"The atoms of the first part/half according to the main COM of
the ligand are C2, C7, C8 and C9. As for the second part they are C3, C4, C5
and C6 atoms."
Think *very* carefully about how you made that decision. Was it
based *only* on the position of the centre of mass, or did you
take other things into account, such as knowledge of which
atoms are bonded to which other atoms?
In other words, if someone just gave you a list of the positions
of the atoms and nothing else, would you be able to figure out
which atoms belonged to which half, without seeing a picture of
the molecule? If so, how would you do it?
If you need information about the bonds, then there's no way
a program could do it from the sample input file you provided,
because it only contains positions.