FAIRMol

NMT-TY0625

Pose ID 10560 Compound 587 Pose 395

DB fairmolDocking 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-TY0625
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
32.1 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.83, Jaccard 0.67
Burial
73%
Hydrophobic fit
70%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.876 kcal/mol/HA) ✓ Good fit quality (FQ -8.17) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (32.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-23.643
kcal/mol
LE
-0.876
kcal/mol/HA
Fit Quality
-8.17
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
32.1 kcal/mol
SASA buried
73%
Lipo contact
70% BSA apolar/total
SASA unbound
636 Ų
Apolar buried
326 Ų

Interaction summary

HB 8 HY 18 PI 0 CLASH 0

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
No clash · clashes detected for this pose.
Final rank3.411Score-23.643
Inter norm-0.855Intra norm-0.020
Top1000noExcludedno
Contacts13H-bonds8
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 32.1
Residues
ALA209 ALA90 ARG74 LEU73 LYS211 LYS89 MET70 PHE83 PRO212 PRO213 SER86 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 overlap10Native recall0.83
Jaccard0.67RMSD-
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
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 - - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 - - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 - - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 - - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 - - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 - - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 - - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 - - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 - - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 - - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 1 0.08 - - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 - - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 10 0.83 - - no Current
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 - - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 - - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 - - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 - - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 - - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 - - no Open
330 5.564206722433145 -0.904232 -20.3369 11 17 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 -23.643kcal/mol
Ligand efficiency (LE) -0.8757kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.170
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -58.81kcal/mol
Minimised FF energy -90.95kcal/mol

SASA & burial

✓ computed
SASA (unbound) 636.1Ų
Total solvent-accessible surface area of free ligand
BSA total 465.9Ų
Buried surface area upon binding
BSA apolar 326.1Ų
Hydrophobic contacts buried
BSA polar 139.8Ų
Polar contacts buried
Fraction buried 73.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3085.3Ų
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 1463.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)