FAIRMol

NMT-TY0371

Pose ID 7693 Compound 515 Pose 241

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
T12
T. brucei R5P T. brucei
Ligand NMT-TY0371
PDB6FXS↗

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
33.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.88, Jaccard 0.67, H-bond role recall 0.40
Burial
95%
Hydrophobic fit
66%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.264 kcal/mol/HA) ✓ Good fit quality (FQ -10.57) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Very high strain energy (33.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-25.274
kcal/mol
LE
-1.264
kcal/mol/HA
Fit Quality
-10.57
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.68
cLogP
Strain ΔE
33.0 kcal/mol
SASA buried
95%
Lipo contact
66% BSA apolar/total
SASA unbound
473 Ų
Apolar buried
297 Ų

Interaction summary

HB 11 HY 9 PI 2 CLASH 6

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
Final rank4.011Score-25.274
Inter norm-1.381Intra norm0.118
Top1000noExcludedno
Contacts19H-bonds11
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; high strain Δ 33.0
Residues
ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ASP13 ASP48 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49 VAL47

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.67RMSD-
HB strict3Strict recall0.25
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:CSD72

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 0 0.00 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 0 0.00 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 5 0.31 0.20 - no Open
251 3.7829044977730146 -1.35705 -25.1409 11 19 14 0.88 0.40 - 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 14 0.88 0.40 - no Current
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 0 0.00 0.00 - no Open
274 4.532558280468934 -1.63443 -31.073 16 21 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 -25.274kcal/mol
Ligand efficiency (LE) -1.2637kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.575
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) 33.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -83.73kcal/mol
Minimised FF energy -116.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 472.9Ų
Total solvent-accessible surface area of free ligand
BSA total 447.4Ų
Buried surface area upon binding
BSA apolar 297.0Ų
Hydrophobic contacts buried
BSA polar 150.4Ų
Polar contacts buried
Fraction buried 94.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2014.5Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 758.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)