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_TB2024_10

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

64.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.71, Jaccard 0.62, H-bond role recall 0.67

Burial

87%

Hydrophobic fit

80%

Reason: strain 64.2 kcal/mol

strain ΔE 64.2 kcal/mol 4 protein-contact clashes 4 intramolecular clashes

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.822 kcal/mol/HA) ✓ Good fit quality (FQ -7.93) ✓ Good H-bonds (4 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (64.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-24.652

kcal/mol

-0.822

kcal/mol/HA

Fit Quality

-7.93

FQ (Leeson)

HAC

heavy atoms

451

LogP

2.83

cLogP

Final rank

2.7471

rank score

Inter norm

-1.008

normalised

Contacts

H-bonds 12

Strain ΔE

64.2 kcal/mol

SASA buried

87%

Lipo contact

80% BSA apolar/total

SASA unbound

679 Å²

Apolar buried

473 Å²

Interaction summary

HBD 4 HY 5 PI 2 CLASH 4

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	15	Native recall	0.71
Jaccard	0.62	RMSD	-
HB strict	4	Strict recall	0.57
HB same residue+role	4	HB role recall	0.67
HB same residue	4	HB residue recall	0.67

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
70	0.5207628594237272	-1.07349	-31.9605	6	20	0	0.00	0.00	-	no	Open
63	2.7470550372729075	-1.00789	-24.6521	12	18	15	0.71	0.67	-	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 -24.652kcal/mol

Ligand efficiency (LE) -0.8217kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.927

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 451.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.83

Lipinski: ≤ 5

Rotatable bonds 10

Conformational strain (MMFF94s)

Strain energy (ΔE) 64.18kcal/mol

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

Docked FF energy -22.50kcal/mol

Minimised FF energy -86.68kcal/mol

SASA & burial

✓ computed

SASA (unbound) 678.9Å²

Total solvent-accessible surface area of free ligand

BSA total 592.4Å²

Buried surface area upon binding

BSA apolar 472.6Å²

Hydrophobic contacts buried

BSA polar 119.8Å²

Polar contacts buried

Fraction buried 87.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 79.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3263.8Å²

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 4428.5Å²

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

Complex non-polar SASA 1716.9Å²

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