On: Penrose – Create diagrams by typing notation in pl...

[shrx]

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

[bmitc → shrx]

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