FAIRMol

NMT-TY0823

Pose ID 10570 Compound 2385 Pose 405

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand NMT-TY0823
PDB6RB5↗

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
24.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.39
Burial
85%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.325 kcal/mol/HA) ✓ Good fit quality (FQ -10.86) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (24.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.180
kcal/mol
LE
-1.325
kcal/mol/HA
Fit Quality
-10.86
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Strain ΔE
24.9 kcal/mol
SASA buried
85%
Lipo contact
75% BSA apolar/total
SASA unbound
472 Ų
Apolar buried
298 Ų

Interaction summary

HB 8 HY 18 PI 0 CLASH 3

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 rank2.000Score-25.180
Inter norm-1.259Intra norm-0.067
Top1000noExcludedno
Contacts13H-bonds8
Artifact reasongeometry warning; 6 clashes; 1 protein clash; moderate strain Δ 24.9
Residues
ALA209 ALA90 ASN208 GLY214 GLY215 LEU73 LYS211 LYS89 MET70 PRO212 PRO213 TYR210 VAL88

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap7Native recall0.58
Jaccard0.39RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT16Atoms7551
Residues493Chains1
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:276; 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
319 0.3637981101771606 -1.21498 -23.7482 11 19 0 0.00 - - no Open
405 1.9997854384566627 -1.25872 -25.1802 8 13 7 0.58 - - no Current
435 2.647455335312565 -1.234 -25.0623 9 14 0 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 -25.180kcal/mol
Ligand efficiency (LE) -1.3253kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.863
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.02
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -148.93kcal/mol
Minimised FF energy -173.87kcal/mol

SASA & burial

✓ computed
SASA (unbound) 472.2Ų
Total solvent-accessible surface area of free ligand
BSA total 399.4Ų
Buried surface area upon binding
BSA apolar 298.4Ų
Hydrophobic contacts buried
BSA polar 101.1Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2967.2Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1444.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)