The 3D ligand-based scorer is supported by the Growing or Linking generators, but not the Fine-Tuning one. Indeed, this 3D feature is most powerful to generate diversity and novelty by exploring novel structural features. The Fine-Tuning generator is designed to stay very close to the reference molecule, in lead optimization cases, therefore, it is not compatible with such fitness function.
Molecules generated with a 3D scorer are scored using the 3D Shape score and the 3D Pharmacophore score. Molecules can be sorted using these scores.
By clicking on See details on any result, in the "3D shape" tab, the generated molecule can be seen superposed in 3D to the reference molecule.
By selecting several molecules and clicking on 3D Ligand Based Results in the top-right "View" module, you can superpose all the molecules simultaneously.