Web Dynpro is a complex framework and it would be tough to integrate it to your Java application. You can use SAP Java Connector JCo. SAP Java Connector can be used to call Remote Function calls on SAP system.
You can use already defined function modules to connect. You can take help from a SAP ABAP developer if you want to customize any function module request.
You can use SAP JCo to make 2 types of calls to system:
By using a JCo connection, you can call an RFC from the R/3. It contains 2 .dll files. These are the 2 .dll files that help in calling an RFC.
A JCO connection to a R/3 system is represented by the JCO.Client Class. This class abstracts all functionalities that surround a connection.
To know more about SAP Java Connector, you can refer below SAP link for configuration: