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Nitroamino is an ideal high-energy group for constructing energetic compounds. The skeletal isomerization of nitroamino to nitroimino forms intramolecular HBs, thus resulting in better density, thermal stability and sensitivity. However, it is difficult to find nitroamino and nitroimino in the same environment for comparative analysis. A new compound, 5-Nitroamino-8-nitroimino-1,4-dihydropyrazino [2,3-d]pyridazine-2,3-dione (3), was designed and synthesized. The symmetric skeleton of pyrazino [2,3-d]pyridazine provides the same environment for both nitroamino and nitroimino groups. By using a variety of computational and graphical methods, a theoretical support for nitroamino-based energetic materials was produced by thoroughly examining the influence between nitroamino and nitroimino.