Photosynthetic reaction centres of the Photosystem(PS)I type contain, with their protein, several small cofactors that participate in channelling energy through the reaction centre. These include chlorophyll molecules, inorganic ligands such as the 4Fe-4S iron-sulfur clusters, and substituted napthaquinones that act as electron acceptors in the electron-transfer chain. Here, molecular dynamics simulations utilizing the Molecular Operating Environment (MOE) software package are used to explore the possible orientations of a quinone and its alkyl tail within the binding site environment - both in the charged and uncharged states of the quinone.