We present a combined computational/experimental study of fluorescent Au nanocluster complexes synthesized using small biological molecules. Using density-functional theory, we calculated the binding energy, HOMO–LUMO gap, charge transfer, and bond length of the ligand–Au nanocluster systems. These calculations suggest the formation of ligand–Au nanocluster complexes. We further simulated the HOMO/LUMO states and the absorption spectra of the complexes. The HOMO and LUMO states of the complexes were confined within the Au nanoclusters, suggesting little ligand intrinsic fluorescence. The simulated absorption spectra agreed reasonably well with the experimental data. The simulation results of different systems demonstrate the strong ligand effects on the fluorescent emissions of ligand–Au nanocluster complexes. Our studies provide valuable information for the rational design of next-generation fluorescent tags.