Benzene ring format changes when molfile sent to Bingo

[Andy Hoffman]

Indigo Team:

I'm hoping I've just missed a configuration setting somewhere, but when I send a molfile structure (MOL file) in Java to be stored in a Bingo NoSQL database, the "display" format of all benzene rings is changing from double-bonded sides to the circle-within-hexagon representation.  I know these are structurally equivalent, and substructure searches indeed still return proper results.  However, it looks "incorrect" to an non-chemistry-aware user when the structure submitted doesn't "match" the structure retrieved visually.

It does look like either the Indigo api or Bingo itself are changing the structure data slightly when saving, as in the example structure below...

... whose molfile was set to the following data:

  Mrv1810 10171819032D          

  0  0  0     0  0            999 V3000

M  V30 BEGIN CTAB

M  V30 COUNTS 20 23 0 0 0

M  V30 BEGIN ATOM

M  V30 1 C -5.5834 2.7484 0 0

M  V30 2 C -6.917 1.9784 0 0

M  V30 3 C -6.917 0.4382 0 0

M  V30 4 C -5.5834 -0.3318 0 0

M  V30 5 C -4.2497 0.4382 0 0

M  V30 6 C -4.2497 1.9784 0 0

M  V30 7 C -5.5835 -1.8719 0 0

M  V30 8 C -4.25 -2.642 0 0

M  V30 9 C -2.9162 -1.8721 0 0

M  V30 10 C -2.9161 -0.3319 0 0

M  V30 11 C -1.5824 0.4381 0 0

M  V30 12 C -0.2488 -0.3318 0 0

M  V30 13 C 1.0851 0.4382 0 0

M  V30 14 C 1.0852 1.9781 0 0

M  V30 15 C -0.2485 2.7482 0 0

M  V30 16 C -1.5824 1.9782 0 0

M  V30 17 C -0.2488 -1.8719 0 0

M  V30 18 C 1.0847 -2.642 0 0

M  V30 19 C 2.4185 -1.8721 0 0

M  V30 20 C 2.4186 -0.3319 0 0

M  V30 END ATOM

M  V30 BEGIN BOND

M  V30 1 2 1 2

M  V30 2 1 2 3

M  V30 3 2 3 4

M  V30 4 1 4 5

M  V30 5 2 5 6

M  V30 6 1 6 1

M  V30 7 2 7 8

M  V30 8 1 8 9

M  V30 9 2 9 10

M  V30 10 1 4 7

M  V30 11 1 10 5

M  V30 12 2 11 12

M  V30 13 1 12 13

M  V30 14 2 13 14

M  V30 15 1 14 15

M  V30 16 2 15 16

M  V30 17 1 16 11

M  V30 18 1 10 11

M  V30 19 2 17 18

M  V30 20 1 18 19

M  V30 21 2 19 20

M  V30 22 1 12 17

M  V30 23 1 20 13

M  V30 END BOND

M  V30 END CTAB

M  END

But when that data is sent into Bingo structure database, and substructure match returns the structure, I get the following image...

And the structure molfile shows as:

  -INDIGO-10171819042D

  0  0  0  0  0  0  0  0  0  0  0 V3000

M  V30 BEGIN CTAB

M  V30 COUNTS 20 23 0 0 0

M  V30 BEGIN ATOM

M  V30 1 C 0.0 0.0 0.0 0

M  V30 2 C 0.0 0.0 0.0 0

M  V30 3 C 0.0 0.0 0.0 0

M  V30 4 C 0.0 0.0 0.0 0

M  V30 5 C 0.0 0.0 0.0 0

M  V30 6 C 0.0 0.0 0.0 0

M  V30 7 C 0.0 0.0 0.0 0

M  V30 8 C 0.0 0.0 0.0 0

M  V30 9 C 0.0 0.0 0.0 0

M  V30 10 C 0.0 0.0 0.0 0

M  V30 11 C 0.0 0.0 0.0 0

M  V30 12 C 0.0 0.0 0.0 0

M  V30 13 C 0.0 0.0 0.0 0

M  V30 14 C 0.0 0.0 0.0 0

M  V30 15 C 0.0 0.0 0.0 0

M  V30 16 C 0.0 0.0 0.0 0

M  V30 17 C 0.0 0.0 0.0 0

M  V30 18 C 0.0 0.0 0.0 0

M  V30 19 C 0.0 0.0 0.0 0

M  V30 20 C 0.0 0.0 0.0 0

M  V30 END ATOM

M  V30 BEGIN BOND

M  V30 1 4 1 2

M  V30 2 4 2 3

M  V30 3 4 3 4

M  V30 4 1 4 5

M  V30 5 4 5 6

M  V30 6 4 6 7

M  V30 7 4 7 8

M  V30 8 4 8 9

M  V30 9 4 9 10

M  V30 10 4 10 11

M  V30 11 4 11 12

M  V30 12 4 12 13

M  V30 13 4 13 14

M  V30 14 4 14 5

M  V30 15 4 14 9

M  V30 16 4 4 15

M  V30 17 4 15 16

M  V30 18 4 16 17

M  V30 19 4 17 18

M  V30 20 4 18 3

M  V30 21 4 18 19

M  V30 22 4 19 20

M  V30 23 4 20 1

M  V30 END BOND

M  V30 END CTAB

M  END

If anyone can tell me why the structures/benzene formats change, and (possibly) how to prevent it... MUCH MUCH appreciated.

Regards,

Andy Hoffman