FAIRMol

OHD_TC1_194

Pose ID 14295 Compound 1399 Pose 57

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 OHD_TC1_194

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 mixed SASA done
Strain ΔE
38.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.37, H-bond role recall 0.36
Burial
72%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 97% of hydrophobic surface is solvent-exposed (29/30 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 (-0.846 kcal/mol/HA) ✓ Good fit quality (FQ -8.84) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (38.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (25)
Score
-33.839
kcal/mol
LE
-0.846
kcal/mol/HA
Fit Quality
-8.84
FQ (Leeson)
HAC
40
heavy atoms
MW
561
Da
LogP
4.23
cLogP
Strain ΔE
38.7 kcal/mol
SASA buried
72%
Lipo contact
80% BSA apolar/total
SASA unbound
853 Ų
Apolar buried
493 Ų

Interaction summary

HB 9 HY 1 PI 0 CLASH 5 ⚠ Exposure 96%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
97% of hydrophobic surface is solvent-exposed (29/30 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 30 Buried (contacted) 1 Exposed 29 LogP 4.23 H-bonds 9
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank5.810Score-33.839
Inter norm-0.829Intra norm-0.017
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasongeometry warning; 25 clashes; 2 protein clashes; high strain Δ 38.7
Residues
ALA24 ASN41 ASN97 ASP94 GLN42 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 LYS127 LYS26 SER100 SER22 SER27 SER28 THR44 THR69 THR96

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 overlap11Native recall0.52
Jaccard0.37RMSD-
HB strict6Strict recall0.40
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
88 2.254954348765645 -0.757962 -31.7056 2 18 0 0.00 0.00 - no Open
103 3.3848326682641656 -0.74453 -25.118 4 20 0 0.00 0.00 - no Open
57 5.810412398343132 -0.828577 -33.8389 9 20 11 0.52 0.36 - 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 -33.839kcal/mol
Ligand efficiency (LE) -0.8460kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.835
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 40HA

Physicochemical properties
Molecular weight 560.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.23
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 39.99kcal/mol
Minimised FF energy 1.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 853.3Ų
Total solvent-accessible surface area of free ligand
BSA total 614.5Ų
Buried surface area upon binding
BSA apolar 492.6Ų
Hydrophobic contacts buried
BSA polar 121.9Ų
Polar contacts buried
Fraction buried 72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1560.7Ų
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 530.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)