FAIRMol

NMT-TY0562

Pose ID 13210 Compound 1625 Pose 331

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 NMT-TY0562
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
26.4 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.62, Jaccard 0.38, H-bond role recall 1.00
Burial
56%
Hydrophobic fit
78%
Reason: 7 internal clashes
7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.897 kcal/mol/HA) ✓ Good fit quality (FQ -7.79) ✓ Strong H-bond network (6 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (26.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-19.727
kcal/mol
LE
-0.897
kcal/mol/HA
Fit Quality
-7.79
FQ (Leeson)
HAC
22
heavy atoms
MW
322
Da
LogP
0.40
cLogP
Strain ΔE
26.4 kcal/mol
SASA buried
56%
Lipo contact
78% BSA apolar/total
SASA unbound
546 Ų
Apolar buried
239 Ų

Interaction summary

HB 6 HY 12 PI 2 CLASH 0
Final rank1.832Score-19.727
Inter norm-0.949Intra norm0.052
Top1000noExcludedno
Contacts10H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash; moderate strain Δ 26.4
Residues
GLU466 GLU467 LEU399 MET400 PHE396 PRO398 SER394 SER395 SER464 THR463

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

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
Jaccard0.38RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
309 0.232933138949205 -1.24137 -25.3727 6 13 0 0.00 0.00 - no Open
289 1.7718411418244264 -1.05343 -18.1033 8 20 0 0.00 0.00 - no Open
331 1.8318489626621886 -0.948695 -19.7272 6 10 5 0.62 1.00 - no Current
380 3.585498242654742 -1.0463 -22.7772 9 12 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 -19.727kcal/mol
Ligand efficiency (LE) -0.8967kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.785
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 322.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.40
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -137.08kcal/mol
Minimised FF energy -163.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 546.5Ų
Total solvent-accessible surface area of free ligand
BSA total 307.7Ų
Buried surface area upon binding
BSA apolar 238.8Ų
Hydrophobic contacts buried
BSA polar 68.9Ų
Polar contacts buried
Fraction buried 56.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2955.0Ų
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 1488.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)