FAIRMol

OHD_Leishmania_133

Pose ID 4759 Compound 348 Pose 18

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_Leishmania_133
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
53.9 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.84, Jaccard 0.67, H-bond role recall 0.80
Burial
87%
Hydrophobic fit
78%
Reason: strain 53.9 kcal/mol
strain ΔE 53.9 kcal/mol 2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.130 kcal/mol/HA) ✓ Good fit quality (FQ -11.48) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (53.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-40.680
kcal/mol
LE
-1.130
kcal/mol/HA
Fit Quality
-11.48
FQ (Leeson)
HAC
36
heavy atoms
MW
495
Da
LogP
-0.34
cLogP
Final rank
3.0487
rank score
Inter norm
-1.119
normalised
Contacts
21
H-bonds 12
Strain ΔE
53.9 kcal/mol
SASA buried
87%
Lipo contact
78% BSA apolar/total
SASA unbound
781 Ų
Apolar buried
534 Ų

Interaction summary

HBD 5 HBA 4 HY 9 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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
Jaccard0.67RMSD-
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
12 1.6392561257972764 -0.859726 -29.8169 8 14 0 0.00 0.00 - no Open
16 2.1036393104027136 -0.742975 -28.9035 8 20 0 0.00 0.00 - no Open
11 2.65940477669851 -0.731382 -24.0508 5 20 0 0.00 0.00 - no Open
15 2.8400958184167666 -1.1447 -44.2495 10 18 14 0.74 0.80 - no Open
12 3.0099859272417073 -0.747145 -28.4943 8 14 0 0.00 0.00 - no Open
12 3.0166469621949865 -0.589367 -22.6096 8 12 0 0.00 0.00 - no Open
18 3.0486529189517513 -1.11879 -40.6803 12 21 16 0.84 0.80 - no Current
5 3.229919745111221 -0.668992 -23.7798 9 19 0 0.00 0.00 - no Open
15 3.8936404298502363 -0.991486 -37.2759 15 23 0 0.00 0.00 - no Open
12 4.894897117783592 -0.855 -26.3168 8 23 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 -40.680kcal/mol
Ligand efficiency (LE) -1.1300kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.485
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.34
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 35.97kcal/mol
Minimised FF energy -17.95kcal/mol

SASA & burial

✓ computed
SASA (unbound) 781.2Ų
Total solvent-accessible surface area of free ligand
BSA total 679.6Ų
Buried surface area upon binding
BSA apolar 533.6Ų
Hydrophobic contacts buried
BSA polar 145.9Ų
Polar contacts buried
Fraction buried 87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1764.5Ų
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 907.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)