FAIRMol

OHD_TC1_221

Pose ID 12983 Compound 2065 Pose 104

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_TC1_221
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
4
Internal clashes
15
Native overlap
contact recall 1.00, Jaccard 0.62, H-bond role recall 0.00
Burial
55%
Hydrophobic fit
91%
Reason: 15 internal clashes
4 protein-contact clashes 15 intramolecular clashes 48% of hydrophobic surface appears solvent-exposed (13/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.552 kcal/mol/HA) ✓ Good fit quality (FQ -5.53) ✓ Good H-bonds (5 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ High strain energy (27.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (15)
Score
-18.776
kcal/mol
LE
-0.552
kcal/mol/HA
Fit Quality
-5.53
FQ (Leeson)
HAC
34
heavy atoms
MW
448
Da
LogP
4.87
cLogP
Strain ΔE
27.0 kcal/mol
SASA buried
55%
Lipo contact
91% BSA apolar/total
SASA unbound
746 Ų
Apolar buried
376 Ų

Interaction summary

HB 5 HY 14 PI 2 CLASH 0 ⚠ Exposure 48%

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
No clash · clashes detected for this pose.
⚠️Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (13/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27 Buried (contacted) 14 Exposed 13 LogP 4.87 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.795Score-18.776
Inter norm-0.630Intra norm0.078
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 15 clashes; 4 protein contact clashes; moderate strain Δ 27.0
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 LYS410 PHE396 PRO398 PRO462 SER394 SER470 THR397 THR463

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.62RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
78 1.6133917115557792 -0.816212 -27.2909 7 18 0 0.00 0.00 - no Open
104 1.7952690213119946 -0.63003 -18.7755 5 13 8 1.00 0.00 - no Current
58 2.994784767622205 -0.958267 -29.2406 7 21 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 -18.776kcal/mol
Ligand efficiency (LE) -0.5522kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.525
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 447.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.87
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 158.00kcal/mol
Minimised FF energy 131.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 745.6Ų
Total solvent-accessible surface area of free ligand
BSA total 412.0Ų
Buried surface area upon binding
BSA apolar 376.0Ų
Hydrophobic contacts buried
BSA polar 36.1Ų
Polar contacts buried
Fraction buried 55.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3175.4Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1550.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)