The problem of deriving three different two-body magnetic couplings in three electrons/three centers in a general geometric arrangement is investigated using the trinuclear Cu(II) HAKKEJ complex as a real case example. In these systems, one quartet and two doublet low lying electronic states exist, which define the magnetic spectra. However, the two possible linearly independent energy differences do not provide enough information to extract the three magnetic coupling constants. Here, we show how to obtain these parameters without making any assumption on the symmetry of the system from a combination of density functional- and wave function-based calculations. The density functional calculations explore various broken symmetry solutions and relate the corresponding energy to the expectation value of the Heisenberg Hamiltonian. This allows one to obtain all magnetic couplings, although their magnitude strongly depends on the exchange-correlation functional. Interestingly, a constant ratio between the magnetic coupling constants along a series of investigated functionals is found. This provides an additional equation to be used when relying on energy differences between spin states, which in turn allow solving the Heisenberg spectrum. The magnetic couplings thus obtained are compared to the experiment. Implications for the appropriate interpretation of the experiment and for the study of more complex systems are discussed.