FAIRMol

OHD_Leishmania_380

Pose ID 4775 Compound 639 Pose 34

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_380
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
20.9 kcal/mol
Protein clashes
3
Internal clashes
6
Native overlap
contact recall 0.58, Jaccard 0.46, H-bond role recall 0.40
Burial
78%
Hydrophobic fit
70%
Reason: 6 internal clashes
3 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.796 kcal/mol/HA) ✓ Good fit quality (FQ -8.31) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (20.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (20)
Score
-31.847
kcal/mol
LE
-0.796
kcal/mol/HA
Fit Quality
-8.31
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Strain ΔE
20.9 kcal/mol
SASA buried
78%
Lipo contact
70% BSA apolar/total
SASA unbound
762 Ų
Apolar buried
413 Ų

Interaction summary

HB 6 HY 22 PI 2 CLASH 6

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 rank2.037Score-31.847
Inter norm-0.817Intra norm0.021
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 20 clashes; 4 protein contact clashes; 1 severe cofactor-context clash; moderate strain Δ 20.9
Residues
ALA96 ARG14 ASN36 ASP161 HIS35 LEU208 LEU209 LYS13 NAP301 PHE171 PHE97 PRO210 PRO99 TYR174 TYR98 VAL211

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 overlap11Native recall0.58
Jaccard0.46RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
34 2.037464332345491 -0.816862 -31.8466 6 16 11 0.58 0.40 - no Current
25 2.378437056644811 -0.79296 -25.1786 11 20 0 0.00 0.00 - no Open
28 3.1939535201530846 -0.720039 -24.3367 8 16 0 0.00 0.00 - no Open
12 3.2679598625087527 -0.927293 -34.1568 6 15 0 0.00 0.00 - no Open
20 3.495100387591973 -0.687709 -25.9631 8 13 0 0.00 0.00 - no Open
26 3.6318101855931193 -0.794213 -29.5742 8 21 0 0.00 0.00 - no Open
25 3.6473712664434346 -0.864399 -31.0091 12 17 0 0.00 0.00 - no Open
11 3.756350175949824 -0.818637 -30.0821 11 18 0 0.00 0.00 - no Open
36 4.328059027755822 -0.664103 -25.5651 8 12 0 0.00 0.00 - no Open
13 4.367243655754057 -0.718582 -25.2048 10 15 0 0.00 0.00 - no Open
30 4.3947619074725255 -0.797581 -32.0325 7 21 0 0.00 0.00 - no Open
27 4.675590440132758 -0.575435 -21.4762 7 13 0 0.00 0.00 - no Open
18 4.709489958919522 -0.661154 -21.8688 6 14 0 0.00 0.00 - no Open
26 4.853888287172083 -0.702973 -26.167 8 19 0 0.00 0.00 - no Open
25 5.0046255959625645 -0.602508 -21.2208 5 13 0 0.00 0.00 - no Open
20 5.305300875417073 -0.744562 -26.4698 11 17 0 0.00 0.00 - no Open
17 5.662829045447725 -0.771959 -29.8084 10 17 0 0.00 0.00 - no Open
12 6.260876601403174 -0.803018 -30.5918 10 16 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 -31.847kcal/mol
Ligand efficiency (LE) -0.7962kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.315
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 40HA

Physicochemical properties
Molecular weight 538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.13
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 141.86kcal/mol
Minimised FF energy 120.97kcal/mol

SASA & burial

✓ computed
SASA (unbound) 761.8Ų
Total solvent-accessible surface area of free ligand
BSA total 592.1Ų
Buried surface area upon binding
BSA apolar 413.3Ų
Hydrophobic contacts buried
BSA polar 178.8Ų
Polar contacts buried
Fraction buried 77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1608.4Ų
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 965.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)