Perhaps we are using "structure" in different senses. Yes, it is possible to generate a molecule with a chemical structure unlike any biological molecule and have it bind to a protein, but it can only do so if its 3D structure is analogous to what naturally binds there. Natural products are a source of drugs because evolution has already done this work for us.
Yes, the chemical structures can look very different when drawn in the 2D manner, but that's why 2D structures aren't very useful for understanding binding, much as primary sequences of proteins aren't that useful. Morphine and fentanyl bind to μ-opioid receptors, just like what naturally binds there (endorphins and enkephalin). But if they are binding to the same receptor, they have to have similar structures in the biologically meaningful 3D sense (at least where they bind).
It appears that you were merely saying that ligands must adopt a 3D conformation that's complementary to the receptor. Sure. That's the entire premise of molecular docking software.
But there can be very dissimilar ligands (like morphine and fentanyl) binding the same receptors. A major goal of drug discovery is to find such novel binders, not to regurgitate known ones.
