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 medium
Native strong
SASA missing
Strain ΔE
28.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.386 kcal/mol/HA)
✓ Good fit quality (FQ -3.86)
✓ Strong H-bond network (7 bonds)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-13.115
kcal/mol
LE
-0.386
kcal/mol/HA
Fit Quality
-3.86
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
2.49
cLogP
Interaction summary
HB 7
HY 24
PI 4
CLASH 3
Interaction summary
HB 7
HY 24
PI 4
CLASH 3
| Final rank | 12.665 | Score | -13.115 |
|---|---|---|---|
| Inter norm | -0.745 | Intra norm | 0.359 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 13 clashes; 3 protein clashes; high strain Δ 55.9 | ||
| Residues |
ALA10
ARG29
ARG71
ASN65
GLN36
ILE61
ILE8
LEU23
LEU28
LEU68
NAP201
PHE32
PHE35
PRO27
PRO62
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 | 0.64 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2295 | 7.976746292991412 | -0.852377 | -23.2574 | 6 | 18 | 13 | 0.62 | 0.20 | - | no | Open |
| 1362 | 8.925522591017504 | -0.725312 | -13.8606 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2299 | 8.398711716189771 | -0.733632 | -22.0466 | 4 | 19 | 15 | 0.71 | 0.40 | - | yes | Open |
| 1366 | 8.933675757609002 | -0.536391 | -15.3595 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2296 | 9.734976409270487 | -0.716884 | -16.4554 | 11 | 16 | 7 | 0.33 | 0.20 | - | yes | Open |
| 2297 | 10.10781661221859 | -0.717401 | -14.2679 | 8 | 19 | 17 | 0.81 | 0.40 | - | yes | Open |
| 2298 | 10.311950229167655 | -0.850057 | -27.0355 | 9 | 19 | 13 | 0.62 | 0.40 | - | yes | Open |
| 1361 | 10.427132919773856 | -0.638504 | -14.8085 | 13 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1363 | 10.479627098128667 | -0.669641 | -11.0816 | 13 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1360 | 10.700916255850332 | -0.751369 | -12.0227 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1365 | 11.751986784324188 | -0.851626 | -25.6904 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2294 | 12.001658807484736 | -0.784603 | -16.9086 | 8 | 18 | 8 | 0.38 | 0.40 | - | yes | Open |
| 1364 | 12.51440994390064 | -0.569733 | -8.23056 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2293 | 12.665368397165075 | -0.744692 | -13.1149 | 7 | 20 | 16 | 0.76 | 0.60 | - | yes | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-13.115kcal/mol
Ligand efficiency (LE)
-0.3857kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.860
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.45kcal/mol
Minimised FF energy
69.28kcal/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.