Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
12.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.026 kcal/mol/HA)
✓ Good fit quality (FQ -9.89)
✓ Good H-bonds (4 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (12.6 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Internal clashes (9)
Score
-30.764
kcal/mol
LE
-1.026
kcal/mol/HA
Fit Quality
-9.89
FQ (Leeson)
HAC
30
heavy atoms
MW
432
Da
LogP
5.94
cLogP
Final rank
1.1899
rank score
Inter norm
-0.977
normalised
Contacts
16
H-bonds 4
Interaction summary
HBD 1
HBA 3
HY 3
PI 4
CLASH 3
Interaction summary
HBD 1
HBA 3
HY 3
PI 4
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.81 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.20 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 619 | 0.2599348264390771 | -0.854274 | -25.8847 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 0.5432662856858713 | -1.0988 | -32.7288 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 1.1898711861443256 | -0.977077 | -30.7641 | 4 | 16 | 13 | 0.81 | 0.20 | - | no | Current |
| 638 | 2.0663861346077406 | -0.799523 | -22.6201 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 2.2748025564410765 | -0.853781 | -23.9237 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 3.282218158019036 | -0.712886 | -19.6109 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.764kcal/mol
Ligand efficiency (LE)
-1.0255kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.892
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
431.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.94
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.75kcal/mol
Minimised FF energy
87.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.9Ų
Total solvent-accessible surface area of free ligand
BSA total
507.2Ų
Buried surface area upon binding
BSA apolar
428.6Ų
Hydrophobic contacts buried
BSA polar
78.6Ų
Polar contacts buried
Fraction buried
75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2221.6Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
827.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)