Nanoparticle mediated drug delivery is an emerging area of research now a days. In our present study, we emphasized on the mode of interaction of a widely used drug, Quercetin with frequently worked metallic nanoparticle, Gold (Au). At first five –OH groups have been attached separately with gold atom and energy minimization was performed using Avogadro Software for windows system. From this, we found that the –OH groups present at 7 position of ‘A’ ring, 3’ and 4’ positions of ‘B’ ring are most suitable site for gold atom to bind. In the next level of study, a gold atom has been interacted with two quercetin molecules at a time. The gold atom was attached to –OH group of 7 position of one quercetin molecule and 4’ position of the other. The calculated energy was found to be 482.319 KJ/Mol. Further, gold atoms were interacted with all –OH groups of quercetin molecule at a time to see its stability and the structure was found to have quite stable with an energy level of 218.074 KJ/Mol. Lastly we tried to make a quercetin–gold nanoparticle model structure which mimics the actual nanocomposite synthesized in vitro where one gold atom was interacted with two quercetin molecules and the other –OH groups of quercetin molecules were again attached with gold atoms. This structure possesses energy of 439.880 KJ/Mol. The bond lengths and bond angle of interacting C, O and Au atoms were measured to characterize the complex.