Experimental and theoretical investigations of iron-sulphur (Fe-S) systems are essential in understanding, optimizing, and designing processes for considering Fe-S minerals as natural resources, synthesizing Fe-S nanoparticles as catalytic systems, and understanding the function of Fe-S metalloenzymes. Our work focuses on the family of [Fe-S] clusters coordinated with a short peptide (9- to 16-mers), also known as ‘maquettes’ of [Fe-S] metalloproteins. We work on specific peptide sequences that contain only three Cys residues (CxxxCxxC) in order to create site-differentiation among the Fe-sites of a [4Fe-4S] cluster that is one of the key requirements for chemical reactivity beyond redox chemistry. Given that the cluster assembly mechanism and the peptide coordination are not known, we devised a computational modelling workflow to monitor favourable peptide conformation for cluster binding as a function of amino acid sequence (AMBER, NVT MD simulations: ), dock pre-assembled [4Fe-4S] clusters to the peptide (PM6), and determine cluster binding affinity, redox activity, and small molecule binding (X-ray spectroscopy validated hybrid DFT: ). The selection of peptide sequences was carried out using bioinformatics methods. The results of computational modelling were followed up with reconstitution experiments, where we find that the yield of [4Fe-4S]-maquettes correlates with the frequency of the peptide forming favourable cluster binding nest and the predicted cluster binding energies. Both the experiments and the computational simulations support the ligand-exchange mechanism between a pre-assembled cluster and the peptide ligand.