In this paper, we investigate the self-organization of NTCDI molecules on Au (111) surface by combining Density Functional Theory (DFT) and experiments based on scanning tunneling microscopy (STM) and infrared spectroscopy measurements. The competition between the cohesive and adsorption energy on the flat surface is discussed. It was shown that the network is mainly stabilized by cohesive interactions explaining the mobility of the network over the surface. The comparison between experimental and infrared spectra enables to confirm the effect and importance of the H-bonds in the network stability. STM images at different voltages and in ambient conditions were interpreted by projected density of states calculations and compared with experiment. The theoretically proposed network geometry was characterized at molecular level reproducing the experimental STM image.