Babylon eclipsed Nippur as the ` holy city ' of Mesopotamia around the time Hammurabi first unified the Babylonian Empire , and became the capital city of the Neo-Babylonian Empire from 612 to 539 BC . Claiming to be the successor of the ancient Eridu , Babylon eclipsed Nippur as the `` holy city '' of Mesopotamia around the time Hammurabi first unified the Babylonian Empire , and again became the seat of the Neo-Babylonian Empire from 612 to 539 BC .