On 11 July 2014 23:41, Wendy Carande <[email protected]> wrote:
> 10104489
> TRC 05231419153D
> PM6 optimization, min free energy conformation
> 14 14 0 0 0 0 0 0 0 0999 V2000
> -0.4307 2.0889 0.2792 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0407 1.1071 0.2148 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.4008 0.9484 0.5227 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.6973 -0.0195 -0.1759 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9941 1.8122 0.8291 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.9923 -0.3134 0.4365 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.1378 -1.2635 -0.2668 N 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1710 0.0301 -0.5321 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0439 -0.4753 0.6673 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1631 -1.3724 0.0355 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.8766 0.5689 0.4954 F 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3775 0.9405 -1.5182 F 0 0 0 0 0 0 0 0 0 0 0 0
> -2.6216 -0.9493 -0.8245 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.6684 -3.1599 -0.1690 Br 0 0 0 0 0 0 0 0 0 0 0 0
> 2 1 1 0 0 0 0
> 2 3 1 0 0 0 0
> 3 5 1 0 0 0 0
> 4 2 1 0 0 0 0
> 6 3 2 0 0 0 0
> 6 9 1 0 0 0 0
> 7 4 2 0 0 0 0
> 7 10 2 0 0 0 0
> 8 4 1 0 0 0 0
> 8 11 1 0 0 0 0
> 10 6 1 0 0 0 0
> 12 8 1 0 0 0 0
> 13 8 1 0 0 0 0
> 14 10 1 0 0 0 0
> M RAD 1 2 2
> M END
>
>
>
This is not a problem with RDKit, but a chemistry problem.
Your structure has a tetra valent N (you have an uncharged nitrogen atom in
the ring with 4 bonds in your structure). If you add a + charge to the
nitrogen (M CHG line in the sdf, see below), RDKit is able to read in your
structure. You can easily do this using a free program such as
MarvinSketch (it also shows you where your original error is).
[image: Inline images 1]
--------------- PYTHON CODE ----------------------------
>>> import rdkit
>>> from rdkit import Chem
>>> s = Chem.SDMolSupplier(/tmp/test_fixed.sdf')
>>> s.next()
<rdkit.Chem.rdchem.Mol object at 0x7fe783d21360>
>>>
--------------- FIXED SDF FILE ----------------------------
Mrv0541 07121410173D -76.23192
PM6 optimization, min free energy conformation
14 14 0 0 0 0 999 V2000
-0.4307 2.0889 0.2792 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0407 1.1071 0.2148 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4008 0.9484 0.5227 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6973 -0.0195 -0.1759 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9941 1.8122 0.8291 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9923 -0.3134 0.4365 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1378 -1.2635 -0.2668 N 0 3 0 0 0 0 0 0 0 0 0 0
-2.1710 0.0301 -0.5321 C 0 0 1 0 0 0 0 0 0 0 0 0
3.0439 -0.4753 0.6673 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1631 -1.3724 0.0355 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8766 0.5689 0.4954 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.3775 0.9405 -1.5182 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.6216 -0.9493 -0.8245 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6684 -3.1599 -0.1690 Br 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
2 3 1 0 0 0 0
3 5 1 0 0 0 0
4 2 1 0 0 0 0
6 3 2 0 0 0 0
6 9 1 0 0 0 0
7 4 2 0 0 0 0
7 10 2 0 0 0 0
8 4 1 0 0 0 0
8 11 1 0 0 0 0
10 6 1 0 0 0 0
12 8 1 0 0 0 0
13 8 1 0 0 0 0
14 10 1 0 0 0 0
M CHG 1 7 1
M RAD 1 2 2
M END
> <Symmetry>
Cs(1)
> <FreeEnergy>
-105.218958525368
> <Freq>
36.3827 1.8490
118.9528 0.6797
121.3287 1.7880
146.7422 3.2258
230.2547 4.6726
300.5702 5.7138
328.8019 1.4348
361.6117 0.5034
402.5823 0.1183
552.4995 20.1778
573.7578 0.7088
621.4207 13.4753
682.9353 27.8339
701.6618 5.4059
844.3396 76.4557
881.5112 51.8745
935.0009 0.0366
986.5135 4.6250
1020.1213 12.4436
1073.2578 27.3170
1132.0055 17.4835
1149.0508 5.7188
1174.1069 3.8183
1193.8903 14.3170
1225.8361 3.1755
1250.0146 94.6662
1258.0689 25.6122
1333.4544 115.3666
1444.9060 96.2140
1474.6392 0.2878
1604.5610 58.4422
1630.9742 34.4613
2636.6222 77.6239
2737.5860 21.2480
2745.9489 233.0648
2756.3587 214.6328
> <gAAFreq>
1046.34084166667
> <gAlpha>
72.95
> <gCOSMO_DPSA1>
-16.3678412270001
> <gCOSMO_DPSA2>
-8.0618952540101
> <gCOSMO_NCD>
-0.00499623410644148
> <gCOSMO_NEG>
-0.492544809359508
> <gCOSMO_PCD>
0.00599090900680561
> <gCOSMO_PNSA1>
98.5832126490001
> <gCOSMO_PNSA2>
-48.5566496802496
> <gCOSMO_POS>
0.492544809149928
> <gCOSMO_PPSA1>
82.215371422
> <gCOSMO_PPSA2>
40.4947544262395
> <gCOSMO_SA>
180.798584071
> <gCOSMO_SKW>
0.546436666002523
> <gCOSMO_VAR>
0.00692393043054713
> <gCOSMO_Vol>
167.141981607954
> <gCvib>
12.6954699037459
> <gDPSA1>
-65.71527629439
> <gDPSA2>
-76.6311751243748
> <gDipole>
2.8934
> <gEN>
-5.447286492133e+02
> <gEnergy>
-76.2319210753677
> <gGAFreq>
745.714161110022
> <gHLgap>
0.33918
> <gHOMO>
-0.37718
> <gIRAFreq>
1836.33033030781
> <gKE>
-3.721651577705e+01
> <gLUMO>
-0.03800
> <gNCD>
-0.0105562568746138
> <gNEG>
-1.166109
> <gNN>
3.105243637196e+02
> <gPCD>
0.0260577959728786
> <gPNSA1>
110.4661447567
> <gPNSA2>
-128.815565596091
> <gPOS>
1.166109
> <gPPSA1>
44.75086846231
> <gPPSA2>
52.1843904717159
> <gSumIR>
1276.4724
> <gVol>
177.358428355517
> <gvdWSA>
155.217013219
> <gvdWV>
120.158277876
$$$$
-
Jean-Paul Ebejer
Early Stage Researcher
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