In view of the fact that the mechanisms of the interaction of organic molecules with the properties of the drug occur in most cases by their binding to the receptors (proteins), we wanted to examine the interactions of small organic molecules that we synthesized and certain proteins. In this paper the comparison between molecules, modeled by different software packages, and experimental results is performed. The series of new molecules are synthesized using Barbier reaction of allylation of carbonyl compounds with 4-(bromomethyl)-1,3-dioxol-2-one as a highly fictionalized allylic synthon. Their structure was determined by spectroscopic methods (NMR-, IR- and UV/VIS-spectroscopy and MS-spectrometry), while for three individual molecules analysis of x-ray diffraction (X-ray analysis) was also performed, which gave the final confirmation of the exact arrangement of all atoms in the space. The molecules are represented in standard chemical format, visualized and prepared for simulations. In order to obtain datasets that further can be used to examine and analyze interactions with well-known proteins, molecular dynamic simulations are performed. The purpose of this research was to present that using powerful computer infrastructure and appropriate software tools, an accurate molecule models can be created.