The Amiga motherboard power connector is wired for a PC style floppy drive and so is the Gotek.
The *correct* cable should connect the same pin numbers on both side together. i.e. pin 1 to pin 1 and so on. (aka a "straight" cable)
The connector is keyed and it should only go in one way.
You really shouldn't messed up unless you were making your own cable and rotated the pinout 180 degrees on one side.
Pin out - See attachment. PCB labeled, table for pinout, PC floppy power connector on the side for colour.
You were lucky as like I said before, there is a 3.3V regulator in the floppy, so the circuits are some what protected.
Last edited by K.C.Lee; 25 October 2014 at 16:57.