FAIRMol

Z223826364

Pose ID 14726 Compound 4300 Pose 488

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 Z223826364

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
38.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.65, H-bond role recall 0.45
Burial
80%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (17/17 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.245 kcal/mol/HA) ✓ Good fit quality (FQ -11.32) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (38.0 kcal/mol) ✗ Geometry warnings
Score
-31.131
kcal/mol
LE
-1.245
kcal/mol/HA
Fit Quality
-11.32
FQ (Leeson)
HAC
25
heavy atoms
MW
365
Da
LogP
2.84
cLogP
Strain ΔE
38.0 kcal/mol
SASA buried
80%
Lipo contact
70% BSA apolar/total
SASA unbound
539 Ų
Apolar buried
303 Ų

Interaction summary

HB 12 HY 0 PI 0 CLASH 5 ⚠ Exposure 100%

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
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (17/17 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) 0 Exposed 17 LogP 2.84 H-bonds 12
Exposed fragments: phenyl (5/7 atoms exposed)phenyl (6/6 atoms exposed)phenyl (8/8 atoms exposed)
Final rank4.206Score-31.131
Inter norm-1.226Intra norm-0.020
Top1000noExcludedno
Contacts17H-bonds12
Artifact reasongeometry warning; 3 clashes; 3 protein clashes; high strain Δ 38.0
Residues
ALA24 ALA40 ASN41 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 LEU39 LYS127 LYS26 PHE38 SER22 SER27 SER28 THR44

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 overlap15Native recall0.71
Jaccard0.65RMSD-
HB strict7Strict recall0.47
HB same residue+role5HB role recall0.45
HB same residue6HB residue recall0.55

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
492 1.6014055927374748 -0.746844 -18.1096 5 7 0 0.00 0.00 - no Open
551 1.6059920393199745 -0.971222 -23.3622 6 9 0 0.00 0.00 - no Open
488 4.206459564715441 -1.22556 -31.1307 12 17 15 0.71 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 -31.131kcal/mol
Ligand efficiency (LE) -1.2452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.320
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 365.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.84
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -15.93kcal/mol
Minimised FF energy -53.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 538.6Ų
Total solvent-accessible surface area of free ligand
BSA total 432.3Ų
Buried surface area upon binding
BSA apolar 302.6Ų
Hydrophobic contacts buried
BSA polar 129.8Ų
Polar contacts buried
Fraction buried 80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1254.3Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 496.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)