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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
16.1 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.00
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.680 kcal/mol/HA)
✓ Good fit quality (FQ -6.56)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-20.407
kcal/mol
LE
-0.680
kcal/mol/HA
Fit Quality
-6.56
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.84
cLogP
Interaction summary
HB 2
HY 24
PI 1
CLASH 9
Interaction summary
HB 2
HY 24
PI 1
CLASH 9
| Final rank | 3.957 | Score | -20.407 |
|---|---|---|---|
| Inter norm | -0.819 | Intra norm | 0.113 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 19 clashes; 1 protein clash | ||
| Residues |
ALA34
ASP54
GLU50
GLY45
ILE160
ILE47
LEU90
MET55
NDP301
PHE58
PHE94
PRO91
SER89
THR184
THR46
THR86
TYR166
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 524 | 1.688891324185852 | -0.910844 | -22.099 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 1.8904526726165263 | -0.855184 | -22.6696 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 503 | 3.2412176734711755 | -1.1393 | -36.6216 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 508 | 3.956584465844293 | -0.818907 | -20.4075 | 2 | 19 | 16 | 0.76 | 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
-20.407kcal/mol
Ligand efficiency (LE)
-0.6802kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.562
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
400.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.65kcal/mol
Minimised FF energy
56.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.7Ų
Total solvent-accessible surface area of free ligand
BSA total
593.7Ų
Buried surface area upon binding
BSA apolar
450.8Ų
Hydrophobic contacts buried
BSA polar
142.9Ų
Polar contacts buried
Fraction buried
89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1730.2Ų
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
1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
601.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)