FAIRMol

OHD_TB2023_28

Pose ID 12955 Compound 5271 Pose 76

DB fairmolDocking 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_TB2023_28
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
50.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.33, H-bond role recall 1.00
Burial
64%
Hydrophobic fit
91%
Reason: strain 50.7 kcal/mol
strain ΔE 50.7 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.716 kcal/mol/HA) ✓ Good fit quality (FQ -6.84) ✓ Good H-bonds (4 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Extreme strain energy (50.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-20.769
kcal/mol
LE
-0.716
kcal/mol/HA
Fit Quality
-6.84
FQ (Leeson)
HAC
29
heavy atoms
MW
524
Da
LogP
2.29
cLogP
Final rank
3.6828
rank score
Inter norm
-0.713
normalised
Contacts
12
H-bonds 6
Strain ΔE
50.7 kcal/mol
SASA buried
64%
Lipo contact
91% BSA apolar/total
SASA unbound
662 Ų
Apolar buried
387 Ų

Interaction summary

HBD 4 HY 3 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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

HY · Hydrophobic contacts

CLASH · Clashes

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 overlap5Native recall0.62
Jaccard0.33RMSD-
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
76 3.682832922842205 -0.712705 -20.7694 6 12 5 0.62 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 -20.769kcal/mol
Ligand efficiency (LE) -0.7162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.837
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 523.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.29
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 50.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 112.55kcal/mol
Minimised FF energy 61.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 662.1Ų
Total solvent-accessible surface area of free ligand
BSA total 424.7Ų
Buried surface area upon binding
BSA apolar 386.7Ų
Hydrophobic contacts buried
BSA polar 38.0Ų
Polar contacts buried
Fraction buried 64.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3110.1Ų
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 1544.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)