  Bio-molecules are active agents in that they consume energy to perform tasks.
The standard theoretical description, however, considers only a system-external
work agent. Fluctuation theorems, for example, do not allow work-exchange
between fluctuating molecules. This tradition leaves `action through work', an
essential characteristic of an active agent, out of proper thermodynamic
consideration. Here, we investigate thermodynamics that considers
internal-work. We find a complementary set of relations that capture the
production of free energy in molecular interactions while obeying the second
law of thermodynamics. This thermodynamic description is in stark contrast to
the traditional one. A choice of an axiom whether one treats a portion of
Hamiltonian as `internal-work' or `internal-energy' decides which of the two
complementary descriptions manifests among the dual. We illustrate, by
examining an allosteric transition and a single-molecule
fluorescence-resonance-energy-transfer measurement of proteins, that the
complementary set is useful in identifying work content by experimental and
numerical observation.
