FAIRMol

Z135082068

Pose ID 13520 Compound 129 Pose 641

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 Z135082068
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
Likely artefact or unreliable pose
Binding strong Geometry high Native strong SASA done
Strain ΔE
25.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.45, H-bond role recall 0.00
Burial
51%
Hydrophobic fit
92%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.459 kcal/mol/HA) ✓ Good fit quality (FQ -4.42) ✓ Strong H-bond network (6 bonds) ✓ Good burial (51% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ High strain energy (25.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (12)
Score
-13.761
kcal/mol
LE
-0.459
kcal/mol/HA
Fit Quality
-4.42
FQ (Leeson)
HAC
30
heavy atoms
MW
443
Da
LogP
4.10
cLogP
Strain ΔE
25.7 kcal/mol
SASA buried
51%
Lipo contact
92% BSA apolar/total
SASA unbound
748 Ų
Apolar buried
351 Ų

Interaction summary

HB 6 HY 17 PI 0 CLASH 2

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.712Score-13.761
Inter norm-0.624Intra norm0.164
Top1000noExcludedno
Contacts8H-bonds6
Artifact reasongeometry warning; 12 clashes; 6 protein contact clashes; moderate strain Δ 25.7
Residues
ASN402 LEU399 LYS407 LYS410 PHE396 PRO398 SER395 THR397

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
Jaccard0.45RMSD-
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
627 1.0001462219980781 -1.0679 -29.9387 7 16 0 0.00 0.00 - no Open
625 1.1234315118959386 -0.879344 -15.7908 7 22 0 0.00 0.00 - no Open
641 1.712445518595198 -0.624042 -13.7612 6 8 5 0.62 0.00 - no Current
648 2.2979713944991356 -0.743596 -18.2288 5 13 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 -13.761kcal/mol
Ligand efficiency (LE) -0.4587kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.425
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 443.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.10
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -137.46kcal/mol
Minimised FF energy -163.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 748.5Ų
Total solvent-accessible surface area of free ligand
BSA total 382.4Ų
Buried surface area upon binding
BSA apolar 351.2Ų
Hydrophobic contacts buried
BSA polar 31.2Ų
Polar contacts buried
Fraction buried 51.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3189.4Ų
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 1527.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)