FAIRMol

Z56902329

Pose ID 14609 Compound 2846 Pose 371

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
T22
L. donovani rab5a L. donovani
Ligand Z56902329

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.41, H-bond role recall 0.27
Burial
87%
Hydrophobic fit
78%
Reason: strain 43.0 kcal/mol
strain ΔE 43.0 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (12/18 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.311 kcal/mol/HA) ✓ Good fit quality (FQ -12.08) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (43.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-34.086
kcal/mol
LE
-1.311
kcal/mol/HA
Fit Quality
-12.08
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Strain ΔE
43.0 kcal/mol
SASA buried
87%
Lipo contact
78% BSA apolar/total
SASA unbound
600 Ų
Apolar buried
409 Ų

Interaction summary

HB 12 HY 3 PI 0 CLASH 3 ⚠ Exposure 66%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 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 18 Buried (contacted) 6 Exposed 12 LogP 1.98 H-bonds 12
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.889Score-34.086
Inter norm-1.331Intra norm0.020
Top1000noExcludedno
Contacts20H-bonds12
Artifact reasongeometry warning; 10 clashes; 3 protein clashes; high strain Δ 43.0
Residues
ALA24 ALA48 ASN41 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 LEU31 LEU39 LEU51 LYS26 SER22 SER27 SER28 THR44 THR69

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap12Native recall0.57
Jaccard0.41RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue4HB residue recall0.36

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
355 1.3986381559687069 -1.35258 -35.2318 12 16 0 0.00 0.00 - no Open
408 1.661138863672402 -0.8999 -20.3371 5 10 0 0.00 0.00 - no Open
371 3.8893457067493027 -1.33147 -34.0855 12 20 12 0.57 0.27 - 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 -34.086kcal/mol
Ligand efficiency (LE) -1.3110kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.98
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 116.21kcal/mol
Minimised FF energy 73.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 600.4Ų
Total solvent-accessible surface area of free ligand
BSA total 523.5Ų
Buried surface area upon binding
BSA apolar 408.9Ų
Hydrophobic contacts buried
BSA polar 114.6Ų
Polar contacts buried
Fraction buried 87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1340.8Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 499.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)