/usr/share/java/biojava4-structure-gui.jar is in libbiojava4.0-java 4.2.11+dfsg-1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/share/java/biojava4-structure-gui-4.2.11.jar
/usr/share/java/biojava4-structure-gui-4.2.11.jar