The properties and applications of metallic nanoparticles are inseparably connected not only to their detailed morphology and composition but also to their structural configuration and mutual interactions. As a result, the assemblies often have superior properties as compared to individual nanoparticles. Although it has been reported that nanoparticles can form highly symmetric clusters, if the configuration can be predicted as a function of the synthesis parameters, more targeted and accurate synthesis will be possible. We present here a theoretical model that accurately predicts the structure and configuration of self-assembled gold nanoclusters. The validity of the model is verified using quantitative experimental data extracted from electron tomography 3D reconstructions of different assemblies. The present theoretical model is generic and can in principle be used for different types of nanoparticles, providing a very wide window of potential applications.