FAIRMol

NMT-TY0959

Pose ID 10581 Compound 527 Pose 416

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-TY0959
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 high Native strong SASA done
Strain ΔE
28.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.67
Burial
74%
Hydrophobic fit
70%
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 (-0.952 kcal/mol/HA) ✓ Good fit quality (FQ -8.88) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (28.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-25.713
kcal/mol
LE
-0.952
kcal/mol/HA
Fit Quality
-8.88
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
28.7 kcal/mol
SASA buried
74%
Lipo contact
70% BSA apolar/total
SASA unbound
645 Ų
Apolar buried
332 Ų

Interaction summary

HB 8 HY 22 PI 0 CLASH 2
Final rank3.387Score-25.713
Inter norm-0.925Intra norm-0.028
Top1000noExcludedno
Contacts13H-bonds8
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 28.7
Residues
ALA209 ALA90 ARG74 GLY85 LEU73 LYS211 LYS89 MET70 PHE83 PRO212 PRO213 TYR210 VAL88

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

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-

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 - - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 - - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 - - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 - - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 - - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 - - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 0 0.00 - - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 - - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 - - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 - - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 - - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 0 0.00 - - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 10 0.83 - - no Current
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 - - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 - - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 - - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 - - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 - - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 - - no Open
453 4.769829786717276 -1.02855 -27.026 8 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 -25.713kcal/mol
Ligand efficiency (LE) -0.9523kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.885
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) 28.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -65.53kcal/mol
Minimised FF energy -94.28kcal/mol

SASA & burial

✓ computed
SASA (unbound) 645.4Ų
Total solvent-accessible surface area of free ligand
BSA total 474.8Ų
Buried surface area upon binding
BSA apolar 331.5Ų
Hydrophobic contacts buried
BSA polar 143.2Ų
Polar contacts buried
Fraction buried 73.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3085.2Ų
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 1473.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)