I've no idea what you mean.
0...100% can be reversed to 100...0% PWM for a "negative pulse" PWM, if that's what you need.
In addition, it may depend on whether the motor case/frame is "ground." In other words, motor ground and your PWM source share a ground.
Do you mean you want to create a PWM signal between 0 and -5V instead of between 0 and 5V?
Then you might try this which doesn't require a negative rail:
https://electronics.stackexchange.com/a/221425/95488The output won't be able to provide a lot of current, but into a high impedance input it should work.