Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T03

L. major DHFR L. major

Ligand OSA_Lib_82

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

28.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.80, Jaccard 0.73, H-bond role recall 0.60

Burial

85%

Hydrophobic fit

92%

Reason: 17 internal clashes

4 protein-contact clashes 17 intramolecular clashes

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.704 kcal/mol/HA) ✓ Good fit quality (FQ -7.20) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (92%) ✗ High strain energy (28.6 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (17)

Score

-26.031

kcal/mol

-0.704

kcal/mol/HA

Fit Quality

-7.20

FQ (Leeson)

HAC

heavy atoms

505

LogP

2.13

cLogP

Final rank

1.8873

rank score

Inter norm

-0.773

normalised

Contacts

H-bonds 3

Strain ΔE

28.6 kcal/mol

SASA buried

85%

Lipo contact

92% BSA apolar/total

SASA unbound

820 Å²

Apolar buried

643 Å²

Interaction summary

HBD 2 HY 8 PI 2 CLASH 0

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

No clash · clashes detected for this pose.

Native ligand reference

★ reference

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

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	16	Native recall	0.80
Jaccard	0.73	RMSD	-
HB strict	3	Strict recall	0.43
HB same residue+role	3	HB role recall	0.60
HB same residue	3	HB residue recall	0.60

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
190	1.887257124812883	-0.773302	-26.0308	3	18	16	0.80	0.60	-	no	Current
128	3.4882773096321715	-0.779999	-28.1657	6	16	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -26.031kcal/mol

Ligand efficiency (LE) -0.7035kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.203

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

Heavy atom count 37HA

Physicochemical properties

Molecular weight 504.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.13

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 28.55kcal/mol

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

Docked FF energy 96.88kcal/mol

Minimised FF energy 68.32kcal/mol

SASA & burial

✓ computed

SASA (unbound) 820.5Å²

Total solvent-accessible surface area of free ligand

BSA total 699.8Å²

Buried surface area upon binding

BSA apolar 643.4Å²

Hydrophobic contacts buried

BSA polar 56.3Å²

Polar contacts buried

Fraction buried 85.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 92.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1788.3Å²

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 796.5Å²

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