Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA missing
Strain ΔE
26.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.465 kcal/mol/HA)
✓ Good fit quality (FQ -4.85)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-18.584
kcal/mol
LE
-0.465
kcal/mol/HA
Fit Quality
-4.85
FQ (Leeson)
HAC
40
heavy atoms
MW
536
Da
LogP
4.73
cLogP
Interaction summary
HB 8
HY 14
PI 2
CLASH 1
Interaction summary
HB 8
HY 14
PI 2
CLASH 1
| Final rank | 9.715 | Score | -18.584 |
|---|---|---|---|
| Inter norm | -0.589 | Intra norm | 0.124 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 20 clashes; 2 protein clashes; high strain Δ 27.5 | ||
| Residues |
ALA10
ARG29
ASN65
ASP22
GLN36
GLY21
ILE61
ILE8
LEU23
NAP201
PHE32
PHE35
PRO27
SER60
THR57
TYR122
VAL116
VAL9
| ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 4 | Strict recall | 0.80 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3215 | 8.793967062661496 | -0.657735 | -25.6467 | 4 | 23 | 19 | 0.90 | 0.40 | - | no | Open |
| 3214 | 9.715144768158227 | -0.588711 | -18.5839 | 8 | 18 | 16 | 0.76 | 0.80 | - | yes | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.584kcal/mol
Ligand efficiency (LE)
-0.4646kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.852
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
535.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.73
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.26kcal/mol
Minimised FF energy
70.65kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.