FAIRMol

KB_chagas_132

Pose ID 5558 Compound 108 Pose 140

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
T09
L. major DHFR-TS L. major
Ligand KB_chagas_132

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
30.5 kcal/mol
Protein clashes
3
Internal clashes
18
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.17
Burial
88%
Hydrophobic fit
79%
Reason: 18 internal clashes
3 protein-contact clashes 18 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.833 kcal/mol/HA) ✓ Good fit quality (FQ -8.33) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (30.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (18)
Score
-28.316
kcal/mol
LE
-0.833
kcal/mol/HA
Fit Quality
-8.33
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
cLogP
Strain ΔE
30.5 kcal/mol
SASA buried
88%
Lipo contact
79% BSA apolar/total
SASA unbound
709 Ų
Apolar buried
490 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 0
Final rank1.615Score-28.316
Inter norm-0.926Intra norm0.093
Top1000noExcludedno
Contacts17H-bonds6
Artifact reasongeometry warning; 18 clashes; 3 protein contact clashes; high strain Δ 30.5
Residues
NDP301 ALA32 ARG48 ASP52 ILE182 ILE45 LEU94 MET53 PHE56 PHE91 PRO88 SER86 THR83 TRP47 VAL156 VAL49 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap13Native recall0.62
Jaccard0.52RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

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
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
116 0.9967124239667426 -0.835107 -24.9422 1 19 0 0.00 0.00 - no Open
145 1.3995751921199313 -0.88415 -27.5642 3 16 0 0.00 0.00 - no Open
182 1.4861130235883124 -0.855269 -26.7745 4 22 0 0.00 0.00 - no Open
140 1.615020829250697 -0.925503 -28.3157 6 17 13 0.62 0.17 - no Current
161 2.662027008092362 -0.751934 -23.4535 3 14 0 0.00 0.00 - no Open
149 3.0092960382301914 -0.757482 -21.0618 2 22 1 0.05 0.00 - no Open
117 3.133913752613804 -0.893126 -27.6382 10 20 0 0.00 0.00 - no Open
92 3.1897154297188073 -0.7343 -24.0617 7 15 0 0.00 0.00 - no Open
109 3.266242765469782 -0.81009 -22.6151 5 16 0 0.00 0.00 - no Open
95 3.6098926606982675 -0.795677 -23.8078 8 16 0 0.00 0.00 - no Open
150 3.6690791561020983 -0.768661 -24.4817 6 18 0 0.00 0.00 - no Open
91 3.8086261390469938 -0.740979 -20.0503 5 21 0 0.00 0.00 - no Open
124 4.692634237226219 -0.64544 -22.9491 7 15 0 0.00 0.00 - no Open
103 4.725842136853786 -0.76159 -22.4824 5 18 0 0.00 0.00 - no Open
118 4.790784883872673 -0.731769 -21.8142 8 17 0 0.00 0.00 - no Open
73 4.7962875837914805 -1.009 -30.2636 11 20 0 0.00 0.00 - no Open
46 5.044122438992116 -0.80531 -23.3978 7 15 0 0.00 0.00 - no Open
87 5.0598912182116695 -0.712441 -22.3133 4 21 1 0.05 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 -28.316kcal/mol
Ligand efficiency (LE) -0.8328kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.333
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 104.07kcal/mol
Minimised FF energy 73.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 708.6Ų
Total solvent-accessible surface area of free ligand
BSA total 622.1Ų
Buried surface area upon binding
BSA apolar 490.0Ų
Hydrophobic contacts buried
BSA polar 132.1Ų
Polar contacts buried
Fraction buried 87.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3330.6Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1649.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)