When I am performing docking studies on PyRx software, the docked molecule picture is incomplete; one of the bonds or arms is missing in the aromatic compound, and I am not able to see 2D picture either. Discovery studio visualizer showing a massage: the ligand is not a single fragment
This issue can be arised due to the input formate of ligand.
You should try to import your ligand in pdb formate and one by one each molecules.
You have to upload one ligand at a time to see the 2D interaction plot in DS
You can check in drop down box where it shows all atom and group. As to what I can see from image is that there is a floating molecule just above the ring and is not joined to it by any bond.
You can check what type of molecule is that and work around that for example, is it a part of structure or not
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