Free online simulator
To use this is pretty easy.
Just type in the chemical symbol for the atom in the 'element' colunm, and type in the cartesian coordinates to the x y and z fields (scientific notation & decimals supported).
To add anoter atom, push tab on the last textbox the 'z' colunm on the last row. If a box turns red, hover over it to find out the problem.
The data is updated realtime (ish).