Deep Eutectic Solvents (DES) are complexes of organic salts and neutral hydrogen bond donors. They are tuneable, low volatility liquids that are environmentally benign. Denitrogenation of fuel oils reduces nitrogen and sulfur oxide emissions from burning petrochemicals in internal combustion engines, but current processes are intensive. A greener denitrogenation process has been developed using DES. Remarkably, the DES can achieve higher extraction efficiency when it contains a small amount of added water. We have analysed data already for the pure DES used in this extraction: choline chloride:malic acid with and without water. Therefore, here we wish to study the structure of this DES containing a small-molecule nitrogen compound (indole) with and without water to discover the mechanism behind the high extraction efficiency of DES and hydrated DES.