We have applied an accurate molecular mechanics force field, parametrized with respect to first-principles calculated reference data, for copper paddle wheel (Cu-2(O2C)(4)) based metal organic frameworks to investigate possible systems with a 3,4-connected network topology. The results explain why the well-known HKUST-1 forms a tbo net, whereas for an extended linker, as in MOF-14, the pto topology is preferred. In particular, the complex structure of the latter system, consisting of two deformed and "interwoven" nets, is accurately predicted, and the necessary deformation energy can be quantified. In this context also all possible forms of interpenetration were considered. Finally, by designing a bromine-substituted extended linker the system can be forced back into the more open tbo topology. This first molecular mechanics investigation of the relative strain energies of MOF network topologies demonstrates that the structure is to a large extent defined by the intrinsic conformational preferences of the building blocks. Our approach allows to analyze and understand the reasons for this preference and can be used as a computational tool for the design of specific topologies.