FAIRMol

NMT-TY0563

Pose ID 14513 Compound 937 Pose 275

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-TY0563

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
33.7 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.57, Jaccard 0.43, H-bond role recall 0.36
Burial
88%
Hydrophobic fit
59%
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes 9 intramolecular clashes 42% of hydrophobic surface appears solvent-exposed (5/12 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 (-1.303 kcal/mol/HA) ✓ Good fit quality (FQ -11.50) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (88% SASA buried) ✗ Very high strain energy (33.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-29.976
kcal/mol
LE
-1.303
kcal/mol/HA
Fit Quality
-11.50
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.19
cLogP
Final rank
5.0062
rank score
Inter norm
-1.352
normalised
Contacts
19
H-bonds 16
Strain ΔE
33.7 kcal/mol
SASA buried
88%
Lipo contact
59% BSA apolar/total
SASA unbound
560 Ų
Apolar buried
294 Ų

Interaction summary

HBD 5 HBA 7 HY 3 PI 0 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 9.

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: 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 overlap12Native recall0.57
Jaccard0.43RMSD-
HB strict6Strict recall0.40
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
287 2.281771617029549 -1.06786 -23.7408 5 18 0 0.00 0.00 - no Open
343 2.4562087162844173 -1.10761 -25.4402 13 17 0 0.00 0.00 - no Open
304 2.461814278287188 -0.94473 -20.9121 7 12 0 0.00 0.00 - no Open
407 2.5036253322923585 -1.19433 -22.7362 8 16 0 0.00 0.00 - no Open
266 2.5178884740350864 -1.23759 -27.3191 9 14 0 0.00 0.00 - no Open
309 3.0017361607070128 -1.11231 -22.3337 10 15 0 0.00 0.00 - no Open
328 3.3135670361627176 -0.980585 -18.4335 10 16 0 0.00 0.00 - no Open
250 4.760381988626865 -1.22455 -27.6963 12 15 0 0.00 0.00 - no Open
275 5.006226701203945 -1.35207 -29.9759 16 19 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 -29.976kcal/mol
Ligand efficiency (LE) -1.3033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.503
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.19
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -72.37kcal/mol
Minimised FF energy -106.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 560.0Ų
Total solvent-accessible surface area of free ligand
BSA total 494.8Ų
Buried surface area upon binding
BSA apolar 294.0Ų
Hydrophobic contacts buried
BSA polar 200.8Ų
Polar contacts buried
Fraction buried 88.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1198.5Ų
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 509.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)