How to implement SDF format?

Question

I have a program that returns a file with SDF format molecule. Now I want to transfer it to SMILES with Open Babel. But I don't get the result I expect. I have visited different websites that show how the SDF must look like, which I think my file does. Can one find a mistake?

CheMGen 1.0

  9  3  0  0  0               999 V2000
    0.0000    0.0000    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
    0.0000    0.0000    0.0000 C  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H  0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  3  2  0  0  0  0
  1  4  1  0  0  0  0
  1  5  1  0  0  0  0
  1  6  1  0  0  0  0
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  9  1  0  0  0  0
M  END
$$$$

This is what I get from Open Babel: CC=C.[HH].[HH].[HH].[HH].[HH] And this I expect: CC=C. In Open Babel I have selected "Delete Hydrogens", but they are shown.

Answer 1

(Chemisty.se is a bit sloppy representing the first line of code if it is an empty one. This equally applies to copy-paste of a.sdf file.)

There is a problem, because the full stop / period is used to concatenate multiple independent molecules into one SMILES string. It may be useful e.g., to describe multiple molecules in a .sdf about a co-crystal; here, it does not seem suitable. Possibly there is a problem generating the connectivty table (below the atom coodinates, regardless if these (still) are all zero) with the program (which one?) you use, how you use it, or a combination of the two.

I assume propene is the structure you target. The freely accessible sketcher of PubChem reports C(=C)C, ChemDraw's JS sample page C=CC as a SMILES string about this molecule. The later is what Openbabel converts the former as canonical SMILES when running

obabel -:'C(=C)C' -ocan

Provision of the canonical SMILES string generates a .sdf with all-zero coordinates by OpenBabel (obabel -:'C=CC' -h -osdf -O test.sdf) similar to the following (there is a leading empty line prior to OpenBabel, but no trailing empty line past $$$$):

 OpenBabel

  9  8  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    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
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3  9  1  0  0  0  0
M  END
$$$$

If you diff both files, you recognize that the line specifying the format in further detail (V2000) as well as the connectivity table differ.