Hi Markus,
Can you send me the mol file? It's not a good format, so the bonds
might missing (and coordinates), but did you try to make a molecule
with the new compound, then assign some of the atoms? That should
work, in principle. Analysis won't be able to display the compound
without coordinates though.
Vega ZZ is supposed to be good, but is only free for academic use.
Also, Babel can be used for conversion of files, not sure if you can
make the mol2 file from scratch with it (though probably it will work
from a SMILES or something similar). Not sure if either of these
generates coordinates... .
Apologies that I can't be of more help!
Wim
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