FAIRMol

KB_chagas_16

Pose ID 2822 Compound 2192 Pose 112

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
T05
L. major PTR1 L. major
Ligand KB_chagas_16
PDB7PXX↗

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
30.0 kcal/mol
Protein clashes
5
Internal clashes
7
Native overlap
contact recall 0.82, Jaccard 0.64, H-bond role recall 0.67
Burial
88%
Hydrophobic fit
86%
Reason: 7 internal clashes
5 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.900 kcal/mol/HA) ✓ Good fit quality (FQ -8.18) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ High strain energy (30.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-22.491
kcal/mol
LE
-0.900
kcal/mol/HA
Fit Quality
-8.18
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
1.35
cLogP
Strain ΔE
30.0 kcal/mol
SASA buried
88%
Lipo contact
86% BSA apolar/total
SASA unbound
590 Ų
Apolar buried
445 Ų

Interaction summary

HB 7 HY 24 PI 4 CLASH 7
Final rank2.675Score-22.491
Inter norm-1.190Intra norm0.290
Top1000noExcludedno
Contacts19H-bonds7
Artifact reasongeometry warning; 14 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 30.0
Residues
ARG17 ASN147 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET183 NDP302 PHE113 SER111 SER112 TYR191 TYR194 TYR283 VAL230 ARG287

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap14Native recall0.82
Jaccard0.64RMSD-
HB strict5Strict recall0.71
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.80

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
112 2.6746012614280077 -1.18978 -22.4905 7 19 14 0.82 0.67 - no Current
148 3.4341378847043953 -0.931263 -22.6396 7 14 0 0.00 0.00 - no Open
170 3.991942354883419 -0.759639 -16.2355 5 10 0 0.00 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 -22.491kcal/mol
Ligand efficiency (LE) -0.8996kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.178
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.35
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -124.16kcal/mol
Minimised FF energy -154.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 590.5Ų
Total solvent-accessible surface area of free ligand
BSA total 519.0Ų
Buried surface area upon binding
BSA apolar 445.4Ų
Hydrophobic contacts buried
BSA polar 73.6Ų
Polar contacts buried
Fraction buried 87.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1665.0Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1022.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)