FAIRMol

NMT-TY0565

Pose ID 9894 Compound 608 Pose 408

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0565
PDB9IFF↗

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
23.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.42
Burial
84%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.212 kcal/mol/HA) ✓ Good fit quality (FQ -9.93) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (23.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-23.023
kcal/mol
LE
-1.212
kcal/mol/HA
Fit Quality
-9.93
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.26
cLogP
Strain ΔE
23.4 kcal/mol
SASA buried
84%
Lipo contact
71% BSA apolar/total
SASA unbound
465 Ų
Apolar buried
277 Ų

Interaction summary

HB 9 HY 19 PI 1 CLASH 1
Final rank2.386Score-23.023
Inter norm-1.288Intra norm0.076
Top1000noExcludedno
Contacts14H-bonds9
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; moderate strain Δ 23.4
Residues
ALA209 ALA67 ALA90 ASN208 GLY66 LEU73 LYS211 LYS89 MET70 PRO212 PRO213 TYR210 TYR69 VAL88

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:204

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap8Native recall0.62
Jaccard0.42RMSD-
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
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
290 1.1542235761146216 -1.3133 -22.9835 5 17 0 0.00 - - no Open
326 2.241892118278962 -1.16101 -21.6592 8 10 0 0.00 - - no Open
408 2.3864433454440244 -1.28783 -23.0227 9 14 8 0.62 - - no Current
340 2.4224499674500235 -1.52753 -26.5605 10 15 0 0.00 - - no Open
242 2.5012839495939683 -1.35686 -25.553 12 13 0 0.00 - - no Open
344 2.970230030733658 -1.42184 -25.8069 7 14 0 0.00 - - no Open
277 3.3258278508067045 -1.67804 -30.7231 16 19 0 0.00 - - no Open
381 3.627532215524071 -1.28108 -23.2122 8 14 0 0.00 - - no Open
357 3.7791067382818606 -1.42538 -25.9702 8 15 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 -23.023kcal/mol
Ligand efficiency (LE) -1.2117kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.932
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.26
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -70.11kcal/mol
Minimised FF energy -93.56kcal/mol

SASA & burial

✓ computed
SASA (unbound) 465.3Ų
Total solvent-accessible surface area of free ligand
BSA total 392.2Ų
Buried surface area upon binding
BSA apolar 276.8Ų
Hydrophobic contacts buried
BSA polar 115.5Ų
Polar contacts buried
Fraction buried 84.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2804.7Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1513.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)