FAIRMol

Z20255081

Pose ID 6494 Compound 678 Pose 398

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 Z20255081

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
20.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.88, H-bond role recall 0.45
Burial
65%
Hydrophobic fit
62%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (13/20 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 (-0.680 kcal/mol/HA) ✓ Good fit quality (FQ -6.56) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (65% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ High strain energy (20.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-20.409
kcal/mol
LE
-0.680
kcal/mol/HA
Fit Quality
-6.56
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.59
cLogP
Strain ΔE
20.8 kcal/mol
SASA buried
65%
Lipo contact
62% BSA apolar/total
SASA unbound
687 Ų
Apolar buried
277 Ų

Interaction summary

HB 13 HY 2 PI 1 CLASH 3 ⚠ Exposure 65%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (13/20 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 20 Buried (contacted) 7 Exposed 13 LogP 4.59 H-bonds 13
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank3.736Score-20.409
Inter norm-0.857Intra norm0.177
Top1000noExcludedno
Contacts15H-bonds13
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; moderate strain Δ 20.8
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 CYS72 GLY73 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 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 overlap15Native recall0.88
Jaccard0.88RMSD-
HB strict6Strict recall0.46
HB same residue+role5HB role recall0.45
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
396 -0.11056417959593262 -1.19533 -34.8331 9 17 0 0.00 0.00 - no Open
419 0.3271797508948459 -0.839972 -24.243 2 13 0 0.00 0.00 - no Open
480 0.4575261200251558 -0.989236 -25.5218 1 21 0 0.00 0.00 - no Open
388 1.3247621968802203 -0.97422 -27.5305 8 15 0 0.00 0.00 - no Open
429 1.5682838105176942 -0.894601 -23.8867 4 14 0 0.00 0.00 - no Open
452 1.7973468440035216 -0.986403 -22.7906 5 13 0 0.00 0.00 - no Open
450 1.8532223899879046 -0.707052 -19.9579 8 16 0 0.00 0.00 - no Open
442 2.056146307025179 -0.886151 -21.9132 8 18 1 0.06 0.00 - no Open
402 2.1313085350777627 -1.15443 -29.8157 14 17 5 0.29 0.27 - no Open
432 2.4339812204281435 -0.65996 -17.4537 6 10 0 0.00 0.00 - no Open
469 2.992470262134781 -0.896028 -22.0828 6 18 0 0.00 0.00 - no Open
408 3.228580280103112 -0.944403 -24.0255 6 19 0 0.00 0.00 - no Open
426 3.390641675980678 -0.781192 -18.2749 8 14 0 0.00 0.00 - no Open
398 3.736159295282282 -0.857475 -20.4087 13 15 15 0.88 0.45 - no Current
409 3.9602894299335802 -0.833689 -21.2615 10 15 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 -20.409kcal/mol
Ligand efficiency (LE) -0.6803kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.562
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.59
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.44kcal/mol
Minimised FF energy 15.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 686.6Ų
Total solvent-accessible surface area of free ligand
BSA total 449.1Ų
Buried surface area upon binding
BSA apolar 277.2Ų
Hydrophobic contacts buried
BSA polar 171.9Ų
Polar contacts buried
Fraction buried 65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2177.3Ų
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 676.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)