FAIRMol

OHD_TB2020_27

Pose ID 10894 Compound 1305 Pose 51

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_27
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
53.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.92, Jaccard 0.48, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
90%
Reason: strain 53.9 kcal/mol
strain ΔE 53.9 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.386 kcal/mol/HA) ✓ Good fit quality (FQ -4.26) ✓ Good H-bonds (3 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (53.9 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (18)
Score
-19.683
kcal/mol
LE
-0.386
kcal/mol/HA
Fit Quality
-4.26
FQ (Leeson)
HAC
51
heavy atoms
MW
741
Da
LogP
6.36
cLogP
Strain ΔE
53.9 kcal/mol
SASA buried
78%
Lipo contact
90% BSA apolar/total
SASA unbound
1077 Ų
Apolar buried
763 Ų

Interaction summary

HB 3 HY 24 PI 2 CLASH 3
Final rank2.337Score-19.683
Inter norm-0.464Intra norm0.078
Top1000noExcludedno
Contacts22H-bonds3
Artifact reasongeometry warning; 18 clashes; 5 protein contact clashes; high strain Δ 46.8
Residues
ALA284 ALA365 ARG287 ARG331 CYS375 GLY196 GLY197 GLY229 GLY286 GLY376 HIS359 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL362 VAL366

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 overlap11Native recall0.92
Jaccard0.48RMSD-
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
51 2.3367390353755515 -0.464314 -19.6831 3 22 11 0.92 0.00 - no Current
53 2.5633739943125504 -0.533989 -16.7478 3 19 0 0.00 0.00 - no Open
36 5.822086808893963 -0.5059 -21.6119 6 17 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 -19.683kcal/mol
Ligand efficiency (LE) -0.3859kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.259
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 51HA

Physicochemical properties
Molecular weight 741.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.36
Lipinski: ≤ 5
Rotatable bonds 16

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 1.45kcal/mol
Minimised FF energy -52.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1076.7Ų
Total solvent-accessible surface area of free ligand
BSA total 844.6Ų
Buried surface area upon binding
BSA apolar 762.7Ų
Hydrophobic contacts buried
BSA polar 82.0Ų
Polar contacts buried
Fraction buried 78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6866.2Ų
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 2069.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)