Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T12

T. brucei R5P T. brucei

Ligand Z30900005

PDB6FXS↗

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

40.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 1.00, Jaccard 0.94, H-bond role recall 0.60

Burial

77%

Hydrophobic fit

71%

Reason: no major geometry red flags detected

5 protein-contact clashes 5 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (10/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-1.096 kcal/mol/HA) ✓ Good fit quality (FQ -9.82) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (40.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)

Score

-26.293

kcal/mol

-1.096

kcal/mol/HA

Fit Quality

-9.82

FQ (Leeson)

HAC

heavy atoms

357

LogP

0.22

cLogP

Final rank

3.9036

rank score

Inter norm

-1.160

normalised

Contacts

H-bonds 13

Strain ΔE

40.7 kcal/mol

SASA buried

77%

Lipo contact

71% BSA apolar/total

SASA unbound

584 Å²

Apolar buried

319 Å²

Interaction summary

HBD 2 HBA 8 HY 3 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

PI · π–π interactions

No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	6FXS	Contacts	16
Pose	Open native pose	HB	0
IFP residues	ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap	16	Native recall	1.00
Jaccard	0.94	RMSD	-
HB strict	8	Strict recall	0.67
HB same residue+role	6	HB role recall	0.60
HB same residue	8	HB residue recall	0.80

Protein summary

302 residues

Protein target	T12	Atoms	4598
Residues	302	Chains	2
Residue summary	ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
578	3.9036429857589163	-1.16046	-26.2933	13	17	16	1.00	0.60	-	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 -26.293kcal/mol

Ligand efficiency (LE) -1.0956kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.818

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 24HA

Physicochemical properties

Molecular weight 357.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.22

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 40.70kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy -91.88kcal/mol

Minimised FF energy -132.58kcal/mol

SASA & burial

✓ computed

SASA (unbound) 584.3Å²

Total solvent-accessible surface area of free ligand

BSA total 448.8Å²

Buried surface area upon binding

BSA apolar 319.0Å²

Hydrophobic contacts buried

BSA polar 129.8Å²

Polar contacts buried

Fraction buried 76.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 71.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2109.8Å²

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 2454.8Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 793.5Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)