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
69.2 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.50
Reason: strain 69.2 kcal/mol
strain ΔE 69.2 kcal/mol
1 protein-contact clashes
3 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.469 kcal/mol/HA)
✓ Good fit quality (FQ -4.65)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Extreme strain energy (69.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-15.470
kcal/mol
LE
-0.469
kcal/mol/HA
Fit Quality
-4.65
FQ (Leeson)
HAC
33
heavy atoms
MW
464
Da
LogP
-0.52
cLogP
Final rank
3.5168
rank score
Inter norm
-0.868
normalised
Contacts
13
H-bonds 12
Interaction summary
HBD 2
HBA 4
PC 1
HY 6
PI 1
CLASH 3
Interaction summary
HBD 2
HBA 4
PC 1
HY 6
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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: strict.
| 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 | 11 | Native recall | 0.65 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 24 | 3.5167520550673474 | -0.867665 | -15.4697 | 12 | 13 | 11 | 0.65 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.470kcal/mol
Ligand efficiency (LE)
-0.4688kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.651
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
464.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.52
Lipinski: ≤ 5
Rotatable bonds
14
Conformational strain (MMFF94s)
Strain energy (ΔE)
69.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.18kcal/mol
Minimised FF energy
12.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
748.6Ų
Total solvent-accessible surface area of free ligand
BSA total
600.9Ų
Buried surface area upon binding
BSA apolar
411.1Ų
Hydrophobic contacts buried
BSA polar
189.8Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1680.2Ų
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
1030.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)