FAIRMol

GemmaOHDUnisi_6

Pose ID 4373 Compound 2874 Pose 310

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
T07
T. brucei PTR1 T. brucei
Ligand GemmaOHDUnisi_6
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
50.8 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.40
Burial
85%
Hydrophobic fit
66%
Reason: strain 50.8 kcal/mol
strain ΔE 50.8 kcal/mol 4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.956 kcal/mol/HA) ✓ Good fit quality (FQ -8.92) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (50.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-25.813
kcal/mol
LE
-0.956
kcal/mol/HA
Fit Quality
-8.92
FQ (Leeson)
HAC
27
heavy atoms
MW
404
Da
LogP
3.60
cLogP
Strain ΔE
50.8 kcal/mol
SASA buried
85%
Lipo contact
66% BSA apolar/total
SASA unbound
630 Ų
Apolar buried
351 Ų

Interaction summary

HB 6 HY 24 PI 6 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 rank1.848Score-25.813
Inter norm-1.122Intra norm0.166
Top1000noExcludedno
Contacts14H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash; 2 cofactor-context clashes; high strain Δ 50.8
Residues
ARG14 CYS168 LEU208 LEU209 MET169 MET213 NAP301 PHE171 PHE97 PRO210 TRP221 TYR174 VAL206 HIS267

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 overlap12Native recall0.63
Jaccard0.57RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
310 1.8475328568645997 -1.12227 -25.8131 6 14 12 0.63 0.40 - no Current
344 2.705377500604715 -0.964566 -22.926 8 18 0 0.00 0.00 - no Open
10 3.6286269820902795 -0.952345 -22.8385 8 18 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 -25.813kcal/mol
Ligand efficiency (LE) -0.9560kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.920
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 404.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.60
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 50.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 15.25kcal/mol
Minimised FF energy -35.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 629.7Ų
Total solvent-accessible surface area of free ligand
BSA total 532.4Ų
Buried surface area upon binding
BSA apolar 351.2Ų
Hydrophobic contacts buried
BSA polar 181.2Ų
Polar contacts buried
Fraction buried 84.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1551.2Ų
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 913.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)