FAIRMol

OHD_TB2020_4

Pose ID 2744 Compound 2134 Pose 34

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
T05
L. major PTR1 L. major
Ligand OHD_TB2020_4
PDB7PXX↗

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
59.9 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.82, Jaccard 0.70, H-bond role recall 0.33
Burial
72%
Hydrophobic fit
90%
Reason: strain 59.9 kcal/mol
strain ΔE 59.9 kcal/mol 3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.544 kcal/mol/HA) ✓ Good fit quality (FQ -5.93) ✓ Good H-bonds (4 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (59.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (17)
Score
-26.118
kcal/mol
LE
-0.544
kcal/mol/HA
Fit Quality
-5.93
FQ (Leeson)
HAC
48
heavy atoms
MW
665
Da
LogP
4.74
cLogP
Strain ΔE
59.9 kcal/mol
SASA buried
72%
Lipo contact
90% BSA apolar/total
SASA unbound
887 Ų
Apolar buried
576 Ų

Interaction summary

HB 4 HY 24 PI 4 CLASH 5

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 rank2.092Score-26.118
Inter norm-0.582Intra norm0.038
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 17 clashes; 4 protein contact clashes; 2 cofactor-context clashes; high strain Δ 59.9
Residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 SER111 SER112 TYR114 TYR191 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap14Native recall0.82
Jaccard0.70RMSD-
HB strict2Strict recall0.29
HB same residue+role2HB role recall0.33
HB same residue2HB residue recall0.40

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
34 2.091947214433606 -0.582244 -26.1177 4 17 14 0.82 0.33 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -26.118kcal/mol
Ligand efficiency (LE) -0.5441kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.928
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 48HA

Physicochemical properties
Molecular weight 664.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.74
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 59.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 177.99kcal/mol
Minimised FF energy 118.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 887.4Ų
Total solvent-accessible surface area of free ligand
BSA total 642.9Ų
Buried surface area upon binding
BSA apolar 576.4Ų
Hydrophobic contacts buried
BSA polar 66.5Ų
Polar contacts buried
Fraction buried 72.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1925.6Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1033.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)