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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
53.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.30
Reason: strain 53.8 kcal/mol
strain ΔE 53.8 kcal/mol
2 protein-contact clashes
66% of hydrophobic surface is solvent-exposed (19/29 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.721 kcal/mol/HA)
✓ Good fit quality (FQ -7.33)
✓ Good H-bonds (4 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Extreme strain energy (53.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (17)
Score
-25.946
kcal/mol
LE
-0.721
kcal/mol/HA
Fit Quality
-7.33
FQ (Leeson)
HAC
36
heavy atoms
MW
496
Da
LogP
2.52
cLogP
Final rank
2.1135
rank score
Inter norm
-0.849
normalised
Contacts
18
H-bonds 6
Interaction summary
HBD 2
HBA 2
HY 5
PI 1
CLASH 2
Interaction summary
HBD 2
HBA 2
HY 5
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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 | 14 | Native recall | 0.88 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.30 |
| HB same residue | 3 | HB residue recall | 0.30 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 207 | 2.113467170645569 | -0.849124 | -25.9458 | 6 | 18 | 14 | 0.88 | 0.30 | - | no | Current |
| 356 | 3.931747155002858 | -0.637183 | -20.0434 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 287 | 4.044818835631979 | -0.617111 | -23.975 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 221 | 4.070800722351716 | -0.741356 | -28.5902 | 5 | 18 | 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
-25.946kcal/mol
Ligand efficiency (LE)
-0.7207kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.325
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.52
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
176.63kcal/mol
Minimised FF energy
122.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
795.7Ų
Total solvent-accessible surface area of free ligand
BSA total
518.2Ų
Buried surface area upon binding
BSA apolar
433.5Ų
Hydrophobic contacts buried
BSA polar
84.8Ų
Polar contacts buried
Fraction buried
65.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2364.3Ų
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
782.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)