We numerically investigate molecular arrangement and orientation in the self-assembled peptide monolayer adsorbed on Sold considering dipoles of each amide group in peptides and a dipole due to the Au-S bond at the chemisorption site. We investigate a single peptide adsorbed on gold and SAM of two dimensional crystal. Comparing their results with that of ignoring Au-S dipole, we show that molecules can take an orientation standing normal to the surface by Au-S dipole.