In this study, we discuss, using molecular dynamics simulations and energy-dispersive x-ray diffraction data, how a conformational isomerism can dramatically alter the nanosegregation phenomena that take place in a prototypical ionic liquid. The diffraction patterns of liquid 2-methoxyethylammonium nitrate are compared with the results from molecular dynamics simulations. The simulations conditions and force field parameters have been varied producing different charge models and different populations of conformers of the cation. We show that, while the short range structure is relatively unchanged in the models, the long range aggregation phenomena deemed responsible for the appearance of low Q peaks in the X-ray patterns strongly depend on the choice of the charge model. In the title compound, the best agreement with the experiment, where no low Q peaks appear, occurs if the point charges are calculated using the gauche conformation of the cation, which is characterized by an intramolecular hydrogen bond between ammonium and ether groups.