FAIRMol

KB_chagas_54

Pose ID 14341 Compound 3036 Pose 103

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 KB_chagas_54

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
17.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.27
Burial
90%
Hydrophobic fit
90%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.028 kcal/mol/HA) ✓ Good fit quality (FQ -9.71) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Moderate strain (17.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-28.798
kcal/mol
LE
-1.028
kcal/mol/HA
Fit Quality
-9.71
FQ (Leeson)
HAC
28
heavy atoms
MW
510
Da
LogP
4.70
cLogP
Strain ΔE
17.0 kcal/mol
SASA buried
90%
Lipo contact
90% BSA apolar/total
SASA unbound
668 Ų
Apolar buried
546 Ų

Interaction summary

HB 6 HY 8 PI 1 CLASH 6 ⚠ Exposure 52%

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
⚠️Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (11/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21 Buried (contacted) 10 Exposed 11 LogP 4.7 H-bonds 6
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.915Score-28.798
Inter norm-1.216Intra norm0.188
Top1000noExcludedno
Contacts22H-bonds6
Artifact reasongeometry warning; 13 clashes; 2 protein clashes
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU73 GLY23 GLY25 GLY71 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 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 overlap19Native recall0.90
Jaccard0.79RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue5HB residue recall0.45

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
171 0.9784121004771374 -1.1891 -31.3276 4 13 0 0.00 0.00 - no Open
141 1.8729061917141898 -0.839296 -16.6469 3 15 0 0.00 0.00 - no Open
103 3.91503943863124 -1.21632 -28.798 6 22 19 0.90 0.27 - 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 -28.798kcal/mol
Ligand efficiency (LE) -1.0285kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.709
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 509.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.70
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 38.80kcal/mol
Minimised FF energy 21.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 668.2Ų
Total solvent-accessible surface area of free ligand
BSA total 605.0Ų
Buried surface area upon binding
BSA apolar 545.9Ų
Hydrophobic contacts buried
BSA polar 59.1Ų
Polar contacts buried
Fraction buried 90.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1457.6Ų
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 519.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)