FAIRMol

NMT-TY0371

Pose ID 14495 Compound 515 Pose 257

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-TY0371

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
30.2 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.57, Jaccard 0.39, H-bond role recall 0.27
Burial
91%
Hydrophobic fit
64%
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes 9 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.515 kcal/mol/HA) ✓ Good fit quality (FQ -12.68) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Very high strain energy (30.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-30.294
kcal/mol
LE
-1.515
kcal/mol/HA
Fit Quality
-12.68
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
30.2 kcal/mol
SASA buried
91%
Lipo contact
64% BSA apolar/total
SASA unbound
485 Ų
Apolar buried
285 Ų

Interaction summary

HB 16 HY 1 PI 0 CLASH 9 ⚠ Exposure 60%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 10 Buried (contacted) 4 Exposed 6 LogP -0.68 H-bonds 16
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank4.360Score-30.294
Inter norm-1.657Intra norm0.142
Top1000noExcludedno
Contacts22H-bonds16
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; high strain Δ 30.2
Residues
ALA24 ALA48 ALA49 ALA70 ASP68 GLN42 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LEU39 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
Jaccard0.39RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
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
291 1.1342832901296953 -1.47243 -28.1213 7 13 0 0.00 0.00 - no Open
308 1.1407956598243199 -1.47271 -28.0966 7 13 0 0.00 0.00 - no Open
287 1.425854450107728 -1.57638 -29.017 10 15 0 0.00 0.00 - no Open
294 1.4368563653499584 -1.58614 -29.0417 10 15 0 0.00 0.00 - no Open
340 1.5199875327590986 -1.30421 -24.1616 12 16 0 0.00 0.00 - no Open
325 1.8929444358902847 -1.09972 -20.59 10 11 0 0.00 0.00 - no Open
264 2.0213778030470935 -1.28263 -24.1424 8 15 0 0.00 0.00 - no Open
272 2.07930378903586 -1.19931 -21.6886 10 17 0 0.00 0.00 - no Open
288 2.272686469792997 -1.20072 -21.8379 10 17 0 0.00 0.00 - no Open
255 2.604134178216891 -1.55444 -29.5672 11 18 0 0.00 0.00 - no Open
395 2.618228131873109 -1.34198 -25.4179 10 16 0 0.00 0.00 - no Open
307 2.6395815071657873 -1.216 -22.6881 12 17 0 0.00 0.00 - no Open
324 2.719858307570968 -0.962258 -19.339 7 11 0 0.00 0.00 - no Open
272 2.890185804928903 -1.24872 -23.3539 7 15 1 0.05 0.00 - no Open
354 2.894301988851109 -1.46517 -27.278 13 19 0 0.00 0.00 - no Open
248 2.9955573621189955 -1.44392 -27.8137 14 18 0 0.00 0.00 - no Open
346 3.086475756889026 -1.42333 -26.6003 13 19 0 0.00 0.00 - no Open
299 3.1992481359795537 -1.24642 -23.7166 13 17 0 0.00 0.00 - no Open
285 3.2187089349618714 -1.29682 -23.427 10 17 1 0.05 0.00 - no Open
379 3.2560466957189305 -1.35838 -25.6607 9 16 0 0.00 0.00 - no Open
369 3.4560880962334983 -1.32647 -25.5936 9 16 0 0.00 0.00 - no Open
254 3.4642926757389616 -1.30203 -24.5606 9 15 0 0.00 0.00 - no Open
406 3.67636034041161 -1.29246 -24.4616 10 16 0 0.00 0.00 - no Open
333 3.717795610400825 -1.4146 -26.5109 10 14 0 0.00 0.00 - no Open
241 3.724783035797209 -1.26416 -21.7498 15 13 0 0.00 0.00 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 0 0.00 0.00 - no Open
330 3.7929991462566486 -0.942708 -18.8834 6 11 0 0.00 0.00 - no Open
241 4.010694369049239 -1.38136 -25.2742 11 19 0 0.00 0.00 - no Open
226 4.299065349056032 -1.39557 -26.9943 14 15 0 0.00 0.00 - no Open
257 4.359761779337785 -1.65662 -30.294 16 22 12 0.57 0.27 - no Current
274 4.532558280468934 -1.63443 -31.073 16 21 11 0.52 0.18 - 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 -30.294kcal/mol
Ligand efficiency (LE) -1.5147kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.675
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.68
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -96.31kcal/mol
Minimised FF energy -126.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 484.6Ų
Total solvent-accessible surface area of free ligand
BSA total 442.7Ų
Buried surface area upon binding
BSA apolar 285.4Ų
Hydrophobic contacts buried
BSA polar 157.3Ų
Polar contacts buried
Fraction buried 91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1186.0Ų
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 505.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)