FAIRMol

OHD_TC2_35

Pose ID 8926 Compound 3734 Pose 118

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand OHD_TC2_35
PDB1NJJ↗

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
39.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.38, H-bond role recall 0.20
Burial
78%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.713 kcal/mol/HA) ✓ Good fit quality (FQ -6.88) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Very high strain energy (39.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-21.399
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-6.88
FQ (Leeson)
HAC
30
heavy atoms
MW
452
Da
LogP
-0.00
cLogP
Strain ΔE
39.9 kcal/mol
SASA buried
78%
Lipo contact
88% BSA apolar/total
SASA unbound
741 Ų
Apolar buried
510 Ų

Interaction summary

HB 2 HY 24 PI 0 CLASH 1
Final rank2.326Score-21.399
Inter norm-0.748Intra norm0.035
Top1000noExcludedno
Contacts18H-bonds2
Artifact reasongeometry warning; 12 clashes; 1 protein clash; high strain Δ 39.9
Residues
ARG22 ARG342 CYS26 GLN341 GLU384 LEU25 LEU339 LEU350 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 THR285 TYR370 TYR371

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap9Native recall0.60
Jaccard0.38RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
96 1.0018275658850255 -0.793266 -23.4285 2 16 0 0.00 0.00 - no Open
118 2.3256254866695896 -0.748369 -21.3992 2 18 9 0.60 0.20 - no Current
83 2.8078260448488805 -0.787138 -23.392 2 19 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 -21.399kcal/mol
Ligand efficiency (LE) -0.7133kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.881
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 452.0Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.00
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 188.21kcal/mol
Minimised FF energy 148.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 740.8Ų
Total solvent-accessible surface area of free ligand
BSA total 580.3Ų
Buried surface area upon binding
BSA apolar 510.0Ų
Hydrophobic contacts buried
BSA polar 70.3Ų
Polar contacts buried
Fraction buried 78.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2644.3Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1368.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)