FAIRMol

KB_chagas_7

Pose ID 6187 Compound 100 Pose 91

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
T10
L. infantum R5P L. infantum
Ligand KB_chagas_7

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 medium Native strong SASA done
Strain ΔE
23.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.55
Burial
71%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.845 kcal/mol/HA) ✓ Good fit quality (FQ -8.23) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-26.185
kcal/mol
LE
-0.845
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Strain ΔE
23.7 kcal/mol
SASA buried
71%
Lipo contact
67% BSA apolar/total
SASA unbound
629 Ų
Apolar buried
300 Ų

Interaction summary

HB 11 HY 9 PI 2 CLASH 4 ⚠ Exposure 35%

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
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 13 Exposed 7 LogP 2.78 H-bonds 11
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.573Score-26.185
Inter norm-0.951Intra norm0.106
Top1000noExcludedno
Contacts15H-bonds11
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; moderate strain Δ 23.7
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 LEU101 THR117 THR74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap14Native recall0.82
Jaccard0.78RMSD-
HB strict8Strict recall0.62
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

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 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 0 0.00 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 13 0.76 0.55 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 5 0.29 0.27 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 14 0.82 0.55 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 0 0.00 0.00 - no Open
91 3.5725886357035477 -0.950541 -26.1853 11 15 14 0.82 0.55 - no Current
89 3.588860201862459 -0.897555 -24.8412 10 10 4 0.24 0.09 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 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 -26.185kcal/mol
Ligand efficiency (LE) -0.8447kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.229
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) 23.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 28.40kcal/mol
Minimised FF energy 4.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 629.1Ų
Total solvent-accessible surface area of free ligand
BSA total 444.5Ų
Buried surface area upon binding
BSA apolar 299.6Ų
Hydrophobic contacts buried
BSA polar 144.9Ų
Polar contacts buried
Fraction buried 70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2161.5Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 664.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)