Undefined stereochemistry in rdkit from mol2

Question

I am about to generate topology from a rdkit mol object with a conformer for a molecule in mol2 format, but receive the error this mol object has 'UndefinedStereochemistry'. As I am from computer science instead of Chemistry, I have no idea what this means and how to fix it.

I think a mol2 conformer file has all bond information and atom stereo position information. why this mol object still has 'UndefinedStereochemistry'? what should I do to make it to have full 'Stereochemistry'?

import rdkit.Chem as Chem
ligand = Chem.MolFromMol2File('test04192/ligand_clean.mol2')
ligand = Chem.AddHs(ligand)

I use this code to load the file to a mol object.below is my conformer file in text form

@<TRIPOS>MOLECULE
TEST
 33 36 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
      1 N          64.6250   41.8100  -29.6810 N.pl3   1  UNL1       -0.1137
      2 N          64.2020   42.7600  -28.7510 N.2     1  UNL1       -0.1528
      3 C          64.4910   44.0110  -28.9750 C.2     1  UNL1        0.1707
      4 C          64.1890   45.1870  -28.2020 C.2     1  UNL1        0.1009
      5 C          65.2330   44.4850  -30.1440 C.2     1  UNL1        0.2922
      6 C          63.4360   45.1650  -26.9130 C.3     1  UNL1        0.0556
      7 N          64.6540   46.2470  -28.7700 N.2     1  UNL1       -0.1739
      8 N          65.3160   45.9130  -29.9790 N.am    1  UNL1       -0.1539
      9 O          65.6880   43.7840  -31.0770 O.2     1  UNL1       -0.2661
     10 C          65.9540   46.7820  -30.8890 C.ar    1  UNL1        0.0768
     11 C          65.2290   47.5060  -31.8040 C.ar    1  UNL1        0.0165
     12 C          65.8320   48.3650  -32.7090 C.ar    1  UNL1       -0.0032
     13 C          67.2020   48.5050  -32.6980 C.ar    1  UNL1       -0.0257
     14 C          67.8430   49.4300  -33.6740 C.3     1  UNL1        0.0307
     15 C          67.9330   47.7860  -31.7880 C.ar    1  UNL1       -0.0245
     16 C          69.4300   47.9550  -31.7930 C.3     1  UNL1        0.0307
     17 C          67.3190   46.9320  -30.8900 C.ar    1  UNL1        0.0123
     18 C          63.6760   40.8990  -30.2480 C.ar    1  UNL1        0.1302
     19 C          63.3690   40.9930  -31.6090 C.ar    1  UNL1        0.0215
     20 C          62.4640   40.1300  -32.1620 C.ar    1  UNL1        0.0016
     21 C          61.8510   39.1660  -31.4010 C.ar    1  UNL1        0.0033
     22 C          62.1320   39.0430  -30.0450 C.ar    1  UNL1        0.0403
     23 C          63.0450   39.9190  -29.5000 C.ar    1  UNL1        0.2124
     24 O          63.3880   39.8630  -28.1340 O.3     1  UNL1       -0.2851
     25 C          61.4920   38.0260  -29.2220 C.ar    1  UNL1        0.0033
     26 C          62.2590   37.2910  -28.3220 C.ar    1  UNL1        0.0001
     27 C          61.6850   36.3120  -27.5150 C.ar    1  UNL1        0.0002
     28 C          60.3350   36.0510  -27.5910 C.ar    1  UNL1        0.0066
     29 C          59.5580   36.7730  -28.4830 C.ar    1  UNL1        0.0798
     30 C          60.1480   37.7360  -29.2720 C.ar    1  UNL1        0.0067
     31 C          58.1320   36.5410  -28.6040 C.2     1  UNL1        0.3878
     32 O          57.6980   36.1020  -29.7120 O.co2   1  UNL1       -0.2406
     33 O          57.2920   36.7990  -27.5370 O.co2   1  UNL1       -0.2406
@<TRIPOS>BOND
     1     1    18    1
     2     1     2    1
     3     2     3    2
     4     3     5    1
     5     3     4    1
     6     4     7    2
     7     4     6    1
     8     5     9    2
     9     5     8   am
    10     7     8    1
    11     8    10    1
    12    10    11   ar
    13    10    17   ar
    14    11    12   ar
    15    12    13   ar
    16    13    14    1
    17    13    15   ar
    18    15    16    1
    19    15    17   ar
    20    18    19   ar
    21    18    23   ar
    22    19    20   ar
    23    20    21   ar
    24    21    22   ar
    25    22    23   ar
    26    22    25    1
    27    23    24    1
    28    25    30   ar
    29    25    26   ar
    30    26    27   ar
    31    27    28   ar
    32    28    29   ar
    33    29    30   ar
    34    29    31    1
    35    31    32   ar
    36    31    33   ar

Answer 1

Currently there is a bug with the Chem.MolFromMol2File, in latest rdkit version: 2023.3.1, which seems to remove Hydrogens from the molecule when creating a mol object.

There is even an open issue on the Github of rdkit. Issue 3106.

Code to reproduce bug behaviour:

from rdkit.Chem.rdMolDescriptors import CalcMolFormula
import rdkit.Chem as Chem
 
ligand = Chem.MolFromMol2File('clean_ligand.mol2', removeHs=False)
CalcMolFormula(ligand)
# This prints out: C25N4O4-3 which is wrongly removing the Hydrogens even though removeHs is False.

Work-around Hack:

The hack is to read the mol2 file into an rdkit molecule, then convert the rdkit molecule to a PDB, and finally read the PDB back to get the rdkit molecule along including the hydrogens.

from rdkit.Chem.rdMolDescriptors import CalcMolFormula
import rdkit.Chem as Chem

ligand = Chem.MolFromMol2File('clean_lignad.mol2', removeHs=False)

Chem.MolToPDBFile(ligand,'clean_ligand.pdb')

clean_lig_pdb = Chem.MolFromPDBFile('clean_ligand.pdb')

CalcMolFormula(clean_lig_pdb)

# This prints out : C25H19N4O4-3 which now includes the hydrogens