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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
37.2 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.00
Reason: 6 internal clashes
5 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.795 kcal/mol/HA)
✓ Good fit quality (FQ -7.59)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Very high strain energy (37.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-23.060
kcal/mol
LE
-0.795
kcal/mol/HA
Fit Quality
-7.59
FQ (Leeson)
HAC
29
heavy atoms
MW
409
Da
LogP
3.65
cLogP
Interaction summary
HB 1
HY 24
PI 1
CLASH 6
Interaction summary
HB 1
HY 24
PI 1
CLASH 6
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 | 2.522 | Score | -23.060 |
|---|---|---|---|
| Inter norm | -0.887 | Intra norm | 0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 30.5 | ||
| Residues |
ALA34
ARG100
ARG59
ASP54
GLN56
GLY161
ILE160
ILE47
LEU90
LEU97
MET55
MET82
NDP301
PHE58
PHE94
THR86
TYR166
VAL32
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 0.5835218828030698 | -0.948247 | -27.8165 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 0.592957583313862 | -0.938475 | -27.9713 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 0.7936629295387901 | -0.906528 | -29.5088 | 1 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 1 | 1.366019553904413 | -0.975299 | -28.4082 | 1 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1 | 2.1682831170699823 | -1.17383 | -32.9705 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 2.513689142209288 | -0.710854 | -21.2765 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 2.5222548743727224 | -0.887327 | -23.0601 | 1 | 19 | 14 | 0.67 | 0.00 | - | no | Current |
| 1 | 3.2001356098827536 | -0.668109 | -18.629 | 3 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.060kcal/mol
Ligand efficiency (LE)
-0.7952kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.591
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
408.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.65
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.26kcal/mol
Minimised FF energy
78.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.9Ų
Total solvent-accessible surface area of free ligand
BSA total
634.8Ų
Buried surface area upon binding
BSA apolar
567.2Ų
Hydrophobic contacts buried
BSA polar
67.6Ų
Polar contacts buried
Fraction buried
92.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1854.8Ų
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
574.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)