FAIRMol

OHD_MAC_53

Pose ID 13254 Compound 4025 Pose 375

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_MAC_53
PDB9IFH↗

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
60.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
52%
Hydrophobic fit
82%
Reason: strain 60.4 kcal/mol
strain ΔE 60.4 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Acceptable LE (-0.283 kcal/mol/HA) ✓ Good fit quality (FQ -2.88) ✓ Strong H-bond network (6 bonds) ✓ Good burial (52% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (60.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-10.201
kcal/mol
LE
-0.283
kcal/mol/HA
Fit Quality
-2.88
FQ (Leeson)
HAC
36
heavy atoms
MW
494
Da
LogP
0.02
cLogP
Strain ΔE
60.4 kcal/mol
SASA buried
52%
Lipo contact
82% BSA apolar/total
SASA unbound
833 Ų
Apolar buried
357 Ų

Interaction summary

HB 6 HY 13 PI 2 CLASH 3

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
Final rank3.805Score-10.201
Inter norm-0.519Intra norm0.216
Top1000noExcludedno
Contacts12H-bonds6
Artifact reasongeometry warning; 15 clashes; 1 protein clash; high strain Δ 60.4
Residues
ASN402 GLU467 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER470 THR397 THR473 TYR392

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
Jaccard0.67RMSD-
HB strict2Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
414 3.2634914229919687 -0.625569 -13.197 9 24 0 0.00 0.00 - no Open
341 3.674652484049885 -0.76243 -16.3654 15 23 0 0.00 0.00 - no Open
375 3.8046081219037604 -0.519069 -10.201 6 12 8 1.00 1.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -10.201kcal/mol
Ligand efficiency (LE) -0.2834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -2.880
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 493.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.02
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 60.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 217.95kcal/mol
Minimised FF energy 157.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 832.9Ų
Total solvent-accessible surface area of free ligand
BSA total 433.4Ų
Buried surface area upon binding
BSA apolar 357.4Ų
Hydrophobic contacts buried
BSA polar 76.1Ų
Polar contacts buried
Fraction buried 52.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3224.1Ų
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 1530.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)