Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand ulfkktlib_1825

PDB7PXX↗

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

89.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.82, Jaccard 0.70, H-bond role recall 0.17

Burial

79%

Hydrophobic fit

78%

Reason: strain 89.0 kcal/mol

strain ΔE 89.0 kcal/mol 3 protein-contact clashes 4 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (16/34 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.540 kcal/mol/HA) ✓ Good fit quality (FQ -5.78) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (89.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (21)

Score

-23.782

kcal/mol

-0.540

kcal/mol/HA

Fit Quality

-5.78

FQ (Leeson)

HAC

heavy atoms

588

LogP

4.68

cLogP

Final rank

2.4291

rank score

Inter norm

-0.664

normalised

Contacts

H-bonds 2

Strain ΔE

89.0 kcal/mol

SASA buried

79%

Lipo contact

78% BSA apolar/total

SASA unbound

831 Å²

Apolar buried

510 Å²

Interaction summary

HBD 2 HY 6 PI 4 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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.

Name	ligand	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	14	Native recall	0.82
Jaccard	0.70	RMSD	-
HB strict	1	Strict recall	0.14
HB same residue+role	1	HB role recall	0.17
HB same residue	2	HB residue recall	0.40

Protein summary

274 residues

Protein target	T05	Atoms	4108
Residues	274	Chains	2
Residue summary	LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
171	2.394722870706949	-0.647782	-23.9689	2	16	13	0.76	0.17	-	no	Open
172	2.42905762727439	-0.664377	-23.7817	2	17	14	0.82	0.17	-	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 -23.782kcal/mol

Ligand efficiency (LE) -0.5405kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.775

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

Heavy atom count 44HA

Physicochemical properties

Molecular weight 587.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.68

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 88.98kcal/mol

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

Docked FF energy 180.92kcal/mol

Minimised FF energy 91.94kcal/mol

SASA & burial

✓ computed

SASA (unbound) 831.5Å²

Total solvent-accessible surface area of free ligand

BSA total 655.6Å²

Buried surface area upon binding

BSA apolar 510.2Å²

Hydrophobic contacts buried

BSA polar 145.4Å²

Polar contacts buried

Fraction buried 78.8%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 77.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1793.9Å²

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 2179.4Å²

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

Complex non-polar SASA 1050.8Å²

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