Database Description

Structure Databases - Small molecules

LigandBox(LIGANDs Data Base Open and eXtensible) is a 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies. It contains the 3D molecular structures including full hydrogen atoms with atomic charges for each compounds.
LigandBox has been developed by JBIC, as one component of the molecular simulation system myPresto, supported by NEDO.
3D conformations of compounds were generated from 2D structural data, kindly provided by Namiki Shoji Co.,Ltd. Compounds from Namiki Shoji Co.,Ltd can be ordered to each company through each inquiry web page.
Chemical structures in this database were computationally generated, may not be identical to structures of compounds stored in supplying companies.

The molecular files are in Sybyl mol2 file format for virtual drug screening, protein-compound docking, and chemo-informatics.The partial atomic charges of each compound is calculated by MOPAC AM1-BCC and the users can adopt these charges in the molecular dynamics simulations.Each compound has physical properties such as solubility and partition coefficient. These information is useful to avoid promiscuous compounds.The compound IDs are the vender’s ID to purchase the compounds and the inventory ratio is high.