FAIRMol

Z276200254

Pose ID 14615 Compound 2197 Pose 377

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
T22
L. donovani rab5a L. donovani
Ligand Z276200254

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
63.6 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.76, Jaccard 0.57, H-bond role recall 0.55
Burial
91%
Hydrophobic fit
69%
Reason: 6 internal clashes, strain 63.6 kcal/mol
strain ΔE 63.6 kcal/mol 6 protein-contact clashes 6 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (11/17 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 (-1.042 kcal/mol/HA) ✓ Good fit quality (FQ -9.72) ✓ Strong H-bond network (15 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Extreme strain energy (63.6 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (13) ✗ Many internal clashes (13)
Score
-28.139
kcal/mol
LE
-1.042
kcal/mol/HA
Fit Quality
-9.72
FQ (Leeson)
HAC
27
heavy atoms
MW
373
Da
LogP
1.08
cLogP
Strain ΔE
63.6 kcal/mol
SASA buried
91%
Lipo contact
69% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
383 Ų

Interaction summary

HB 15 HY 8 PI 1 CLASH 6 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 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 17 Buried (contacted) 6 Exposed 11 LogP 1.08 H-bonds 15
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
Final rank2.536Score-28.139
Inter norm-1.126Intra norm0.084
Top1000noExcludedno
Contacts23H-bonds15
Artifact reasongeometry warning; 13 clashes; 13 protein contact clashes; high strain Δ 63.6
Residues
ALA158 ALA24 ASN126 ASP129 GLN42 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LEU130 LYS127 LYS159 LYS26 PHE38 SER157 SER27 SER28 THR44 THR45 THR69

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

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 overlap16Native recall0.76
Jaccard0.57RMSD-
HB strict8Strict recall0.53
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

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
377 2.536139453384206 -1.12609 -28.1392 15 23 16 0.76 0.55 - no Current
342 2.710124874786965 -1.07187 -24.041 14 15 0 0.00 0.00 - no Open
353 3.4397813385699 -0.886304 -20.0261 10 17 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 -28.139kcal/mol
Ligand efficiency (LE) -1.0422kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.723
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 373.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.08
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 63.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 149.53kcal/mol
Minimised FF energy 85.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 613.6Ų
Total solvent-accessible surface area of free ligand
BSA total 556.4Ų
Buried surface area upon binding
BSA apolar 383.1Ų
Hydrophobic contacts buried
BSA polar 173.3Ų
Polar contacts buried
Fraction buried 90.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1283.2Ų
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 499.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)