FAIRMol

NMT-TY0547

Pose ID 14510 Compound 3084 Pose 272

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-TY0547

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.57, Jaccard 0.41, H-bond role recall 0.36
Burial
88%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 58% of hydrophobic surface appears solvent-exposed (7/12 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 (-1.305 kcal/mol/HA) ✓ Good fit quality (FQ -11.33) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ High strain energy (27.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-28.704
kcal/mol
LE
-1.305
kcal/mol/HA
Fit Quality
-11.33
FQ (Leeson)
HAC
22
heavy atoms
MW
322
Da
LogP
0.40
cLogP
Strain ΔE
27.0 kcal/mol
SASA buried
88%
Lipo contact
69% BSA apolar/total
SASA unbound
535 Ų
Apolar buried
328 Ų

Interaction summary

HB 16 HY 2 PI 0 CLASH 4 ⚠ Exposure 58%

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
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12 Buried (contacted) 5 Exposed 7 LogP 0.4 H-bonds 16
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.359Score-28.704
Inter norm-1.402Intra norm0.097
Top1000noExcludedno
Contacts20H-bonds16
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; moderate strain Δ 27.0
Residues
ALA24 ALA70 ASP68 GLN42 GLU21 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LYS127 LYS26 PHE38 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
Jaccard0.41RMSD-
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
275 1.5462981432240444 -1.47118 -32.4771 9 12 0 0.00 0.00 - no Open
245 2.6909937967378683 -1.28992 -25.0477 14 18 0 0.00 0.00 - no Open
272 3.359287914114204 -1.40206 -28.7036 16 20 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 -28.704kcal/mol
Ligand efficiency (LE) -1.3047kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 322.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.40
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -83.33kcal/mol
Minimised FF energy -110.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 534.8Ų
Total solvent-accessible surface area of free ligand
BSA total 472.5Ų
Buried surface area upon binding
BSA apolar 327.9Ų
Hydrophobic contacts buried
BSA polar 144.6Ų
Polar contacts buried
Fraction buried 88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1236.0Ų
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 506.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)