PDBQT to SDF
Export ligand poses from Meeko-prepared PDBQT to SDF while recovering chemical connectivity.
How to convert docking PDBQT files to SDF?
Upload a ligand PDBQT containing Meeko chemical reconstruction remarks. The PDBQT to SDF converter reconstructs connectivity and exports ligand poses as SDF records. Download the SDF for chemical inspection or further analysis. Plain PDBQT without the required metadata cannot be reconstructed reliably.
- Upload a ligand
.pdbqtwith Meeko reconstruction metadata. - Choose whether to keep all poses or only cluster representatives.
- Run the export.
- Download the SDF and inspect its pose records.
Worked example
Input .pdbqt:
REMARK SMILES CCO
REMARK SMILES IDX 1 1 2 2 3 3
REMARK H PARENT 3 4
ROOT
ATOM 1 C UNL 1 -0.954 0.048 0.043 1.00 0.00 0.034 C
ATOM 2 C UNL 1 0.488 -0.322 -0.189 1.00 0.00 0.152 C
ENDROOT
BRANCH 2 3
ATOM 3 O UNL 1 1.277 0.325 0.738 1.00 0.00 -0.397 OA
ATOM 4 H UNL 1 1.833 1.048 0.389 1.00 0.00 0.210 HD
ENDBRANCH 2 3
TORSDOF 1Actual .sdf output:
RDKit 3D
9 8 0 0 0 0 0 0 0 0999 V2000
-0.9540 0.0480 0.0430 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4880 -0.3220 -0.1890 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2770 0.3250 0.7380 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.1502 0.0984 1.1242 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1590 1.0279 -0.4129 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6055 -0.7121 -0.4129 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6106 -1.4098 -0.0812 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7880 -0.0212 -1.2037 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8330 1.0480 0.3890 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
1 4 1 0
1 5 1 0
1 6 1 0
2 7 1 0
2 8 1 0
3 9 1 0
M END
> <meeko> (1)
{"is_sidechain": [false]}
$$$$The blocks show the complete input and output for one ethanol molecule. Coordinates and chemistry shown here come from this conversion run.
Input
| Input | Accepted format | Requirements |
|---|---|---|
| Molecules | .pdbqt upload | Ligand PDBQT with Meeko reconstruction remarks; multiple poses supported. Maximum file size: 50 MiB. |
Settings
| Setting | Default | What it does |
|---|---|---|
Only cluster representatives | Off | Export only cluster representative poses when the input contains clustering information. Off exports all reconstructable poses. |
Keep flexible residues | Off | Keep reconstructed flexible receptor residues in the SDF. Off exports the ligand without those flexible residues. |
Results
| Output | Contents |
|---|---|
| Results table | Name, Poses, Output file. |
molecule_1.sdf | Reconstructed ligand pose records with coordinates. |
results.tsv | Tab-separated table with the same rows and values. |
report.json | Result rows, resolved settings and warnings. |
run.log | Tool, settings, result count and warnings; failures include their error. |
Downloads are available from Files. Inspect both the structure preview and the chemical content of the downloaded file.
Why PDBQT reconstruction needs metadata
PDBQT stores coordinates, docking atom types and charges, without a complete, unambiguous bond-order description. Meeko preparation writes REMARK SMILES, atom-index mappings and hydrogen-parent information. SDF export uses these remarks to reconstruct the molecular graph instead of guessing from distances.
Retain these remarks in docking outputs. A coordinate and torsion file can be usable for docking but lack what this exporter needs. Renaming the extension cannot restore missing chemical information.
Meeko reconstructs explicit hydrogens during export. SDF atom counts and hydrogen coordinates need not be identical to the raw PDBQT list. Multiple reconstructable poses become separate records. Only cluster representatives applies when supported clustering metadata is present.
Choosing a structure conversion
| File available | Tool | Requirement |
|---|---|---|
| Meeko-prepared PDBQT | PDBQT to SDF | Reconstruction remarks retained. |
| Ligand PDB | PDB to SDF | Inspect bond orders and charge. |
| Original 3D SDF | SDF to PDBQT | Prefer the original chemistry for new preparation. |
FAQ
Can any PDBQT file become SDF?
No. This exporter needs metadata that Meeko can reconstruct. Files without it fail explicitly.
Can I export several docking poses?
Yes, when reconstructable. The table reports exported pose counts and the SDF has one record per pose.
Does SDF retain the docking torsion tree?
It retains the reconstructed graph and pose coordinates, rather than a PDBQT torsion-tree representation. Prepare it again if another docking file is needed.
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