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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
44.8 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.00
Reason: 10 internal clashes, strain 44.8 kcal/mol
strain ΔE 44.8 kcal/mol
10 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 (-0.630 kcal/mol/HA)
✓ Good fit quality (FQ -5.95)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (44.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-17.632
kcal/mol
LE
-0.630
kcal/mol/HA
Fit Quality
-5.95
FQ (Leeson)
HAC
28
heavy atoms
MW
408
Da
LogP
1.21
cLogP
Final rank
1.8691
rank score
Inter norm
-0.855
normalised
Contacts
18
H-bonds 2
Interaction summary
HBA 2
HY 9
PI 3
CLASH 0
Interaction summary
HBA 2
HY 9
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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: strict.
| Name | 8RHT | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA34
ASP54
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
SER89
THR184
THR86
TRP49
TYR166
TYR57
VAL32
VAL33
| ||
| Current overlap | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
223 residues
| Protein target | T06 | Atoms | 3452 |
|---|---|---|---|
| Residues | 223 | Chains | 1 |
| Residue summary | ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74 | ||
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:NDP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 1.8691352553791356 | -0.855188 | -17.6319 | 2 | 18 | 15 | 0.71 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.632kcal/mol
Ligand efficiency (LE)
-0.6297kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.945
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.21
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
44.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-88.57kcal/mol
Minimised FF energy
-133.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
704.6Ų
Total solvent-accessible surface area of free ligand
BSA total
666.1Ų
Buried surface area upon binding
BSA apolar
496.9Ų
Hydrophobic contacts buried
BSA polar
169.2Ų
Polar contacts buried
Fraction buried
94.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1766.0Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
577.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)