sci-chemistry/kemistry-0.7 appears to have an internal copy of openbabel, whose version.h claims it to be version 1.99.1.
The last commit was 24 October 2004, the project looks pretty dead. I am not sure it would be worth the effort to port it to use a modern OpenBabel at this stage. If there is no activity it would likely be better to remove the package from the Gentoo tree.
Removed from portage.