How to determine IBM USB 6 pin header pinout?
Going with the conventional numbering 


┌── ──┐
│5 3 1│
│6 4 2│
└─────┘


From the measurements. 1 and 4 appear to be ground, 2 is 5V/VUSB, and 3 is the chassis. That also matches the components, and the track widths - the DRC has made the power and ground lines thicker than the chassis ground (Which the DRC probably doesn't know is a power net). The component south of pin 2 is a suppression choke, and a little capacitor between chassis ground and ground to help EMI, but double check your measurements before you hook it up.

That just leaves the thin signal tracks on pins 5 and 6 for D+ and D-. Fortunately nothing terrible happens if you have these swapped - just things don't work. Given sod's law you'll probably get this wrong first time round...

The only USB cable for that motherboard, that I can find pictures of on the web, is an IBM 46K4646.  That has an 8 pin header - but with the pinout


1 brown
2 red
3 shield
4 black
5 green
6 white
7 nc
8 nc


That looks like a plausible match for your connector, so as a first guess
I'd go with green (D+) to pin 5 and white (D-) to pin 6.

so long as you don't short 5V to ground you should be fine. The USB spec. says that host controllers have to be tolerant of D+ and D- being shorted to +5V (originally for ever, but now for minutes) and ground.