Deus Ex: GOTY PC version and Deus Ex: Conspiracy PS2 versions are said to be a bit different in design, level-size, UI, and a few other things:
https://steamcommunity.com/sharedfiles/filedetails/?id=185990038
I think the biggest issue w/ Deus Ex: GOTY PC with a gamepad is there are tons of hot-keys. So, yeah - I don't know if trying to get this one set-up onto a controller would & could be the wisest of ideas here. Honestly, this is a FPS - and those are best played, especially old ones w/ tons of hot-keys, with KB/mouse.
Out-the-box and even with
KenTie's EXE Mod installed (yes, I recommend the mod highly, to stop audio from not playing properly issues and other weird issues), it ain't recognizing my X360 GamePad straight-up. Same with Revision mod too.
You might have to mess w/ a mod (can't seem to find one), KB-to-controller app's, gamepad app's,
or just use Steam's built-in features to force a controller set-up...or something of the sort. Same seems to go for Deus Ex: Revision (free mod) too.
I would try Steam's built-in controller set-up first; start with that. See if it's okay to you.
If you want to go further, here's some app's you can use, to try to force keyboard strokes to be mapped with a gamepad and/or set-up gamepads to work with a game; you'll have to run the proper app when running the game:
JoyToPad -
https://joytokey.net/en/
Pinnacle Game Profiler (costs $ and has profiles) -
http://pinnaclegameprofiler.com/
There is a Deus Ex profile, BTW -
http://pinnaclegameprofiler.com/game-profiles/d
Controller Companion (costs $ and does have profiles in the Workshop players made) -
https://steamcommunity.com/sharedfiles/filedetails/?id=791925680&searchtext=deus+ex
CC Profile for Deus Ex: GOTY (set-up with X360 pad w/ controls similar to PS2 version) -
https://steamcommunity.com/sharedfiles/filedetails/?id=791925680&searchtext=deus+ex
I don't have Pinnacle, but I do have Controller Companion. Maybe I'll check the CC Profile out, for the heck of it.
EDIT:
Yeah, not thrilled w/ how the CC profile's set-up. Controls are in old-school control set-up spots, not how most games would do them in this era. Would have to edit or make a new one myself.