FAIRMol

NMT-TY0581

Pose ID 11178 Compound 532 Pose 335

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand NMT-TY0581
PDB5S9T↗

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 mixed SASA done
Strain ΔE
26.7 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.33, Jaccard 0.20, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
60%
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.233 kcal/mol/HA) ✓ Good fit quality (FQ -10.31) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✗ High strain energy (26.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-24.652
kcal/mol
LE
-1.233
kcal/mol/HA
Fit Quality
-10.31
FQ (Leeson)
HAC
20
heavy atoms
MW
297
Da
LogP
-0.56
cLogP
Final rank
1.6375
rank score
Inter norm
-1.162
normalised
Contacts
12
H-bonds 13
Strain ΔE
26.7 kcal/mol
SASA buried
80%
Lipo contact
60% BSA apolar/total
SASA unbound
475 Ų
Apolar buried
229 Ų

Interaction summary

HBD 2 HBA 3 HY 4 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

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.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap4Native recall0.33
Jaccard0.20RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
335 1.6374603727918098 -1.16238 -24.6517 13 12 4 0.33 0.00 - no Current
295 2.1906893103294434 -1.18283 -22.6868 9 14 0 0.00 0.00 - no Open
347 2.571610966863597 -1.29978 -26.4017 8 16 0 0.00 0.00 - no Open
412 2.5959669276222557 -1.25601 -23.6443 10 16 0 0.00 0.00 - no Open
362 3.049217149686972 -1.37348 -25.3455 8 15 0 0.00 0.00 - no Open
344 3.608446794378311 -1.40534 -27.9146 11 14 0 0.00 0.00 - no Open
246 4.361509766167529 -1.27482 -22.0905 15 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 -24.652kcal/mol
Ligand efficiency (LE) -1.2326kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.315
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 297.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.56
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -50.85kcal/mol
Minimised FF energy -77.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 475.1Ų
Total solvent-accessible surface area of free ligand
BSA total 382.5Ų
Buried surface area upon binding
BSA apolar 228.6Ų
Hydrophobic contacts buried
BSA polar 153.9Ų
Polar contacts buried
Fraction buried 80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6273.0Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2088.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)