Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T03

L. major DHFR L. major

Ligand OHD_Leishmania_71

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

62.0 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.60, Jaccard 0.55, H-bond role recall 0.40

Burial

78%

Hydrophobic fit

83%

Reason: strain 62.0 kcal/mol

strain ΔE 62.0 kcal/mol 1 protein-contact clashes

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.669 kcal/mol/HA) ✓ Good fit quality (FQ -6.75) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (62.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-23.404

kcal/mol

-0.669

kcal/mol/HA

Fit Quality

-6.75

FQ (Leeson)

HAC

heavy atoms

498

LogP

4.85

cLogP

Strain ΔE

62.0 kcal/mol

SASA buried

78%

Lipo contact

83% BSA apolar/total

SASA unbound

785 Å²

Apolar buried

503 Å²

Interaction summary

HB 4 HY 24 PI 2 CLASH 1

HB · H-bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Final rank	4.138	Score	-23.404
Inter norm	-0.782	Intra norm	0.113
Top1000	no	Excluded	no
Contacts	14	H-bonds	4
Artifact reason	geometry warning; 16 clashes; 2 protein clashes; high strain Δ 61.9
Residues	ARG97 ILE45 LEU94 LYS57 LYS95 MET53 MET79 NDP301 PHE56 PHE91 THR83 TYR162 VAL156 VAL87

Native ligand reference

★ reference

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

Name	3CL9	Contacts	20
Pose	Open native pose	HB	0
IFP residues	ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap	12	Native recall	0.60
Jaccard	0.55	RMSD	-
HB strict	3	Strict recall	0.43
HB same residue+role	2	HB role recall	0.40
HB same residue	2	HB residue recall	0.40

Protein summary

225 residues

Protein target	T03	Atoms	3428
Residues	225	Chains	2
Residue summary	LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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
4	4.137626863486307	-0.782176	-23.4037	4	14	12	0.60	0.40	-	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 -23.404kcal/mol

Ligand efficiency (LE) -0.6687kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.745

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 497.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.85

Lipinski: ≤ 5

Rotatable bonds 10

Conformational strain (MMFF94s)

Strain energy (ΔE) 61.95kcal/mol

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

Docked FF energy 66.32kcal/mol

Minimised FF energy 4.37kcal/mol

SASA & burial

✓ computed

SASA (unbound) 784.9Å²

Total solvent-accessible surface area of free ligand

BSA total 608.6Å²

Buried surface area upon binding

BSA apolar 502.6Å²

Hydrophobic contacts buried

BSA polar 106.0Å²

Polar contacts buried

Fraction buried 77.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 82.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1648.8Å²

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 1820.7Å²

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

Complex non-polar SASA 801.8Å²

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