The information about 3D atomic coordinates of chemical structures is valuable knowledge in many respect. For large sets of different structures, the computation or measurement of these coordinates is an expensive process. Therefore, the originator of such a data set is interested in enforcing his intellectual property right. In this paper, a method for copyright protection of chemical structure sets based on digital watermarking is proposed. A complete watermarking system including synchronization of the watermark detector and verification of the decoded watermark message is presented. The basic embedding scheme, denoted SCS (Scalar Costa Scheme) watermarking, is based on considering watermarking as a communications problem with side information at the encoder.