[Zinc-fans] non-unique ZINC ids in Zinc7

Jens Auer auer at bit.uni-bonn.de
Fri Feb 15 03:12:00 PST 2008


Hi,

we have just found several molecules in the Zinc7 database which are
different in structure but have the same ZINC id. The complete list includes 
~23000 ids, where most of the time two or three entries correspond the same
SMILES string (it also include the  ZINC01278699 from the errata which matches 
more than a hundred SMILES strings). I can send you the list of these ids if you're interested, but 
it is too large to be posted here on the mailing list. I've attached a samle sd-file with
two compounds with the same id but different structure for illustration.

Best regards,
  Jens
 
-- 
Jens Auer
Life Science Informatics
B-IT Intl. Center for Information Technology
Rheinische Friedrich-Wilhelms-University Bonn
Dahlmannstraße 2
D-53113 Bonn
phone: +49 (228) 2699 314
email: auer at bit.uni-bonn.de
-------------- next part --------------
ZINC00000308
  MOE2007           3D

 55 58  0  0  1  0  0  0  0  0999 V2000
    7.0050   11.3100   -1.5430 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8640   11.9320   -0.7350 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5060   12.0740   -2.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760   13.5990   -2.7240 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3480   10.1300   -1.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1840    9.6930    0.1580 C   0  0  3  0  0  0  0  0  0  0  0  0
    5.0500   10.0170    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0700    8.1920    0.2220 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8500    7.5840    0.2470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7690    6.1840    0.3070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8520    5.4310    0.3440 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0730    5.9720    0.3160 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2210    7.3810    0.2560 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5080    7.9410    0.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5990    7.1270    0.2680 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4550    5.7420    0.3270 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2230    5.1640    0.3510 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4360    5.5360    0.3340 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2760    6.3280    0.3010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9570    5.7590    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0840    4.3590    0.3840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3490    3.7470    0.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4400    2.3900    0.4610 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2960    1.5940    0.5000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0550    2.1520    0.4770 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0790    3.5500    0.4180 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3440    4.1580    0.3930 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0020   10.2840    0.7020 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9500   11.4750   -1.0250 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8330   10.2390   -1.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0460   11.7720   -2.5290 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9770   13.0160   -0.7230 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8930   11.5520    0.2860 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4110   11.7910   -3.2700 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6380   11.6390   -3.2300 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4840   13.8840   -2.1650 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2560   14.0360   -2.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2950   13.9640   -3.7480 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1980    9.6110   -1.7410 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4440    9.8860   -1.8560 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9480    8.1780    0.2220 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6330    9.0130    0.1880 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5880    7.5590    0.2490 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3360    5.1170    0.3530 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1300    4.0890    0.3970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3660    7.4030    0.2560 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8400    6.3810    0.2980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2440    4.3500    0.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4130    1.9220    0.4760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3960    0.5200    0.5450 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8230    1.5230    0.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2390    3.5530    0.4190 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1900   10.0400    0.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5580   11.5930   -1.3380 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.8140   12.0510   -0.7990 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 29  1  0  0  0  0
  1 30  1  0  0  0  0
  1 31  1  0  0  0  0
  2 32  1  0  0  0  0
  2 33  1  0  0  0  0
  2 54  1  0  0  0  0
  3  4  1  0  0  0  0
  3 34  1  0  0  0  0
  3 35  1  0  0  0  0
  3 54  1  0  0  0  0
  4 36  1  0  0  0  0
  4 37  1  0  0  0  0
  4 38  1  0  0  0  0
  5  6  1  0  0  0  0
  5 39  1  0  0  0  0
  5 40  1  0  0  0  0
  5 54  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 28  1  0  0  0  0
  8  9  2  0  0  0  0
  8 13  1  0  0  0  0
  9 10  1  0  0  0  0
  9 41  1  0  0  0  0
 10 11  2  0  0  0  0
 10 18  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 17  2  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 42  1  0  0  0  0
 15 16  2  0  0  0  0
 15 43  1  0  0  0  0
 16 17  1  0  0  0  0
 16 44  1  0  0  0  0
 17 45  1  0  0  0  0
 18 19  1  0  0  0  0
 18 27  2  0  0  0  0
 19 20  2  0  0  0  0
 19 46  1  0  0  0  0
 20 21  1  0  0  0  0
 20 47  1  0  0  0  0
 21 22  1  0  0  0  0
 21 26  2  0  0  0  0
 22 23  2  0  0  0  0
 22 48  1  0  0  0  0
 23 24  1  0  0  0  0
 23 49  1  0  0  0  0
 24 25  2  0  0  0  0
 24 50  1  0  0  0  0
 25 26  1  0  0  0  0
 25 51  1  0  0  0  0
 26 27  1  0  0  0  0
 27 52  1  0  0  0  0
 28 53  1  0  0  0  0
 54 55  1  0  0  0  0
M  CHG  1  54   1
M  END
>  <name>
ZINC00000308

$$$$
ZINC00000308
  MOE2007           3D

 41 42  0  0  0  0  0  0  0  0999 V2000
    2.4960    4.2870    0.4940 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1980    3.5220    0.4960 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0830    4.1400    0.7170 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0820    5.3400    0.9250 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1120    5.9210    1.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1250    5.2510    1.1370 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1820    7.2460    1.3840 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1990    2.0680    0.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4020    1.4000    0.0050 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    0.0410   -0.2300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2060   -0.6650   -0.2290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0020   -0.0050    0.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0040    1.3570    0.2460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1660   -0.7000    0.0090 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3720    0.0570    0.1350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7000    0.2830    1.6250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2450    0.1820    1.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5580   -0.9530    0.6860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5520   -0.7280   -0.4620 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2100   -2.0040   -0.4610 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4790   -2.6170   -0.6980 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7050    4.6460   -0.5140 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4180    5.1360    1.1730 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3040    3.6330    0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3730    7.7810    1.3930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0420    7.6650    1.5450 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3330    1.9470    0.0040 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3310   -0.4740   -0.4150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9360    1.8710    0.4260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2650    1.0160   -0.3730 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2400   -0.4910    2.2390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3680    1.2710    1.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7070    1.1170    1.3760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5740   -0.0900    2.6950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5810   -0.8670    0.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3980   -1.9280    1.1470 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0190   -0.1510   -1.2600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2060   -1.6870   -0.8490 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3400   -3.6850   -0.8680 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9420   -2.1670   -1.5760 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1220   -2.4680    0.1690 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 22  1  0  0  0  0
  1 23  1  0  0  0  0
  1 24  1  0  0  0  0
  2  3  2  0  0  0  0
  2  8  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  7 25  1  0  0  0  0
  7 26  1  0  0  0  0
  8  9  1  0  0  0  0
  8 13  2  0  0  0  0
  9 10  2  0  0  0  0
  9 27  1  0  0  0  0
 10 11  1  0  0  0  0
 10 28  1  0  0  0  0
 11 12  2  0  0  0  0
 11 20  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 13 29  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 19  1  0  0  0  0
 15 30  1  0  0  0  0
 16 17  1  0  0  0  0
 16 31  1  0  0  0  0
 16 32  1  0  0  0  0
 17 18  1  0  0  0  0
 17 33  1  0  0  0  0
 17 34  1  0  0  0  0
 18 19  1  0  0  0  0
 18 35  1  0  0  0  0
 18 36  1  0  0  0  0
 19 37  1  0  0  0  0
 19 38  1  0  0  0  0
 20 21  1  0  0  0  0
 21 39  1  0  0  0  0
 21 40  1  0  0  0  0
 21 41  1  0  0  0  0
M  END
>  <name>
ZINC00000308

$$$$


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