FAIRMol

NMT-TY0671

Pose ID 9916 Compound 1300 Pose 430

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0671
PDB9IFF↗

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
77.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
74%
Hydrophobic fit
67%
Reason: strain 77.4 kcal/mol
strain ΔE 77.4 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.941 kcal/mol/HA) ✓ Good fit quality (FQ -8.98) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (77.4 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (12) ✗ Many internal clashes (11)
Score
-27.279
kcal/mol
LE
-0.941
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.49
cLogP
Final rank
2.3253
rank score
Inter norm
-0.939
normalised
Contacts
16
H-bonds 10
Strain ΔE
77.4 kcal/mol
SASA buried
74%
Lipo contact
67% BSA apolar/total
SASA unbound
634 Ų
Apolar buried
315 Ų

Interaction summary

HBD 2 HBA 4 HY 8 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap10Native recall0.77
Jaccard0.53RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
327 1.113016812929585 -0.837606 -23.8962 1 14 0 0.00 - - no Open
430 2.3252787033319144 -0.938777 -27.2792 10 16 10 0.77 - - no Current
360 2.515614498002701 -1.00043 -29.7334 5 14 0 0.00 - - no Open
401 3.832792503061684 -0.889515 -25.6391 11 18 0 0.00 - - no Open
277 3.8876534768210544 -1.08809 -28.9894 10 19 0 0.00 - - no Open
276 3.987457950263569 -0.9943 -24.6113 10 15 0 0.00 - - no Open
301 3.991224331337767 -0.914304 -27.8504 10 14 0 0.00 - - no Open
355 4.515890243073721 -0.794133 -23.2595 9 20 0 0.00 - - no Open
278 5.236654933239286 -0.9719 -21.9883 11 22 0 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 -27.279kcal/mol
Ligand efficiency (LE) -0.9407kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.979
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.49
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 77.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -19.34kcal/mol
Minimised FF energy -96.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 633.9Ų
Total solvent-accessible surface area of free ligand
BSA total 470.7Ų
Buried surface area upon binding
BSA apolar 315.1Ų
Hydrophobic contacts buried
BSA polar 155.7Ų
Polar contacts buried
Fraction buried 74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2881.3Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1515.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)