In this study, novel ionic liquids formed between the 1-ethyl-3-methylimidazolium cation [emim](+) and the glycine anion [Gly](-) have been investigated theoretically. The relevant geometrical characteristics, energy properties, the characters of the intermolecular hydrogen bonds (H bonds), and the possibility of proton transfer as well as IR characteristics have been systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses have also been applied to understand the nature of the interactions between ionic pairs in ionic liquids. The most stable geometries have been determined by analyzing the relative energies and interaction energies, where the C-H center dot center dot center dot O intermolecular H bonds involving the protons attached to the imidazolium ring have been found to possess partial covalent character in nature. Electron transfers from the lone pairs of the carbonyl O atom of [Gly](-) to the C-H antibonding orbital of the [emim](+) can explain the elongation and red shift of the C-H stretching frequency. The interaction modes are more favorable when the carbonyl O atoms of [Gly](-) interact with the C2-H of the imidazolium ring and the C-H of the methyl group through the formation of double H bonds. The origin of the high stability of the amino acid ionic liquids observed experimentally may be attributed to the nonexistence of the proton-transferred products (neutral pairs) together with the large energy needed for separation of the ionic pairs. Additionally, the characteristics of the IR spectra have been analyzed to demonstrate the variants of the molecular structure of the [emim](+)[Gly](-) ionic liquids.