The states and properties of materials are governed by the constituent atomic structures defined by the positions of nuclei and electrons. Although quantum chemical simulations and other measurements, such as synchrotron X-ray scattering, are used to elucidate the atomic structures of materials under development, experimental data are required for verification and adjustment. Scattering measurements, based on empirical models focused on nucleus positions, are at the core of experimental analyses. However, structure determination way sensitive to the electron shape is limited and not applicable to materials in any state of matter. In this study, electronic pair distribution functions were derived from X-ray scattering data and were used to validate the electron positions in covalent materials on a sub-angstrom scale. This approach is expanded from atomic pair distribution functions analysing wide materials including crystalline and non-crystalline materials, and enables direct comparison of experimental and theoretical electronic structures to validate material's structures beyond atomic configurations.