Conceptuallly, an atom is an indivisible unit.  In physics, it turns out the what were first identified as atomic turned out to be have component parts.  What turned out to be critical was what the quanta were that mediate the relationships within and between the atomic units.  Atoms are atoms in terms of chemistry and not ultimate in terms of the physics of higher energies and smaller scales.

If the atoms of a Currency Systems are taken at the level of financial systems, which are ultimately social architectures, then the atoms are objects that have a value.  The Financial Transaction is the sub-atomic event, and in theory we could describe our systems in terms of financial Feynman Diagrams.  The atoms are the financial instraments, money, checks, stocks, bonds, etc.  Well, some of those could be systems (think molecules are crystal) composed of groups of atoms.  Many of these components have quantities, that are like the energy in a photon.  Currency units like dollars or Euros are like energy units in physics.