FAIRMol

NMT-TY0940

Pose ID 7741 Compound 241 Pose 289

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-TY0940
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
29.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.76, H-bond role recall 0.60
Burial
74%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 64% of hydrophobic surface is solvent-exposed (9/14 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 (-1.056 kcal/mol/HA) ✓ Good fit quality (FQ -9.47) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (29.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-25.351
kcal/mol
LE
-1.056
kcal/mol/HA
Fit Quality
-9.47
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.63
cLogP
Strain ΔE
29.1 kcal/mol
SASA buried
74%
Lipo contact
70% BSA apolar/total
SASA unbound
606 Ų
Apolar buried
311 Ų

Interaction summary

HB 13 HY 4 PI 3 CLASH 4 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (9/14 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 14 Buried (contacted) 5 Exposed 9 LogP 1.63 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.672Score-25.351
Inter norm-1.124Intra norm0.068
Top1000noExcludedno
Contacts14H-bonds13
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 29.1
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 MET101 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 SER74

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

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
Jaccard0.76RMSD-
HB strict8Strict recall0.67
HB same residue+role6HB role recall0.60
HB same residue6HB residue recall0.60

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
306 1.2631873093929213 -1.34941 -30.1267 13 17 0 0.00 0.00 - no Open
381 1.6357487501015966 -1.24508 -30.9111 6 15 0 0.00 0.00 - no Open
395 1.6502547563641763 -1.23395 -30.8008 7 15 0 0.00 0.00 - no Open
323 1.840957912270202 -1.14049 -27.563 10 15 0 0.00 0.00 - no Open
328 2.162352905157436 -0.96164 -21.6733 6 22 0 0.00 0.00 - no Open
344 2.3366599065068105 -0.856748 -22.4171 7 13 0 0.00 0.00 - no Open
446 2.3492674163877334 -1.02269 -23.8404 10 15 0 0.00 0.00 - no Open
355 2.861871233912479 -0.808224 -17.4676 8 10 0 0.00 0.00 - no Open
325 2.919717690817132 -1.00604 -21.4293 6 17 0 0.00 0.00 - no Open
370 3.568230353766292 -1.00298 -25.4418 10 18 0 0.00 0.00 - no Open
289 3.671940099102461 -1.12425 -25.3507 13 14 13 0.81 0.60 - no Current
277 4.192295277504068 -1.02312 -22.1326 15 13 4 0.25 0.30 - 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 -25.351kcal/mol
Ligand efficiency (LE) -1.0563kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.466
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.63
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -58.10kcal/mol
Minimised FF energy -87.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 605.8Ų
Total solvent-accessible surface area of free ligand
BSA total 447.3Ų
Buried surface area upon binding
BSA apolar 310.7Ų
Hydrophobic contacts buried
BSA polar 136.6Ų
Polar contacts buried
Fraction buried 73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2126.6Ų
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 772.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)