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
20.4 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.33
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.056 kcal/mol/HA)
✓ Good fit quality (FQ -10.08)
✓ Good H-bonds (3 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-30.617
kcal/mol
LE
-1.056
kcal/mol/HA
Fit Quality
-10.08
FQ (Leeson)
HAC
29
heavy atoms
MW
442
Da
LogP
4.76
cLogP
Final rank
3.3301
rank score
Inter norm
-0.982
normalised
Contacts
14
H-bonds 8
Interaction summary
HBA 3
PC 1
HY 5
PI 3
CLASH 5
Interaction summary
HBA 3
PC 1
HY 5
PI 3
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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
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 | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 12 | Native recall | 0.71 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 626 | 3.3300902874820757 | -0.981773 | -30.617 | 8 | 14 | 12 | 0.71 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.617kcal/mol
Ligand efficiency (LE)
-1.0558kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
441.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.76
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.88kcal/mol
Minimised FF energy
-18.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.0Ų
Total solvent-accessible surface area of free ligand
BSA total
489.3Ų
Buried surface area upon binding
BSA apolar
365.8Ų
Hydrophobic contacts buried
BSA polar
123.5Ų
Polar contacts buried
Fraction buried
77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1554.6Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1131.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)