Currently, the BioJava unit test: TestBond.testHydrogenToProteinBondMissing fails, because on 2018-03-29 the hydrogen names for EDO were modified, however, the PDB structures were not updated (see snippets below). Note, the same issue may affect other ligands where atom names were updated.

edo.cif
_chem_comp.pdbx_modified_date 2018-03-29
...
EDO H1 H1 H 0 1 N N N 40.269 18.578 -36.179 -0.626 0.552 -1.391 H1 EDO 5
EDO H2 H2 H 0 1 N N N 38.845 17.541 -35.829 -1.224 1.508 -0.013 H2 EDO 6
EDO H3 H3 H 0 1 N N N 40.451 16.981 -38.299 1.224 1.508 0.014 H3 EDO 7
EDO H4 H4 H 0 1 N N N 38.587 16.690 -39.453 2.328 -0.604 0.176 H4 EDO 8
EDO H5 H5 H 0 1 N N N 40.908 16.123 -36.247 -2.328 -0.604 -0.177 H5 EDO 9
EDO H6 H6 H 0 1 N N N 39.425 18.451 -38.410 0.626 0.551 1.391 H6 EDO 10

4txr.cif
HETATM 4078 H H11 . EDO E 5 . ? -2.936 -17.609 18.748 1.00 14.13 ? 202 EDO A H11 1
HETATM 4079 H H12 . EDO E 5 . ? -1.441 -18.486 18.410 1.00 14.13 ? 202 EDO A H12 1
HETATM 4080 H HO1 . EDO E 5 . ? -3.099 -19.869 19.278 1.00 16.64 ? 202 EDO A HO1 1
HETATM 4081 H H21 . EDO E 5 . ? -2.090 -18.733 16.039 1.00 15.08 ? 202 EDO A H21 1
HETATM 4082 H H22 . EDO E 5 . ? -2.056 -17.033 16.508 1.00 15.08 ? 202 EDO A H22 1
HETATM 4083 H HO2 . EDO E 5 . ? -3.968 -17.575 15.297 1.00 15.81 ? 202 EDO A HO2 1