Babel does not correctly recognizes S=O groups in output MOPAC 7.14 file.
Instead of producing a double bond, it creates just one single bond. Here is
an example. I used
CS(=O)C
to produce input file to MOPAC 7.14 (Ubuntu), optimized structure with
MOPAC, and after conversion of the output file I got
CSC
The output file from MOPAC is enclosed.
There's no good way to establish this S=O bond at the moment -- it could be an S-OH with a missing hydrogen. I'm leaving this on the tracker for future versions.