There are 2 things to consider if you want to run java standalone applications with Notes.
It is not preferred to run standalone Notes Java Applications with a different VM than Notes does.
In your case, you should take the VM located in “/app/pkqno01a/lotus/notes/latest/ibmpow/jvm”.
This could be a probably a problem, because this is an IBM VM 1.3.x. If you need to access external code, which is not compatible with JSE2 1.3 you must take a different one.
If you must use a different (newer) VM, compile your stuff as 1.3 code. This means you must call javac with the params -source 1.3 and -target 1.3 to make your code compatible with the Notes Java packages. Changing this params should also be possible in your preferred IDE. You have to add the required Notes archives (Notes.jar, jsdk.jar, XML4j.jar and LotusXSL.jar) to your classpath. If you have compiled your code as 1.3 code, you cannot use newer language features like generic code etc.
Setting the LD_LIBRARY_PATH is not enough to load needed native libraries. The Notes Java API expect that you run your code in the directory where your notes.ini is located.