Using usb port to communicate with standalone atmega328p circuit
The ATmega328 does not have any native USB capability, so there is nowhere appropriate to connect D+/D- to the ATmega328.

Assuming you are emulating an Arduino Uno, then something like this:

https://www.jaycar.com.au/arduino-compatible-usb-to-serial-adaptor-module/p/XC4464

is what will come closest to mimicking the USB function on an Uno (ie a serial connection).

This shows how such a device would be connected:

https://www.jaycar.com.au/usb-serial-converter