Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T09

L. major DHFR-TS L. major

Ligand OHD_TbNat_129

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 mixed SASA done

Strain ΔE

47.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.52, Jaccard 0.44, H-bond role recall 0.33

Burial

71%

Hydrophobic fit

78%

Reason: strain 47.2 kcal/mol

strain ΔE 47.2 kcal/mol 1 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (26/40 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.

✓ Good LE (-0.379 kcal/mol/HA) ✓ Good fit quality (FQ -4.29) ✓ Good H-bonds (5 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (47.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)

Score

-21.976

kcal/mol

-0.379

kcal/mol/HA

Fit Quality

-4.29

FQ (Leeson)

HAC

heavy atoms

823

LogP

0.27

cLogP

Final rank

3.7634

rank score

Inter norm

-0.446

normalised

Contacts

H-bonds 6

Strain ΔE

47.2 kcal/mol

SASA buried

71%

Lipo contact

78% BSA apolar/total

SASA unbound

1102 Å²

Apolar buried

608 Å²

Interaction summary

HBA 5 HY 6 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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: strict.

Name	3CL9	Contacts	21
Pose	Open native pose	HB	0
IFP residues	NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap	11	Native recall	0.52
Jaccard	0.44	RMSD	-
HB strict	3	Strict recall	0.43
HB same residue+role	2	HB role recall	0.33
HB same residue	2	HB residue recall	0.33

Protein summary

511 residues

Protein target	T09	Atoms	8170
Residues	511	Chains	2
Residue summary	LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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:NDP301

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
67	3.763354080232624	-0.445618	-21.9763	6	15	11	0.52	0.33	-	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 -21.976kcal/mol

Ligand efficiency (LE) -0.3789kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.287

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

Heavy atom count 58HA

Physicochemical properties

Molecular weight 822.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.27

Lipinski: ≤ 5

Rotatable bonds 15

Conformational strain (MMFF94s)

Strain energy (ΔE) 47.18kcal/mol

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

Docked FF energy 184.57kcal/mol

Minimised FF energy 137.39kcal/mol

SASA & burial

✓ computed

SASA (unbound) 1102.4Å²

Total solvent-accessible surface area of free ligand

BSA total 778.0Å²

Buried surface area upon binding

BSA apolar 607.8Å²

Hydrophobic contacts buried

BSA polar 170.2Å²

Polar contacts buried

Fraction buried 70.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 78.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3648.1Å²

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 4428.5Å²

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

Complex non-polar SASA 1654.4Å²

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