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In order to improve the environment for researchers on computational chemistry, a database management system named SimChemDB was developed. SimChemDB provides the facilities for data management, including storing chemical files, displaying and editing chemical structure. It made use of Apache Derby, which served as database engine. The database schema was created for the storage of various data. A TableViewer was designed for the visualization of chemical data. Finally, SimChemDB system was demonstrated through an application on anti-malarial drug design process, where the steps of data preparation were expatiated. The results indicate that SimChemDB is an effective tool for computational chemistry, and it facilitates the management of chemical data.