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 mixed
SASA done
Strain ΔE
24.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.20
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 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 (-0.621 kcal/mol/HA)
✓ Good fit quality (FQ -6.21)
✓ Good H-bonds (3 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Many internal clashes (18)
Score
-21.118
kcal/mol
LE
-0.621
kcal/mol/HA
Fit Quality
-6.21
FQ (Leeson)
HAC
34
heavy atoms
MW
449
Da
LogP
3.52
cLogP
Final rank
2.2914
rank score
Inter norm
-0.975
normalised
Contacts
20
H-bonds 6
Interaction summary
HBA 3
HY 7
PI 0
CLASH 6
Interaction summary
HBA 3
HY 7
PI 0
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 2WOV | Contacts | 27 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA284
ALA365
ARG222
ARG228
ARG287
ASN223
ASN254
GLN165
GLU202
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
LEU334
LYS60
MET333
NDP800
PHE198
PHE367
PRO167
SER200
TYR221
VAL194
VAL366
| ||
| Current overlap | 8 | Native recall | 0.30 |
| Jaccard | 0.21 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
Protein summary
493 residues
| Protein target | T19 | Atoms | 7541 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221 | ||
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
C:NDP800
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 466 | 2.2914150691266615 | -0.974852 | -21.1177 | 6 | 20 | 8 | 0.30 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.118kcal/mol
Ligand efficiency (LE)
-0.6211kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.52
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-5.09kcal/mol
Minimised FF energy
-29.23kcal/mol
SASA & burial
✓ computed
SASA (unbound)
702.5Ų
Total solvent-accessible surface area of free ligand
BSA total
629.4Ų
Buried surface area upon binding
BSA apolar
510.4Ų
Hydrophobic contacts buried
BSA polar
119.0Ų
Polar contacts buried
Fraction buried
89.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3174.3Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1460.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)