FAIRMol

OHD_Leishmania_124

Pose ID 4750 Compound 1448 Pose 9

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
T08
T. brucei PTR1 T. brucei
Ligand OHD_Leishmania_124
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.73, H-bond role recall 0.80
Burial
82%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.926 kcal/mol/HA) ✓ Good fit quality (FQ -9.34) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (32.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (17)
Score
-32.406
kcal/mol
LE
-0.926
kcal/mol/HA
Fit Quality
-9.34
FQ (Leeson)
HAC
35
heavy atoms
MW
475
Da
LogP
1.25
cLogP
Strain ΔE
32.0 kcal/mol
SASA buried
82%
Lipo contact
78% BSA apolar/total
SASA unbound
780 Ų
Apolar buried
500 Ų

Interaction summary

HB 8 HY 24 PI 3 CLASH 3

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 rank1.828Score-32.406
Inter norm-1.062Intra norm0.136
Top1000noExcludedno
Contacts19H-bonds8
Artifact reasongeometry warning; 17 clashes; 6 protein contact clashes; 1 cofactor-context clash; high strain Δ 32.0
Residues
ARG14 ASP161 CYS168 GLU217 GLY205 LEU208 LEU209 LYS220 MET163 MET213 NAP301 PHE171 PHE97 PRO210 SER207 SER95 TRP221 TYR174 VAL206

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 overlap16Native recall0.84
Jaccard0.73RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
9 1.8278753700939747 -1.06159 -32.4057 8 19 16 0.84 0.80 - no Current
3 3.458347873613621 -1.02586 -32.7223 8 14 0 0.00 0.00 - no Open
7 4.4128156040438125 -0.863725 -24.7338 11 22 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 -32.406kcal/mol
Ligand efficiency (LE) -0.9259kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.339
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.25
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 7.01kcal/mol
Minimised FF energy -24.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 780.1Ų
Total solvent-accessible surface area of free ligand
BSA total 637.9Ų
Buried surface area upon binding
BSA apolar 500.1Ų
Hydrophobic contacts buried
BSA polar 137.8Ų
Polar contacts buried
Fraction buried 81.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1755.7Ų
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 910.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)