I wrote this program as a visual aid for my engineering chemistry professor.
It is 3 water molecules which bonds to a central +3 aluminum. I implemented it by integrating the force and torque from the coloumb forces of Hydrogen and Oxygen. It is 'correct,' except that I modified the variables such that the reaction would not happen instantaneously.
The molecule that emerges is similar to the real thing, e.g. a central aluminum with 3 water molecules evenly spaced around it (equal angles). I didn't specifically tell it to do this, it emerges from the physics. This model limits it to a single plane.
I plan on implementing more complex molecules/compounds.