I have not done connecting to Qlik Sense server (Standalone) from other Web based Server (Custom web based Java coding). But I have connected to QRS and QPS in Qliksense. All are having almost same configuration steps.
You need to check some steps here that may help you to understand... https://help.qlik.com/en-US/sense/November2017/Subsystems/ManagementConsole/Content/configure-QDS-with-certificates.htm
In my case, I copied my security certificates from Qlik Sense server to my local Windows OS in my desired path folder.
After that you need to click on the client.pfx to allow the access and check via MMC in your local machine to allow the certificates to work.
Otherwise you can contact Qlik Team to guide you!