FAIRMol

TC488

Pose ID 6272 Compound 1436 Pose 176

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
T10
L. infantum R5P L. infantum
Ligand TC488

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
28.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 1.00, Jaccard 0.81, H-bond role recall 0.45
Burial
67%
Hydrophobic fit
78%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 70% of hydrophobic surface is solvent-exposed (21/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.668 kcal/mol/HA) ✓ Good fit quality (FQ -6.88) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (28.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-25.376
kcal/mol
LE
-0.668
kcal/mol/HA
Fit Quality
-6.88
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Strain ΔE
28.1 kcal/mol
SASA buried
67%
Lipo contact
78% BSA apolar/total
SASA unbound
856 Ų
Apolar buried
450 Ų

Interaction summary

HB 12 HY 7 PI 3 CLASH 6 ⚠ Exposure 70%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
70% of hydrophobic surface is solvent-exposed (21/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 30 Buried (contacted) 9 Exposed 21 LogP 5.18 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (7 atoms exposed)
Final rank5.856Score-25.376
Inter norm-0.791Intra norm0.097
Top1000noExcludedno
Contacts21H-bonds12
Artifact reasongeometry warning; 15 clashes; 3 protein clashes; moderate strain Δ 28.1
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 ASP44 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 SER46 THR45 THR74 TYR17 TYR49

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

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 overlap17Native recall1.00
Jaccard0.81RMSD-
HB strict6Strict recall0.46
HB same residue+role5HB role recall0.45
HB same residue7HB residue recall0.64

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 4.097676844008653 -0.78523 -28.0312 5 20 0 0.00 0.00 - no Open
215 4.595874156107308 -0.890462 -29.8082 11 22 0 0.00 0.00 - no Open
176 5.855540308270551 -0.790924 -25.3763 12 21 17 1.00 0.45 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -25.376kcal/mol
Ligand efficiency (LE) -0.6678kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.885
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.18
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 137.26kcal/mol
Minimised FF energy 109.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 855.5Ų
Total solvent-accessible surface area of free ligand
BSA total 574.1Ų
Buried surface area upon binding
BSA apolar 449.6Ų
Hydrophobic contacts buried
BSA polar 124.4Ų
Polar contacts buried
Fraction buried 67.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2460.3Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 685.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)