FAIRMol

GemmaOHDUnisi_38

Pose ID 14576 Compound 3024 Pose 338

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 GemmaOHDUnisi_38

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.27
Burial
80%
Hydrophobic fit
84%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes 74% of hydrophobic surface is solvent-exposed (17/23 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 (-0.919 kcal/mol/HA) ✓ Good fit quality (FQ -8.57) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (14.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-24.812
kcal/mol
LE
-0.919
kcal/mol/HA
Fit Quality
-8.57
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
5.41
cLogP
Final rank
4.3491
rank score
Inter norm
-1.123
normalised
Contacts
18
H-bonds 10
Strain ΔE
14.7 kcal/mol
SASA buried
80%
Lipo contact
84% BSA apolar/total
SASA unbound
641 Ų
Apolar buried
429 Ų

Interaction summary

HBD 1 HBA 5 HY 2 PI 1 CLASH 7

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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 overlap13Native recall0.62
Jaccard0.50RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

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
322 0.8278075936041438 -1.32071 -32.9059 6 14 0 0.00 0.00 - no Open
356 0.9693317372851367 -0.896093 -18.51 4 17 0 0.00 0.00 - no Open
339 3.6612808815022593 -0.956451 -23.6271 4 17 1 0.05 0.00 - no Open
348 4.023415965506665 -0.910424 -13.4768 8 14 0 0.00 0.00 - no Open
338 4.349104779598979 -1.12272 -24.8121 10 18 13 0.62 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 -24.812kcal/mol
Ligand efficiency (LE) -0.9190kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.574
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.41
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 81.67kcal/mol
Minimised FF energy 66.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 641.2Ų
Total solvent-accessible surface area of free ligand
BSA total 512.0Ų
Buried surface area upon binding
BSA apolar 429.4Ų
Hydrophobic contacts buried
BSA polar 82.6Ų
Polar contacts buried
Fraction buried 79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1376.3Ų
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 543.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)