FAIRMol

Z1541758605

Pose ID 14791 Compound 1404 Pose 553

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 Z1541758605

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
55.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.45
Burial
84%
Hydrophobic fit
78%
Reason: strain 55.9 kcal/mol
strain ΔE 55.9 kcal/mol 1 protein-contact clashes 71% of hydrophobic surface is solvent-exposed (17/24 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.891 kcal/mol/HA) ✓ Good fit quality (FQ -8.84) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (55.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-29.399
kcal/mol
LE
-0.891
kcal/mol/HA
Fit Quality
-8.84
FQ (Leeson)
HAC
33
heavy atoms
MW
448
Da
LogP
3.08
cLogP
Strain ΔE
55.9 kcal/mol
SASA buried
84%
Lipo contact
78% BSA apolar/total
SASA unbound
724 Ų
Apolar buried
475 Ų

Interaction summary

HB 16 HY 5 PI 1 CLASH 1 ⚠ Exposure 70%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (17/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 24 Buried (contacted) 7 Exposed 17 LogP 3.08 H-bonds 16
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (1/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank5.063Score-29.399
Inter norm-0.919Intra norm0.028
Top1000noExcludedno
Contacts22H-bonds10
Artifact reasongeometry warning; 11 clashes; 3 protein clashes; high strain Δ 55.8
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 GLY47 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28 THR44

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

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 overlap19Native recall0.90
Jaccard0.79RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

HB · H-bonds
Mode: permissive. 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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
556 3.5029826523423684 -0.842178 -28.4054 4 15 0 0.00 0.00 - no Open
555 4.855569708198166 -0.57865 -24.0527 6 10 0 0.00 0.00 - no Open
553 5.063067709584083 -0.91929 -29.3989 10 22 19 0.90 0.45 - 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 -29.399kcal/mol
Ligand efficiency (LE) -0.8909kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.839
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 447.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.08
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 55.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 142.16kcal/mol
Minimised FF energy 86.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 724.5Ų
Total solvent-accessible surface area of free ligand
BSA total 607.4Ų
Buried surface area upon binding
BSA apolar 475.3Ų
Hydrophobic contacts buried
BSA polar 132.1Ų
Polar contacts buried
Fraction buried 83.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1448.1Ų
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 504.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)