BIOVIA Direct may not parse molfiles in V2000 format correctly if they include at least one line in the atom block that ends with the atom symbol plus exact one trailing space character. In particular, such atoms will be considered pseudo atoms rather than just standard atom types. The following molfile provides an example for such specific format of the lines in the atom block:

  ACCLDraw09092111232D

  5  5  0  0  0  0  0  0  0  0999 V2000
   10.6875  -10.8395    0.0000 N 
    9.7325  -11.5334    0.0000 C 
   10.0972  -12.6562    0.0000 C 
   11.2778  -12.6562    0.0000 C 
   11.6425  -11.5334    0.0000 C 
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  1  1  0  0  0  0
M  END

If you try to use such molfiles e.g. with Direct's mol() operator, the pseudo atoms with be considered unknown atom types and query features:

SELECT mol('/home/biovia/pyrrole.mol') CTAB FROM DUAL;

ORA-20100: MDL-1919: Molecule failed registration check: 
Error: (root) No query features allowed for registration
Error: (root) Unknown atom symbols: N,C
MDL-0633: Unable to convert molfile string to binary molecule ctab
ORA-06512: at "C\$DIRECT2021.MDLAUXOP", line 343
ORA-06512: at "C\$DIRECT2021.MDLAUXOP", line 336
ORA-06512: at "C\$DIRECT2021.MDLAUXOP", line 319

As a workaround, you can remove the single trailing space, or add a second one: 

  ACCLDraw09092111062D

  5  5  0  0  0  0  0  0  0  0999 V2000
   10.6875  -10.8395    0.0000 N
    9.7325  -11.5334    0.0000 C
   10.0972  -12.6562    0.0000 C
   11.2778  -12.6562    0.0000 C
   11.6425  -11.5334    0.0000 C
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  1  1  0  0  0  0
M  END

The source of the problem is a bug in an underlying Pipeline Pilot Chemistry Library​​​​​​​. BIOVIA Draw is not impacted by this issue. The issue will be fixed in the BIOVIA Direct and Pipeline Pilot 2022 releases.