A bottom-up approach was followed to create a CG model for the C8S3 molecule. During this procedure different aspects of the CG features were optimised to ensure that the final model accurately represents the structural and chemical properties of the cyanine dyes. Initially, QM methods were used to obtain optimal parameters for the description of the polymethine bridge dihedrals and different sets of partial charges. Then, the obtained parameters were tested on available crystal structures for cyanine dyes with the same aromatic core. The best set of parameters was used for atomistic simulations that provided the reference point for constructing the cyanine dye CG model. The CG model was further optimised to reproduce better the structural features of the monomer conformation when aggregates are formed. The final CG model represented with great detail structural/spatial properties of the cyanine dyes. Our results provide guidelines and best practices for constructing CG models for simple or complex nanomaterials.