FAIRMol

OHD_TB2020_29

Pose ID 10896 Compound 562 Pose 53

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_TB2020_29
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
57.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.83, Jaccard 0.34, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
84%
Reason: 6 internal clashes, strain 57.2 kcal/mol
strain ΔE 57.2 kcal/mol 6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good fit quality (FQ -1.79) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (57.2 kcal/mol) ✗ Low LE (-0.163 kcal/mol/HA) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (19)
Score
-8.297
kcal/mol
LE
-0.163
kcal/mol/HA
Fit Quality
-1.79
FQ (Leeson)
HAC
51
heavy atoms
MW
725
Da
LogP
6.19
cLogP
Strain ΔE
57.2 kcal/mol
SASA buried
80%
Lipo contact
84% BSA apolar/total
SASA unbound
1011 Ų
Apolar buried
676 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 6
Final rank3.184Score-8.297
Inter norm-0.438Intra norm0.275
Top1000noExcludedno
Contacts27H-bonds7
Artifact reasongeometry warning; 19 clashes; 9 protein contact clashes; high strain Δ 54.8
Residues
ALA284 ALA363 ALA365 ARG228 ARG361 CYS375 GLY196 GLY197 GLY229 GLY286 GLY376 HIS428 ILE199 ILE285 ILE378 LEU332 LEU334 LEU377 PHE198 PHE230 SER200 SER364 THR360 THR374 VAL362 VAL366 VAL381

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap10Native recall0.83
Jaccard0.34RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
53 3.1843385243565816 -0.438163 -8.29736 7 27 10 0.83 0.00 - no Current
55 3.259793348076267 -0.524383 -22.9259 5 18 0 0.00 0.00 - no Open
64 3.3123104589459818 -0.521754 -24.5294 3 20 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -8.297kcal/mol
Ligand efficiency (LE) -0.1627kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -1.795
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 51HA

Physicochemical properties
Molecular weight 724.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.19
Lipinski: ≤ 5
Rotatable bonds 16

Conformational strain (MMFF94s)
Strain energy (ΔE) 57.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -30.27kcal/mol
Minimised FF energy -87.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1010.9Ų
Total solvent-accessible surface area of free ligand
BSA total 805.7Ų
Buried surface area upon binding
BSA apolar 676.0Ų
Hydrophobic contacts buried
BSA polar 129.7Ų
Polar contacts buried
Fraction buried 79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6812.7Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2075.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)