FAIRMol

OHD_MAC_68

Pose ID 5110 Compound 3135 Pose 369

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
T08
T. brucei PTR1 T. brucei
Ligand OHD_MAC_68
PDB6RX6↗

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
46.7 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.80
Burial
85%
Hydrophobic fit
80%
Reason: strain 46.7 kcal/mol
strain ΔE 46.7 kcal/mol 3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.894 kcal/mol/HA) ✓ Good fit quality (FQ -8.95) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (46.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-30.406
kcal/mol
LE
-0.894
kcal/mol/HA
Fit Quality
-8.95
FQ (Leeson)
HAC
34
heavy atoms
MW
494
Da
LogP
1.32
cLogP
Strain ΔE
46.7 kcal/mol
SASA buried
85%
Lipo contact
80% BSA apolar/total
SASA unbound
722 Ų
Apolar buried
488 Ų

Interaction summary

HB 9 HY 24 PI 3 CLASH 4
Final rank2.460Score-30.406
Inter norm-1.032Intra norm0.138
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasongeometry warning; 14 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 46.7
Residues
ALA212 ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LEU263 LYS178 MET163 NAP301 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206 VAL211 HIS267

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap15Native recall0.79
Jaccard0.62RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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
369 2.4598161032641923 -1.03229 -30.4064 9 20 15 0.79 0.80 - no Current
324 3.5962351800416785 -0.742386 -23.4425 9 21 0 0.00 0.00 - no Open
376 4.043057395500419 -0.557853 -17.636 9 13 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 -30.406kcal/mol
Ligand efficiency (LE) -0.8943kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.948
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 493.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.32
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.24kcal/mol
Minimised FF energy 110.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 722.1Ų
Total solvent-accessible surface area of free ligand
BSA total 611.6Ų
Buried surface area upon binding
BSA apolar 488.1Ų
Hydrophobic contacts buried
BSA polar 123.5Ų
Polar contacts buried
Fraction buried 84.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1635.4Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1012.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)