The origin of the exceptional stability of molecular glasses grown by physical vapor deposition (PVD) is not well understood. Differences in glass density have been correlated with thermodynamic stability for thin films of N,N′-Bis(3-methylphenyl)-N,N′-diphenylbenzidine (TPD) grown by PVD at specific substrate temperatures below the glass transition temperature. However, the relationship between the internal conformation of glass molecules and the thermodynamic properties of molecular glasses is not well studied. We use carbon 1s near edge x-ray absorption fine structure (NEXAFS) spectroscopy to examine different TPD sample preparations in which differences in the thermodynamic stability of the glass are known. Density functional theory simulations of the NEXAFS spectra of TPD allow us to attribute spectroscopic differences to changes in the internal conformation of the TPD molecule and relate this conformation to the stability of the TPD glass. This provides a direct experimental measurement of the internal conformation of molecules forming an organic glass.