I thought the nucleus rim was the first ring, you made me doubt if I know hydrogen correctly >:D
Then carbon came I put 6N and 6P in the nucleus (in an overlapping way; I clicked proton and neutron 6 times and they just spawned on top of each other, also moved together, I assume, when I dragged them. I checked with a little offsetted pair, they moved together.) and 2 electron in the first ring, 4 electrons in the second but it didn't register I get frustrated lolz. 
I did that again without overlapping and I don't know what I did wrong O.o electron collision is annoying to find too, there needs to be a feedback, because at first I thought if I put electrons on green lines then it'll be good but at the first level it only registered if I put them slightly inwards, so I assume this electron placement is on colliders.
This game was frustrating sry :'3 we can't even delete these particles as far as I know. Would be nice if we could delete with right click.
Nice idea tho, atoms are neat.