FAIRMol

NMT-TY0116

Pose ID 11159 Compound 1467 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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand NMT-TY0116
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
7.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.33, Jaccard 0.18, H-bond role recall 1.00
Burial
100%
Hydrophobic fit
37%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.0 kcal/mol) ✓ Excellent LE (-1.923 kcal/mol/HA) ✓ Good fit quality (FQ -12.14) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (100% SASA buried) ✗ Geometry warnings
Score
-21.155
kcal/mol
LE
-1.923
kcal/mol/HA
Fit Quality
-12.14
FQ (Leeson)
HAC
11
heavy atoms
MW
169
Da
LogP
-0.67
cLogP
Strain ΔE
7.0 kcal/mol
SASA buried
100%
Lipo contact
37% BSA apolar/total
SASA unbound
311 Ų
Apolar buried
116 Ų

Interaction summary

HB 13 HY 11 PI 1 CLASH 5

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 rank2.420Score-21.155
Inter norm-2.018Intra norm0.000
Top1000noExcludedno
Contacts14H-bonds13
Artifact reasongeometry warning; 2 clashes; 3 protein clashes
Residues
ALA338 ARG331 ASP327 ASP330 FAD501 GLU341 GLY326 HIS359 LEU332 LEU334 MET333 THR329 THR335 VAL337

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap4Native recall0.33
Jaccard0.18RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
271 -1.8035287957311457 -2.77782 -30.556 8 7 0 0.00 0.00 - no Open
316 2.4195092939240896 -2.01759 -21.1554 13 14 4 0.33 1.00 - 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 -21.155kcal/mol
Ligand efficiency (LE) -1.9232kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 11HA

Physicochemical properties
Molecular weight 169.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.67
Lipinski: ≤ 5
Rotatable bonds 0

Conformational strain (MMFF94s)
Strain energy (ΔE) 7.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -39.80kcal/mol
Minimised FF energy -46.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 311.2Ų
Total solvent-accessible surface area of free ligand
BSA total 311.0Ų
Buried surface area upon binding
BSA apolar 115.6Ų
Hydrophobic contacts buried
BSA polar 195.3Ų
Polar contacts buried
Fraction buried 99.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 37.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6111.7Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2067.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)