FAIRMol

NMT-TY0920

Pose ID 7737 Compound 544 Pose 285

DB SELECTIONDocking 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-TY0920
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
41.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.50
Burial
77%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.251 kcal/mol/HA) ✓ Good fit quality (FQ -11.81) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (41.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-35.027
kcal/mol
LE
-1.251
kcal/mol/HA
Fit Quality
-11.81
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
41.5 kcal/mol
SASA buried
77%
Lipo contact
75% BSA apolar/total
SASA unbound
654 Ų
Apolar buried
376 Ų

Interaction summary

HB 11 HY 10 PI 4 CLASH 1

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 rank1.847Score-35.027
Inter norm-1.101Intra norm-0.150
Top1000noExcludedno
Contacts16H-bonds11
Artifact reasongeometry warning; 9 clashes; 1 protein clash; high strain Δ 41.5
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74

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 overlap13Native recall0.81
Jaccard0.68RMSD-
HB strict7Strict recall0.58
HB same residue+role5HB role recall0.50
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
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 0 0.00 0.00 - no Open
320 1.0669444827431311 -0.878088 -31.4505 3 16 0 0.00 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 0 0.00 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 13 0.81 0.50 - no Current
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 0 0.00 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 16 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 -35.027kcal/mol
Ligand efficiency (LE) -1.2510kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.810
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -25.46kcal/mol
Minimised FF energy -66.94kcal/mol

SASA & burial

✓ computed
SASA (unbound) 654.0Ų
Total solvent-accessible surface area of free ligand
BSA total 502.4Ų
Buried surface area upon binding
BSA apolar 376.4Ų
Hydrophobic contacts buried
BSA polar 126.1Ų
Polar contacts buried
Fraction buried 76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2183.7Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 773.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)