FAIRMol

GemmaOHDUnisi_36

Pose ID 14575 Compound 2877 Pose 337

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_36

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
22.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.50, H-bond role recall 0.27
Burial
86%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 75% of hydrophobic surface is solvent-exposed (18/24 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 (-0.917 kcal/mol/HA) ✓ Good fit quality (FQ -8.75) ✓ Good H-bonds (3 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ High strain energy (22.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-26.581
kcal/mol
LE
-0.917
kcal/mol/HA
Fit Quality
-8.75
FQ (Leeson)
HAC
29
heavy atoms
MW
385
Da
LogP
4.86
cLogP
Final rank
4.1210
rank score
Inter norm
-1.061
normalised
Contacts
21
H-bonds 8
Strain ΔE
22.1 kcal/mol
SASA buried
86%
Lipo contact
85% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
481 Ų

Interaction summary

HBD 1 HBA 2 HY 2 PI 1 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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: 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 overlap14Native recall0.67
Jaccard0.50RMSD-
HB strict3Strict recall0.20
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
348 0.7097099713471693 -0.928736 -24.4899 6 14 0 0.00 0.00 - no Open
321 0.7414515178002574 -1.28064 -37.1559 6 15 0 0.00 0.00 - no Open
457 1.0013317596324351 -0.895256 -16.9261 5 16 0 0.00 0.00 - no Open
346 1.3116209126168636 -1.01701 -27.3469 8 17 0 0.00 0.00 - no Open
386 1.6562451370699631 -0.778291 -20.4118 8 17 0 0.00 0.00 - no Open
313 1.869078421749205 -1.05744 -21.2439 6 14 0 0.00 0.00 - no Open
355 2.4041395187131402 -0.777914 -17.359 4 14 0 0.00 0.00 - no Open
419 3.1271929319738234 -0.869189 -23.9867 6 18 0 0.00 0.00 - no Open
359 3.178043498913507 -0.693471 -19.6333 4 13 0 0.00 0.00 - no Open
295 3.228938024541079 -1.08489 -29.5785 6 21 0 0.00 0.00 - no Open
337 4.121022873227579 -1.06073 -26.5805 8 21 14 0.67 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 -26.581kcal/mol
Ligand efficiency (LE) -0.9166kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.749
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 385.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.86
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.12kcal/mol
Minimised FF energy 64.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 656.0Ų
Total solvent-accessible surface area of free ligand
BSA total 565.0Ų
Buried surface area upon binding
BSA apolar 480.9Ų
Hydrophobic contacts buried
BSA polar 84.2Ų
Polar contacts buried
Fraction buried 86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1405.4Ų
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 505.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)