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I'm designing a PCB with 3 Atmel ATmega16U4-AU micro-controllers on it.

I will be programming them through SPI.

Therefore, I will not be using D+ and D- ports on the USB interface. Then how do I deal with those pins.

Shall I:

  1. Leave them unconnected?

  2. Or Connect them to three different usb ports? (This way looks stupid. I don't want so many usb ports on the PCB)

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    \$\begingroup\$ Why are you using such a sophisticated chip if you're not using one of the largest selling points for it? \$\endgroup\$ – Ignacio Vazquez-Abrams Apr 25 '16 at 21:30
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    \$\begingroup\$ @Ignacio Once, I've selected a PIC with USB because it happened to have the most Flash and RAM in its family. I didn't need the USB. \$\endgroup\$ – Nick Alexeev♦ Apr 26 '16 at 1:11
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You can leave the pins unconnected.

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With pretty much any modern micro, unless explicitly stated in the manual, unused IO can be left unconnected

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