FAIRMol

NMT-TY0929

Pose ID 14554 Compound 484 Pose 316

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-TY0929

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
40.6 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.67, Jaccard 0.50, H-bond role recall 0.36
Burial
84%
Hydrophobic fit
72%
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes 10 intramolecular clashes 59% of hydrophobic surface appears solvent-exposed (10/17 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 (-1.058 kcal/mol/HA) ✓ Good fit quality (FQ -9.87) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (40.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.553
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.87
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
40.6 kcal/mol
SASA buried
84%
Lipo contact
72% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
395 Ų

Interaction summary

HB 9 HY 9 PI 1 CLASH 10 ⚠ Exposure 58%

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
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 7 Exposed 10 LogP 2.03 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)
Final rank4.705Score-28.553
Inter norm-1.178Intra norm0.121
Top1000noExcludedno
Contacts21H-bonds9
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 40.6
Residues
ALA24 ALA40 ALA70 ASN126 ASN41 ASP68 GLU43 GLU73 GLY23 GLY25 GLY71 ILE29 LYS127 LYS159 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 overlap14Native recall0.67
Jaccard0.50RMSD-
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
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 1 0.05 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 14 0.67 0.36 - no Current
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 17 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.553kcal/mol
Ligand efficiency (LE) -1.0575kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.866
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.95kcal/mol
Minimised FF energy -57.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 649.5Ų
Total solvent-accessible surface area of free ligand
BSA total 546.1Ų
Buried surface area upon binding
BSA apolar 394.6Ų
Hydrophobic contacts buried
BSA polar 151.5Ų
Polar contacts buried
Fraction buried 84.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1328.5Ų
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 523.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)