FAIRMol

Z13702152

Pose ID 14825 Compound 2299 Pose 587

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 Z13702152

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
53.6 kcal/mol
Protein clashes
13
Internal clashes
13
Native overlap
contact recall 0.57, Jaccard 0.40, H-bond role recall 0.36
Burial
87%
Hydrophobic fit
70%
Reason: 13 protein-contact clashes, 13 internal clashes, strain 53.6 kcal/mol
strain ΔE 53.6 kcal/mol 13 protein-contact clashes 13 intramolecular clashes 39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.701 kcal/mol/HA) ✓ Good fit quality (FQ -7.01) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Extreme strain energy (53.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-23.826
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-7.01
FQ (Leeson)
HAC
34
heavy atoms
MW
497
Da
LogP
3.29
cLogP
Strain ΔE
53.6 kcal/mol
SASA buried
87%
Lipo contact
70% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
449 Ų

Interaction summary

HB 10 HY 7 PI 0 CLASH 13 ⚠ Exposure 39%

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23 Buried (contacted) 14 Exposed 9 LogP 3.29 H-bonds 10
Exposed fragments: phenyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
Final rank6.615Score-23.826
Inter norm-0.941Intra norm0.240
Top1000noExcludedno
Contacts21H-bonds10
Artifact reasongeometry warning; 16 clashes; 3 protein clashes; high strain Δ 53.6
Residues
ALA24 ALA48 ALA70 ASN41 ASP68 GLN42 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LEU31 LEU39 LYS127 LYS26 SER22 SER27 SER28 THR44 THR69

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 overlap12Native recall0.57
Jaccard0.40RMSD-
HB strict6Strict recall0.40
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
559 1.3577561097961066 -0.680404 -15.1312 0 22 0 0.00 0.00 - no Open
558 4.265525184151839 -0.88899 -24.9878 8 16 0 0.00 0.00 - no Open
587 6.614825177450811 -0.940543 -23.8259 10 21 12 0.57 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 -23.826kcal/mol
Ligand efficiency (LE) -0.7008kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.012
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 496.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.29
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 20.31kcal/mol
Minimised FF energy -33.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 741.0Ų
Total solvent-accessible surface area of free ligand
BSA total 642.3Ų
Buried surface area upon binding
BSA apolar 449.2Ų
Hydrophobic contacts buried
BSA polar 193.1Ų
Polar contacts buried
Fraction buried 86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1415.3Ų
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 494.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)