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
35.9 kcal/mol
Protein clashes
13
Internal clashes
14
Native overlap
contact recall 0.90, Jaccard 0.79, H-bond role recall 0.00
Reason: 13 protein-contact clashes, 14 internal clashes
13 protein-contact clashes
14 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.384 kcal/mol/HA)
✓ Good fit quality (FQ -3.84)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (35.9 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (16)
✗ Many internal clashes (13)
Score
-13.055
kcal/mol
LE
-0.384
kcal/mol/HA
Fit Quality
-3.84
FQ (Leeson)
HAC
34
heavy atoms
MW
528
Da
LogP
4.37
cLogP
Interaction summary
HB 2
HY 24
PI 4
CLASH 14
Interaction summary
HB 2
HY 24
PI 4
CLASH 14
| Final rank | 3.230 | Score | -13.055 |
|---|---|---|---|
| Inter norm | -0.718 | Intra norm | 0.330 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 16 protein contact clashes; 2 cofactor-context clashes; high strain Δ 35.9 | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
GLN56
HIS182
ILE160
ILE47
LEU90
LEU97
MET55
NDP301
PHE233
PHE58
PHE94
PRO91
THR184
THR86
TYR166
TYR57
VAL32
VAL33
| ||
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
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 | 19 | Native recall | 0.90 |
| Jaccard | 0.79 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 509 | 3.2297838390728724 | -0.718177 | -13.0551 | 2 | 22 | 19 | 0.90 | 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
-13.055kcal/mol
Ligand efficiency (LE)
-0.3840kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.842
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
527.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.23kcal/mol
Minimised FF energy
6.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
723.9Ų
Total solvent-accessible surface area of free ligand
BSA total
687.5Ų
Buried surface area upon binding
BSA apolar
472.4Ų
Hydrophobic contacts buried
BSA polar
215.1Ų
Polar contacts buried
Fraction buried
95.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1737.5Ų
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
574.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)