Molecular metrics status: missing
Molecular metrics have not been computed yet for this pose.
No cached metrics
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
Metrics pending
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA pending
Strain ΔE
34.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.43, Jaccard 0.35, H-bond role recall 0.36
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (7/7 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Interaction summary
HB 15
HY 0
PI 0
CLASH 6
⚠ Exposure 100%
Interaction summary
HB 15
HY 0
PI 0
CLASH 6
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (7/7 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 7
Buried (contacted) 0
Exposed 7
LogP 0.3
H-bonds 15
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.877 | Score | -31.099 |
|---|---|---|---|
| Inter norm | -2.218 | Intra norm | -0.003 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 15 |
| Artifact reason | excluded; geometry warning; 5 clashes; 5 protein clashes; high strain Δ 34.2 | ||
| Residues |
ALA24
ALA70
ASP68
GLN42
GLU73
GLY23
GLY25
GLY71
LYS26
SER22
SER27
SER28
THR44
THR69
| ||
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 9 | Native recall | 0.43 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 245 | 4.876545490828688 | -2.2181 | -31.0988 | 15 | 14 | 9 | 0.43 | 0.36 | - | yes | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.