As this years Nobel in Chemistry was won by 3 boffins, one of whom had assembled molecules (or groups of molecules) to perform computation functions.
BTW most atom sizes are still measured in Angstroms, IE 0.1nm.
According to http://antoine.frostburg.edu/chem/senese/101/periodic/faq/what-atom-is-largest.shtml this Cesium is the biggest atom at up to 0.273nm atomic radius, so 0.546nm in diameter.
So a cube 50nm on a side is a cube 91.5 Cesium atoms on a side. That's 753571 whole Cesium atoms in volume.
Seems like there should be enough space if you're doing proper molecular nanotechnology.