FAIRMol

OHD_Leishmania_310

Pose ID 4087 Compound 243 Pose 24

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
T07
T. brucei PTR1 T. brucei
Ligand OHD_Leishmania_310
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
37.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.60
Burial
99%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.288 kcal/mol/HA) ✓ Good fit quality (FQ -12.02) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (99% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (37.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (14)
Score
-34.775
kcal/mol
LE
-1.288
kcal/mol/HA
Fit Quality
-12.02
FQ (Leeson)
HAC
27
heavy atoms
MW
360
Da
LogP
2.42
cLogP
Strain ΔE
37.5 kcal/mol
SASA buried
99%
Lipo contact
80% BSA apolar/total
SASA unbound
613 Ų
Apolar buried
487 Ų

Interaction summary

HB 10 HY 24 PI 4 CLASH 2

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 rank0.755Score-34.775
Inter norm-1.594Intra norm0.306
Top1000noExcludedno
Contacts20H-bonds10
Artifact reasongeometry warning; 14 clashes; 4 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 37.5
Residues
ALA96 ARG14 ASN175 ASP161 CYS168 GLY205 LEU208 LEU209 MET163 NAP301 PHE171 PHE97 PRO167 PRO210 SER207 SER95 TRP221 TYR174 VAL164 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 overlap15Native recall0.79
Jaccard0.62RMSD-
HB strict4Strict recall0.67
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

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
24 0.7549739333923433 -1.59413 -34.7747 10 20 15 0.79 0.60 - no Current
329 0.8698098052673956 -1.45049 -32.341 12 17 15 0.79 0.60 - no Open
317 0.8946384457594485 -1.58597 -34.0011 11 20 15 0.79 0.60 - no Open
28 1.0656347282420564 -1.45916 -33.2626 11 19 16 0.84 0.60 - no Open
356 1.3049353307334395 -0.979504 -15.9888 7 14 0 0.00 0.00 - no Open
18 1.588420314889381 -0.911019 -18.1341 8 13 0 0.00 0.00 - no Open
422 1.6628478945064362 -1.05644 -21.9746 9 14 0 0.00 0.00 - no Open
20 3.0361155172718495 -1.0181 -22.5996 8 16 0 0.00 0.00 - no Open
23 3.1202537945072804 -1.07531 -24.183 8 16 0 0.00 0.00 - no Open
27 3.3132689308519394 -0.966783 -22.6379 4 18 0 0.00 0.00 - no Open
356 3.328134667714495 -0.944168 -25.3759 8 17 0 0.00 0.00 - no Open
344 3.624100808087315 -0.981092 -22.542 4 18 0 0.00 0.00 - no Open
388 4.022832904360227 -0.998263 -23.0614 8 15 0 0.00 0.00 - no Open
13 4.626933943246996 -0.776058 -21.6728 5 15 0 0.00 0.00 - no Open
28 4.830200145190352 -0.821899 -16.9858 6 13 0 0.00 0.00 - no Open
345 4.977153414468411 -0.945005 -21.6885 10 15 0 0.00 0.00 - no Open
317 5.527148258279148 -1.01223 -15.9467 14 19 0 0.00 0.00 - no Open
317 5.568677730743583 -1.13532 -21.0205 16 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 -34.775kcal/mol
Ligand efficiency (LE) -1.2880kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.016
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 360.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.42
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 127.65kcal/mol
Minimised FF energy 90.16kcal/mol

SASA & burial

✓ computed
SASA (unbound) 612.9Ų
Total solvent-accessible surface area of free ligand
BSA total 605.2Ų
Buried surface area upon binding
BSA apolar 487.0Ų
Hydrophobic contacts buried
BSA polar 118.2Ų
Polar contacts buried
Fraction buried 98.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1625.2Ų
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 920.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)