We investigate the impact of ligands on the morphology, electronic structure, and optical response of the Cd(33)Se(33) cluster, which overlaps in size with the smallest synthesized CdSe nanocrystal quantum dots (QDs). Our density functional theory calculations demonstrate significant surface reorganization for both the bare cluster and the cluster capped with amine or phosphine oxide model ligands. We observe strong surface-ligand interactions leading to substantial charge redistribution and polarization effects on the surface. These effects result in the development of hybridized states, for which the electronic density is spread over the cluster and the ligands. The loss of one of the passivating ligands leads to either optically dark or bright additional states inside of the band gap, depending on the position of the leaving ligand on the QD surface. However, for fully ligated QDs, neither the ligand-localized nor hybridized molecular orbitals appear as trap states inside or near the band gap of the QD. Instead, being mostly optically dark, dense hybridized states could open new relaxation channels for high-energy photoexcitations. Comparing QDs passivated by different ligands, we also found that hybridized states are denser at the edge of the conduction band of the cluster ligated with phosphine oxide molecules than that with primary amines. Such a different manifestation of ligand binding may potentially lead to faster electron relaxation in QDs passivated by phosphine oxide than by amine ligands.