plugin.setProtectCharge(False);

plugin.setMaximumTautomerizationPathLength(4);

plugin.setRationalTautomerGenerationMode(False);

plugin.setTakeCanonicalForm(True);

plugin.setCleanResultStructures(True);

plugin.setMaxStructureCount(1000);

output

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

  -INDIGO-10141316292D



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    0.2707  -17.7484    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0

    0.3496  -16.9271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    1.0604  -16.5084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    1.0530  -15.6834    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

    1.7638  -15.2646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

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    2.4897  -15.6841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0

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 57 63  1  0  0  0  0

 23 26  4  0  0  0  0

 63 64  1  0  0  0  0

 15 16  1  0  0  0  0

 47 65  4  0  0  0  0

 27 32  4  0  0  0  0

 65 66  4  0  0  0  0

  7  8  1  0  0  0  0

 65 67  2  0  0  0  0

 66 68  4  0  0  0  0

 30 33  1  0  0  0  0

 34 35  2  0  0  0  0

 15 17  1  1  0  0  0

  3  4  4  0  0  0  0

 68 69  4  0  0  0  0

 69 70  4  0  0  0  0

 70 71  4  0  0  0  0

 71 66  4  0  0  0  0

 13 18  4  0  0  0  0

 70 72  4  0  0  0  0

  7  9  1  0  0  0  0

 72 73  4  0  0  0  0

 11  6  4  0  0  0  0

 18 19  4  0  0  0  0

  3 74  4  0  0  0  0

 35 36  1  0  0  0  0

 74 75  2  0  0  0  0

 74 73  4  0  0  0  0

 36 37  2  0  0  0  0

 76 72  1  0  0  0  0

 76 62  1  6  0  0  0

 37 38  1  0  0  0  0

 76 77  1  0  0  0  0

 38 34  1  0  0  0  0

 77 78  1  1  0  0  0

 29 34  1  0  0  0  0

 77 79  1  0  0  0  0

 32 39  4  0  0  0  0

 79 80  2  0  0  0  0

 79 64  1  0  0  0  0

  4  5  4  0  0  0  0

 81 78  1  6  0  0  0

 81 82  1  0  0  0  0

 19 20  4  0  0  0  0

  9 10  1  0  0  0  0

 19 21  2  0  0  0  0

 39 40  4  0  0  0  0

 40 41  4  0  0  0  0

 81 86  1  0  0  0  0

 83 82  1  0  0  0  0

 84 83  1  0  0  0  0

 84 85  1  0  0  0  0

 85 86  1  0  0  0  0

 41 42  4  0  0  0  0

 85 87  1  1  0  0  0

 42 32  4  0  0  0  0

 84 88  1  1  0  0  0

 20 22  4  0  0  0  0

 83 89  1  1  0  0  0

 36 43  1  0  0  0  0

 88 90  1  0  0  0  0

  5  1  4  0  0  0  0

 88 91  1  0  0  0  0

 43 44  2  0  0  0  0

 83 92  1  6  0  0  0

  1  2  4  0  0  0  0

 81 93  1  1  0  0  0

M  STY  5   1 DAT   2 DAT   3 DAT   4 DAT   5 DAT

M  SLB  5   1   1   2   2   3   3   4   4   5   5

M  SAL   1  1  18

M  SDT   1 MRV_IMPLICIT_H                F

M  SDD   1     0.0000    0.0000    DR    ALL  1       1  

M  SED   1 IMPL_H1

M  SAL   2  1  42

M  SDT   2 MRV_IMPLICIT_H                F

M  SDD   2     0.0000    0.0000    DR    ALL  1       1  

M  SED   2 IMPL_H1

M  SAL   3  1  47

M  SDT   3 MRV_IMPLICIT_H                F

M  SDD   3     0.0000    0.0000    DR    ALL  1       1  

M  SED   3 IMPL_H1

M  SAL   4  1  71

M  SDT   4 MRV_IMPLICIT_H                F

M  SDD   4     0.0000    0.0000    DR    ALL  1       1  

M  SED   4 IMPL_H1

M  SAL   5  1  73

M  SDT   5 MRV_IMPLICIT_H                F

M  SDD   5     0.0000    0.0000    DR    ALL  1       1  

M  SED   5 IMPL_H1

M  END

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

Question: why output is aromatized? how to avoid aromatization?

User 851ac690a0

15-10-2013 09:00:55

Hi,

Could you send your input files as a mrv or sdf file format?

The output file is dearomatized automatically according to the default settings.

I can not reproduce this problem. Which version do you use?

Jozsi

User 162d60ff7f

15-10-2013 11:11:22

File is attached. I use JCHem_NET_API_6_0_0_181.

User 851ac690a0

15-10-2013 11:49:16

Hi,

Thanks.

I can not open this file in my system. It seems to be corrupted anywhere.

Could you send another molecule formatum ,for example smiles?

How do you create these sdf files?

Jozsi

User 162d60ff7f

15-10-2013 14:22:08

The record is from ChEMBL compound collection:

https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL501954

You can download molfile yourself:

https://www.ebi.ac.uk/chembl/download_helper/getmol/482142

User 851ac690a0

15-10-2013 22:44:56

Hi,

Thanks. Now I was able to reproduce the problem.

There is a bug , this is why an aromatic form of the canonical tautomer is generated instead of the dearomatized structure. I try to fix this bug.

Jozsi