FAIRMol

KB_Leish_4

Pose ID 9600 Compound 100 Pose 114

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 KB_Leish_4
PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
23.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.85, Jaccard 0.65
Burial
73%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.650 kcal/mol/HA) ✓ Good fit quality (FQ -6.33) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ High strain energy (23.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (10)
Score
-20.144
kcal/mol
LE
-0.650
kcal/mol/HA
Fit Quality
-6.33
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
23.8 kcal/mol
SASA buried
73%
Lipo contact
64% BSA apolar/total
SASA unbound
653 Ų
Apolar buried
304 Ų

Interaction summary

HB 8 HY 15 PI 0 CLASH 5

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 rank1.801Score-20.144
Inter norm-0.767Intra norm0.117
Top1000noExcludedno
Contacts15H-bonds8
Artifact reasongeometry warning; 10 clashes; 9 protein contact clashes; moderate strain Δ 23.8
Residues
ALA209 ALA90 ARG74 ASN208 ASN245 GLY214 GLY215 GLY246 LEU73 LYS211 LYS89 MET70 PRO212 PRO213 VAL88

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 overlap11Native recall0.85
Jaccard0.65RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 - - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 - - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 - - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 - - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 11 0.85 - - no Current
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 - - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 - - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 - - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 - - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 0 0.00 - - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 0 0.00 - - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 - - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 0 0.00 - - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 - - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 0 0.00 - - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 0 0.00 - - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 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 -20.144kcal/mol
Ligand efficiency (LE) -0.6498kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.331
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 31.27kcal/mol
Minimised FF energy 7.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.8Ų
Total solvent-accessible surface area of free ligand
BSA total 476.9Ų
Buried surface area upon binding
BSA apolar 304.2Ų
Hydrophobic contacts buried
BSA polar 172.7Ų
Polar contacts buried
Fraction buried 73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2890.3Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1539.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)