FAIRMol

Z29467616

Pose ID 6696 Compound 3412 Pose 600

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 Z29467616

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
24.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.84, H-bond role recall 0.64
Burial
76%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.131 kcal/mol/HA) ✓ Good fit quality (FQ -10.42) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (24.3 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (16) ✗ Internal clashes (7)
Score
-29.418
kcal/mol
LE
-1.131
kcal/mol/HA
Fit Quality
-10.42
FQ (Leeson)
HAC
26
heavy atoms
MW
388
Da
LogP
3.09
cLogP
Strain ΔE
24.3 kcal/mol
SASA buried
76%
Lipo contact
72% BSA apolar/total
SASA unbound
638 Ų
Apolar buried
350 Ų

Interaction summary

HB 16 HY 5 PI 3 CLASH 5 ⚠ Exposure 35%
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 3.09 H-bonds 16
Exposed fragments: phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.416Score-29.418
Inter norm-1.010Intra norm-0.121
Top1000noExcludedno
Contacts18H-bonds16
Artifact reasongeometry warning; 7 clashes; 16 protein contact clashes; moderate strain Δ 24.3
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLU138 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 LEU101 LEU136 THR74 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 overlap16Native recall0.94
Jaccard0.84RMSD-
HB strict7Strict recall0.54
HB same residue+role7HB role recall0.64
HB same residue9HB residue recall0.82

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
600 2.4160132425637864 -1.01049 -29.4178 16 18 16 0.94 0.64 - no Current
599 2.9447681812716744 -1.23975 -34.9413 9 18 0 0.00 0.00 - no Open
48 3.0042415447161783 -1.12646 -23.1716 16 17 15 0.88 0.73 - 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 -29.418kcal/mol
Ligand efficiency (LE) -1.1315kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.424
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 388.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.09
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -4.58kcal/mol
Minimised FF energy -28.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 638.4Ų
Total solvent-accessible surface area of free ligand
BSA total 485.1Ų
Buried surface area upon binding
BSA apolar 349.8Ų
Hydrophobic contacts buried
BSA polar 135.3Ų
Polar contacts buried
Fraction buried 76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2202.9Ų
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 686.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)