to get the desired result, I suggest you to create a new database such as:
You should remove the duplicate tables from the Data Model, if any. When the Data Model is correct and it contains the needed tables, you can synchronize your Data Model with the database. During the synchronization process, you only have to Export the entities and relationships to the database. At the end, the tables will be created in the database and they will be mapped with the Data Model elements.
For more details, you can refer to this wiki article:
The Data Model Mapping
The User, Group and Module entities cannot be removed from the Data Model, because they are needed for the user profiling and the user authentication.
The problem that you get while executing the delete command could be related to the dependencies among the tables. For example, you cannot delete the User table if other existing tables, such as the Group table, depends on it.