In recent years, Fragment Based Drug Discovery (FBDD) is focused in the drug discovery technique. The FBDD approach employs a number of sensitive biophysical techniques to detect the binding of small molecular compounds (fragments) to the target protein. The various combinations of the detection techniques have been employed by each research organization. It is one of the reasons that FBDD approach could provide unique lead compound for each organization. Generally, Fragment Library consists of small numbers (typically 500-3,000 fragments) of low molecular weight (typically 150-250 Da) compounds that have relatively weak binding affinities typically from 10-3 to 10-5 M. Fragments have a potent for growing up to be the novel lead compounds which suitable for the future drug candidate by structure modification. The more accurate binding information is important to conduct such suitable structure modification. During FBDD introduction study using our original Fragment Library for new anti-Influenza drug (RNA Polymerase PB2 inhibitor) discovery project, we have found a fragment which stabilizes target protein structure in spite of the weak binding affinity. By using this fragment in a purification step, the new apo-crystal structure of the target protein is obtained with 1.3Å resolution. Additionally, some new crystal complex structures with weak binders are obtained by using soaking method with this apo-crystal. These obtained binding modes must be useful for the effective structure modification of initial weak binders. In this presentation, we will propose that search for the agents which stabilize protein structure is one of the effective methods for FBDD approach.