In this work, an atom-based molecular modelling technique is applied to determine the structures of smectic E, A, and C phases composed of phenyl ester mesogens. These mesogenic molecules are abbreviated as MDn21B. A computer search with molecular mechanics calculations is performed to identify the possible low energy configurations of two adjacent molecules. According to these results, the isolated molecules with their optimized structures approach dimer associations, and the favourable alignments are antiparallel. Depending on the lowest energy associations, ten different initial models for each phase, to simulate X-ray diffraction patterns, are developed by packing the dimers with an antiparallel association into periodic boxes. Also, relaxed models are obtained by applying cycles of energy minimization and molecular dynamics under (NVT) conditions at 500 K to these initial models. Molecular dynamics runs under (NPT) conditions are then performed on these relaxed models at a temperature of each smectic phase chosen to approach equilibrated structures in these phases. Simulations are also performed, and detailed molecular structures analysed, on the basis of these equilibrated structures. The simulated X-ray diffraction patterns for smectics E, A, and C are in good agreement with those obtained experimentally. The distributions of the dihedral angles at the bonds in the aromatic cores indicate that more fluctuations occur in the smectic A and C phases than in the smectic E. The average values of the aromatic core overlap, as calculated between neighbouring mesogens in the smectic phases, are in the range 4.78-5.91 A. These values are slightly higher than those found in experimental X-ray diffraction patterns at the position 2 theta 20. Total pair correlation functions have a similar appearance for smectics E and A. Also, these pair correlation functions are similar to the results for amorphous polymers, i.e. the total pair correlation functions lose their order outside a spherical shell with radius gamma greater than 5 A.