The holy roman empire was dissolved by Francis II, with it the position of emperor.

the last emperor to actually be crowned by the papal was Charles V

There was no agreement or treaties, it was a tradition that died out, it was an unneeded hassle

The HRE was dissolved after its last emperor, Francis II, was beaten by Napoleon at Austerlitz in 1806. Francis had founded the Austrian Empire in 1804, becoming (weirdly enough) both Francis I of Austria and simultaneously Francis II of the HRE. So there's no longer any HRE to be crowned emperor of.

Much of the territory of the HRE had been being mediatized and/or secularized during the wars of the French Revolution, so the final loss of territory after Austerlitz was the end of the empire as a workable territory in any case. After Austerlitz, most of the territory of the HRE became part of the Confederation of the Rhine, which underwent further reorganizations to become the precursor states to the German empire.

Incidentally, Francis I went on to suffer several more defeats at the hands of Napoleon, but Austria's leading role in the War of the Sixth Coalition means that it emerged as one of the main allied powers in that war, and hosted the Congress of Vienna, which reorganized Europe in the post-Napoleonic era.