FAIRMol

Z68563450

Pose ID 14864 Compound 5544 Pose 626

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 Z68563450

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
45.9 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.90, Jaccard 0.68, H-bond role recall 0.36
Burial
91%
Hydrophobic fit
91%
Reason: 11 protein-contact clashes, 11 internal clashes, strain 45.9 kcal/mol
strain ΔE 45.9 kcal/mol 11 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.717 kcal/mol/HA) ✓ Good fit quality (FQ -6.99) ✓ Good H-bonds (3 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Extreme strain energy (45.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-22.228
kcal/mol
LE
-0.717
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
31
heavy atoms
MW
429
Da
LogP
0.89
cLogP
Final rank
4.2287
rank score
Inter norm
-0.981
normalised
Contacts
26
H-bonds 7
Strain ΔE
45.9 kcal/mol
SASA buried
91%
Lipo contact
91% BSA apolar/total
SASA unbound
739 Ų
Apolar buried
611 Ų

Interaction summary

HBA 3 HY 4 PI 1 CLASH 11

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap19Native recall0.90
Jaccard0.68RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
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
626 4.228662591470237 -0.981352 -22.2282 7 26 19 0.90 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 -22.228kcal/mol
Ligand efficiency (LE) -0.7170kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.986
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 428.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.89
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 231.66kcal/mol
Minimised FF energy 185.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 739.0Ų
Total solvent-accessible surface area of free ligand
BSA total 671.8Ų
Buried surface area upon binding
BSA apolar 610.6Ų
Hydrophobic contacts buried
BSA polar 61.2Ų
Polar contacts buried
Fraction buried 90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1548.8Ų
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 493.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)