Chlorophyll and sucrose

Theobromine (cocoa) and caffeine

Valium and nicotine

What makes the structure consisting of the mean relative positions of a molecule's constituent nuclei visualizable as it is is the fact that the fuzziness of the relative position of each pair of nuclei, given by the standard deviation of the corresponding probability distribution, is small compared to the mean value of this distribution.

It is the bigger things, starting with molecules, that have visualizable aspects, not the "smaller" ones that make up atoms.

If the "ultimate constituents" of matter are formless objects, then the shapes of things are sets of spatial relations (ultimately between formless objects), and what space contains (in the proper, set-theoretic sense of "containment") is spatial relations. It thus contains the shapes of all things that have shapes, but it does not contain the formless "constituents" of matter. It exists "between" them. It is the "web" spun by their spatial relations.