FAIRMol

Z14342059

Pose ID 14826 Compound 10 Pose 588

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 Z14342059

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
20.7 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.36
Burial
89%
Hydrophobic fit
66%
Reason: 11 protein-contact clashes, 11 internal clashes
11 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.851 kcal/mol/HA) ✓ Good fit quality (FQ -8.44) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ High strain energy (20.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-28.078
kcal/mol
LE
-0.851
kcal/mol/HA
Fit Quality
-8.44
FQ (Leeson)
HAC
33
heavy atoms
MW
488
Da
LogP
5.57
cLogP
Final rank
3.9088
rank score
Inter norm
-0.969
normalised
Contacts
22
H-bonds 9
Strain ΔE
20.7 kcal/mol
SASA buried
89%
Lipo contact
66% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
410 Ų

Interaction summary

HBA 7 HY 4 PI 1 CLASH 11

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 overlap17Native recall0.81
Jaccard0.65RMSD-
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
585 0.2569287082877208 -0.794756 -22.3755 0 17 0 0.00 0.00 - no Open
580 0.6899638235943697 -0.911895 -24.8311 2 13 0 0.00 0.00 - no Open
570 0.774398796580156 -0.808344 -21.7394 3 11 0 0.00 0.00 - no Open
587 1.684180210553361 -0.748881 -14.6809 3 15 0 0.00 0.00 - no Open
566 1.8476754197172935 -1.0664 -31.6066 4 23 0 0.00 0.00 - no Open
593 2.3429760084794173 -0.743852 -21.1563 12 14 0 0.00 0.00 - no Open
603 2.4614585551832606 -0.716776 -18.8166 4 15 0 0.00 0.00 - no Open
559 3.860075508321798 -0.916895 -22.0869 8 13 0 0.00 0.00 - no Open
588 3.908763500807694 -0.968638 -28.0781 9 22 17 0.81 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 -28.078kcal/mol
Ligand efficiency (LE) -0.8509kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.442
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 487.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.57
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 19.39kcal/mol
Minimised FF energy -1.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 694.0Ų
Total solvent-accessible surface area of free ligand
BSA total 620.8Ų
Buried surface area upon binding
BSA apolar 410.4Ų
Hydrophobic contacts buried
BSA polar 210.4Ų
Polar contacts buried
Fraction buried 89.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1328.2Ų
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 515.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)