Both molecules will in general be chemically equal. However, unequal molecules may be fitted as well (usually in the form of two concatenated 'PDB-style' datafiles as input.
Atoms to be used for the fit (at least 5 pairs) should be clicked in pairs. The Fit sequence starts and ends by clicking on the menu-item FITbyCLICK.
For more information on molecule fitting see FIT and AUTOFIT.
The Left click position attempts the best fit including inversion.