The internal Zend Studio debugger does not support i5/OS functions. The way to use Studio for i5/OS with your i5 is to use Remote Debugging.
When remotely debugging a PHP application running on a Windows server (Zend Server), an error message appears. This article provides a workaround for the cases when the problem is caused by a FastCGI timeout.
In many environments it may be the case that the debugging session is prevented by some network obstacles (firewalls, routers, proxy servers, etc.). To allow safe and effective bypassing of network obstructions you can setup an SSH Tunnel for remote debugging with Zend Studio.
This article provides the list of GET parameters that can be used to trigger and control a debug session.
The way to use Studio for i5/OS with your i5 is to use Remote Debugging. This will allow you to compose a script on your PC and run it in Studio using the php engine running on your i5. You will need to do this to access the i5 Toolkit Functions such as i5_connect(), as well as the ibm_db2 extensions, such as db2_connect().
This article explains how to use the Zend Debugger to debug command line PHP scripts without a dedicated web server, i.e. how to start a debug session from the command line.