It's completely, utterly wrong. To point out just one problem, the two central rings should be planar. Good thing they picked this one to show in the landing page carousel. That example was enough for me to close the page again.

The displayed structure has nothing to do with how it really looks like [0].

It seems they just used a naive algorithm for automatic atom placement with a goal to minimize overlaps between the atoms.

[0] https://en.wikipedia.org/wiki/Caffeine

That naive algorithm isn't even good since it can clearly be laid out without any edge crossings.

By the way, just for clarity, note that the comments in this subthread were written before we updated the random seed for that example to result in a much better diagram: https://github.com/penrose/penrose/commit/134533830dab25642a...