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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
23.7 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.48, H-bond role recall 0.25
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.705 kcal/mol/HA)
✓ Good fit quality (FQ -6.73)
✓ Good H-bonds (5 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ High strain energy (23.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (12)
Score
-20.439
kcal/mol
LE
-0.705
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
29
heavy atoms
MW
397
Da
LogP
3.10
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 3
Interaction summary
HB 5
HY 24
PI 2
CLASH 3
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
| Final rank | 1.359 | Score | -20.439 |
|---|---|---|---|
| Inter norm | -0.807 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 5 protein contact clashes; 2 cofactor-context clashes; moderate strain Δ 23.7 | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
GLN56
ILE47
LEU90
LEU97
LYS93
MET55
NDP301
PHE58
PHE94
PRO91
PRO96
SER98
THR184
TYR57
VAL33
| ||
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.48 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 1 | HB role recall | 0.25 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 208 | 1.359179259741825 | -0.806574 | -20.4387 | 5 | 19 | 13 | 0.62 | 0.25 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.439kcal/mol
Ligand efficiency (LE)
-0.7048kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.728
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
397.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.10
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.66kcal/mol
Minimised FF energy
26.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
705.2Ų
Total solvent-accessible surface area of free ligand
BSA total
643.8Ų
Buried surface area upon binding
BSA apolar
469.3Ų
Hydrophobic contacts buried
BSA polar
174.5Ų
Polar contacts buried
Fraction buried
91.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1752.5Ų
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
583.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)