FAIRMol

NMT-TY0626

Pose ID 14536 Compound 973 Pose 298

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 NMT-TY0626

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 mixed SASA done
Strain ΔE
39.2 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.52, Jaccard 0.37, H-bond role recall 0.36
Burial
95%
Hydrophobic fit
68%
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes 9 intramolecular clashes 50% of hydrophobic surface appears solvent-exposed (7/14 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 (-1.412 kcal/mol/HA) ✓ Good fit quality (FQ -12.66) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (39.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-33.896
kcal/mol
LE
-1.412
kcal/mol/HA
Fit Quality
-12.66
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.87
cLogP
Final rank
4.7293
rank score
Inter norm
-1.320
normalised
Contacts
20
H-bonds 16
Strain ΔE
39.2 kcal/mol
SASA buried
95%
Lipo contact
68% BSA apolar/total
SASA unbound
561 Ų
Apolar buried
359 Ų

Interaction summary

HBD 2 HBA 8 HY 3 PI 0 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

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

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 overlap11Native recall0.52
Jaccard0.37RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
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
356 2.6032865444136504 -1.32222 -31.3752 9 15 0 0.00 0.00 - no Open
312 2.6588734209874447 -1.03898 -24.7483 6 18 1 0.05 0.00 - no Open
272 2.8069113310207094 -1.15287 -26.7627 12 14 0 0.00 0.00 - no Open
365 2.88321056510472 -1.17359 -27.9475 7 16 0 0.00 0.00 - no Open
298 4.729317408455978 -1.32032 -33.8956 16 20 11 0.52 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 -33.896kcal/mol
Ligand efficiency (LE) -1.4123kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.657
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.87
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -57.81kcal/mol
Minimised FF energy -97.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 560.8Ų
Total solvent-accessible surface area of free ligand
BSA total 531.0Ų
Buried surface area upon binding
BSA apolar 359.2Ų
Hydrophobic contacts buried
BSA polar 171.8Ų
Polar contacts buried
Fraction buried 94.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1247.6Ų
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 498.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)