FAIRMol

GemmaOHDUnisi_30

Pose ID 4375 Compound 2870 Pose 312

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_30
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
12.5 kcal/mol
Protein clashes
6
Internal clashes
8
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.20
Burial
97%
Hydrophobic fit
80%
Reason: 8 internal clashes
6 protein-contact clashes 8 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.313 kcal/mol/HA) ✓ Good fit quality (FQ -11.20) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (12.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.569
kcal/mol
LE
-1.313
kcal/mol/HA
Fit Quality
-11.20
FQ (Leeson)
HAC
21
heavy atoms
MW
279
Da
LogP
3.48
cLogP
Strain ΔE
12.5 kcal/mol
SASA buried
97%
Lipo contact
80% BSA apolar/total
SASA unbound
519 Ų
Apolar buried
403 Ų

Interaction summary

HB 6 HY 24 PI 2 CLASH 8

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 rank1.782Score-27.569
Inter norm-1.437Intra norm0.124
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 8 clashes; 1 protein clash; 4 cofactor-context clashes
Residues
ARG14 ASN175 ASP161 CYS168 MET163 NAP301 PHE171 PHE97 PRO167 SER95 TRP221 TYR174 VAL164

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 overlap9Native recall0.47
Jaccard0.39RMSD-
HB strict2Strict recall0.33
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
320 0.25828970369132925 -1.52526 -28.4236 4 14 10 0.53 0.20 - no Open
347 1.5679916420256366 -1.23715 -25.0233 5 15 0 0.00 0.00 - no Open
312 1.7818278313920717 -1.4367 -27.5687 6 13 9 0.47 0.20 - 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 -27.569kcal/mol
Ligand efficiency (LE) -1.3128kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.198
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.48
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 62.83kcal/mol
Minimised FF energy 50.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 519.0Ų
Total solvent-accessible surface area of free ligand
BSA total 501.1Ų
Buried surface area upon binding
BSA apolar 402.8Ų
Hydrophobic contacts buried
BSA polar 98.3Ų
Polar contacts buried
Fraction buried 96.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1542.0Ų
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 929.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)