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_DCM_36

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

56.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.48, Jaccard 0.40, H-bond role recall 0.33

Burial

85%

Hydrophobic fit

72%

Reason: strain 56.0 kcal/mol

strain ΔE 56.0 kcal/mol 1 protein-contact clashes

Molecular report

Full metrics ↗

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

✓ Excellent LE (-1.179 kcal/mol/HA) ✓ Good fit quality (FQ -10.57) ✓ Good H-bonds (4 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Extreme strain energy (56.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)

Score

-28.305

kcal/mol

-1.179

kcal/mol/HA

Fit Quality

-10.57

FQ (Leeson)

HAC

heavy atoms

339

LogP

3.95

cLogP

Final rank

2.0243

rank score

Inter norm

-1.141

normalised

Contacts

H-bonds 10

Strain ΔE

56.0 kcal/mol

SASA buried

85%

Lipo contact

72% BSA apolar/total

SASA unbound

565 Å²

Apolar buried

347 Å²

Interaction summary

HBD 1 HBA 3 HY 7 PI 1 CLASH 1

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	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	10	Native recall	0.48
Jaccard	0.40	RMSD	-
HB strict	1	Strict recall	0.14
HB same residue+role	2	HB role recall	0.33
HB same residue	3	HB residue recall	0.50

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
388	2.0243210769246227	-1.1409	-28.3055	10	14	10	0.48	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 -28.305kcal/mol

Ligand efficiency (LE) -1.1794kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.570

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 339.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.95

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 55.98kcal/mol

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

Docked FF energy 126.62kcal/mol

Minimised FF energy 70.64kcal/mol

SASA & burial

✓ computed

SASA (unbound) 565.4Å²

Total solvent-accessible surface area of free ligand

BSA total 478.7Å²

Buried surface area upon binding

BSA apolar 347.1Å²

Hydrophobic contacts buried

BSA polar 131.6Å²

Polar contacts buried

Fraction buried 84.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 72.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3150.6Å²

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 1711.2Å²

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