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
Reject
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA missing
Strain ΔE
48.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.20
Reason: strain 48.7 kcal/mol
strain ΔE 48.7 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.558 kcal/mol/HA)
✓ Good fit quality (FQ -5.58)
✓ Good H-bonds (3 bonds)
✗ Extreme strain energy (48.7 kcal/mol)
✗ Geometry warnings
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-18.974
kcal/mol
LE
-0.558
kcal/mol/HA
Fit Quality
-5.58
FQ (Leeson)
HAC
34
heavy atoms
MW
514
Da
LogP
2.43
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 3
Interaction summary
HB 3
HY 24
PI 2
CLASH 3
| Final rank | 10.812 | Score | -18.974 |
|---|---|---|---|
| Inter norm | -0.663 | Intra norm | 0.104 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 1 protein clash; high strain Δ 61.1 | ||
| Residues |
ALA10
ARG29
ASN65
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
TRP25
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: permissive.
| 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 | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3206 | 4.948815307706374 | -0.684734 | -23.3162 | 1 | 18 | 17 | 0.81 | 0.00 | - | no | Open |
| 3703 | 5.418972328285989 | -0.620116 | -19.2603 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2378 | 8.222562756337524 | -0.79336 | -24.4281 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3702 | 7.61940434743973 | -0.745467 | -24.4793 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2376 | 8.192807940647587 | -0.845605 | -25.0189 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2379 | 10.032734323736642 | -0.838117 | -20.277 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3207 | 10.811693932797503 | -0.662537 | -18.9743 | 1 | 15 | 11 | 0.52 | 0.20 | - | yes | Current |
| 3704 | 11.093703929308662 | -0.700711 | -22.7493 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3205 | 11.162627935924707 | -0.691385 | -18.3515 | 4 | 19 | 15 | 0.71 | 0.00 | - | yes | Open |
| 3701 | 59.59594328498775 | -0.634484 | -20.5254 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3204 | 60.01081702260929 | -0.798969 | -26.4833 | 1 | 19 | 18 | 0.86 | 0.00 | - | yes | Open |
| 2377 | 62.61832617806778 | -0.717906 | -21.9928 | 12 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.974kcal/mol
Ligand efficiency (LE)
-0.5581kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.584
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
513.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.32kcal/mol
Minimised FF energy
-0.41kcal/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.