How Do You Make A 3D Atom Model Of Oxygen?

Back in the dinosaur days, we made them with a wooden base which supported a wooden dowel, with a ball on top to be the nucleus.  The ball had colored thumb tacks to indicate protons and neutrons (had to be the correct number of each).  Then a stiff wire like a coat hanger was pushed through the center of the ball.  The wire held circular orbits with beads on the orbit wires based on the number of electrons for each element.
The instructor liked the girls so he gave them elements with the least orbits and the boys got the ones with many orbits and electrons.

There is some good 3D (but not really) software out there, some free, some Very expensive. 3D modeling is often done in lieu of actual chemistry to see what is possible, likely. 20 years ago we had to reserve time on a VAX computer to do these simulations but now days any new PC works well.