FAIRMol

Z31546448

Pose ID 14624 Compound 1835 Pose 386

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 Z31546448

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
52.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.67, H-bond role recall 0.36
Burial
89%
Hydrophobic fit
72%
Reason: strain 52.6 kcal/mol
strain ΔE 52.6 kcal/mol 3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.706 kcal/mol/HA) ✓ Good fit quality (FQ -7.00) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (52.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-23.300
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-7.00
FQ (Leeson)
HAC
33
heavy atoms
MW
514
Da
LogP
1.15
cLogP
Strain ΔE
52.6 kcal/mol
SASA buried
89%
Lipo contact
72% BSA apolar/total
SASA unbound
798 Ų
Apolar buried
510 Ų

Interaction summary

HB 11 HY 9 PI 1 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank4.470Score-23.300
Inter norm-0.962Intra norm0.256
Top1000noExcludedno
Contacts24H-bonds11
Artifact reasongeometry warning; 9 clashes; 3 protein clashes; high strain Δ 52.5
Residues
ALA158 ALA40 ALA48 ASN126 ASN41 ASP129 ASP160 GLN42 GLU73 GLY23 GLY25 GLY47 ILE46 LEU130 LEU31 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER27 SER28 THR44

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 overlap18Native recall0.86
Jaccard0.67RMSD-
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
394 1.663146631070567 -0.733808 -21.4 2 11 0 0.00 0.00 - no Open
360 2.218437220773212 -0.755466 -22.9464 11 14 0 0.00 0.00 - no Open
386 4.4701261769287655 -0.962162 -23.3 11 24 18 0.86 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 -23.300kcal/mol
Ligand efficiency (LE) -0.7061kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.005
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 513.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.15
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 52.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 87.07kcal/mol
Minimised FF energy 34.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 797.7Ų
Total solvent-accessible surface area of free ligand
BSA total 712.1Ų
Buried surface area upon binding
BSA apolar 509.9Ų
Hydrophobic contacts buried
BSA polar 202.2Ų
Polar contacts buried
Fraction buried 89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1444.9Ų
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 491.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)