A practical guide to preparing MOL and SDF files

A structure file is the brief for your whole project, so it's worth thirty seconds of checking before you upload it.

#Which format to use

#What a Molfile looks like

The header is followed by a counts line and one line per atom and bond. This is benzene:

benzene
  ChemOS  demo

  6  6  0  0  0  0  0  0  0  0999 V2000
    1.2124    0.7000    0.0000 C   0  0
    0.0000    1.4000    0.0000 C   0  0
   -1.2124    0.7000    0.0000 C   0  0
   -1.2124   -0.7000    0.0000 C   0  0
    0.0000   -1.4000    0.0000 C   0  0
    1.2124   -0.7000    0.0000 C   0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  1  1  0
M  END

#Checklist

1. Stereochemistry is explicit. Wedge and hash bonds should match the isomer you need.
2. Salts and solvents are separate. Draw the counter-ion as its own fragment.
3. No query atoms. Generic labels like R or X can't be planned.
4. One target per file, unless you mean to quote several at once.