We study Andreev reflection in a normal conductor-molecule-superconductor junction using a first principles approach. In particular, we focus on a family of molecules consisting of a molecular backbone and a weakly coupled side group. We show that the presence of the side group can lead to a Fano resonance in the Andreev reflection. We use a simple theoretical model to explain the results of the numerical calculations and to make predictions about the possible sub-gap resonance structures in the Andreev reflection coefficient.