Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
14.9 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.40
Reason: 15 internal clashes
15 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 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 Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.118 kcal/mol/HA)
✓ Good fit quality (FQ -10.55)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Moderate strain (14.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-31.292
kcal/mol
LE
-1.118
kcal/mol/HA
Fit Quality
-10.55
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
4.45
cLogP
Final rank
0.5186
rank score
Inter norm
-1.158
normalised
Contacts
21
H-bonds 2
Interaction summary
HBD 1
PC 1
HY 9
PI 0
CLASH 0
Interaction summary
HBD 1
PC 1
HY 9
PI 0
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 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 | 7 | Native recall | 0.26 |
| Jaccard | 0.17 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 139 | 0.518615896362834 | -1.15784 | -31.292 | 2 | 21 | 7 | 0.26 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.292kcal/mol
Ligand efficiency (LE)
-1.1176kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.550
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
417.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.45
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.91kcal/mol
Minimised FF energy
60.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.5Ų
Total solvent-accessible surface area of free ligand
BSA total
615.7Ų
Buried surface area upon binding
BSA apolar
602.5Ų
Hydrophobic contacts buried
BSA polar
13.2Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3215.6Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1485.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)