FAIRMol

NMT-TY0625

Pose ID 13222 Compound 587 Pose 343

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-TY0625
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
33.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 0.00
Burial
55%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.877 kcal/mol/HA) ✓ Good fit quality (FQ -8.18) ✓ Strong H-bond network (9 bonds) ✓ Good burial (55% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Very high strain energy (33.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-23.669
kcal/mol
LE
-0.877
kcal/mol/HA
Fit Quality
-8.18
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.44
cLogP
Strain ΔE
33.3 kcal/mol
SASA buried
55%
Lipo contact
83% BSA apolar/total
SASA unbound
643 Ų
Apolar buried
291 Ų

Interaction summary

HB 9 HY 16 PI 1 CLASH 2
Final rank2.359Score-23.669
Inter norm-0.896Intra norm0.020
Top1000noExcludedno
Contacts12H-bonds9
Artifact reasongeometry warning; 9 clashes; 1 protein clash; high strain Δ 33.2
Residues
ARG472 ASN402 GLU467 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER395 SER470 THR397

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 overlap8Native recall1.00
Jaccard0.67RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 0.00 - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 8 1.00 0.00 - no Current
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 0.00 - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 0.00 - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 17 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 -23.669kcal/mol
Ligand efficiency (LE) -0.8766kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.179
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.44
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -47.28kcal/mol
Minimised FF energy -80.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 643.2Ų
Total solvent-accessible surface area of free ligand
BSA total 352.2Ų
Buried surface area upon binding
BSA apolar 291.4Ų
Hydrophobic contacts buried
BSA polar 60.8Ų
Polar contacts buried
Fraction buried 54.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3031.5Ų
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 1512.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)