Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
45.6 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.81, Jaccard 0.61, H-bond role recall 0.64
Reason: 11 protein-contact clashes, 11 internal clashes, strain 45.6 kcal/mol
strain ΔE 45.6 kcal/mol
11 protein-contact clashes
11 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.727 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (45.6 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (19)
✗ Many internal clashes (22)
Score
-28.362
kcal/mol
LE
-0.727
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
39
heavy atoms
MW
544
Da
LogP
0.00
cLogP
Interaction summary
HB 16
HY 10
PI 1
CLASH 11
Interaction summary
HB 16
HY 10
PI 1
CLASH 11
| Final rank | 4.544 | Score | -28.362 |
|---|---|---|---|
| Inter norm | -0.794 | Intra norm | 0.065 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 16 |
| Artifact reason | geometry warning; 22 clashes; 19 protein contact clashes; high strain Δ 41.6 | ||
| Residues |
ALA24
ALA40
ASN126
ASN41
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE29
ILE46
LEU130
LEU31
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 9 | Strict recall | 0.60 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 501 | 4.259353633259846 | -0.672638 | -29.6878 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 4.543875081931204 | -0.79425 | -28.3621 | 16 | 24 | 17 | 0.81 | 0.64 | - | no | Current |
| 440 | 5.2996161546053635 | -0.975202 | -38.9957 | 16 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 469 | 6.678919219716884 | -0.621114 | -21.645 | 8 | 15 | 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
-28.362kcal/mol
Ligand efficiency (LE)
-0.7272kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.547
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
543.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.00
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
45.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
156.74kcal/mol
Minimised FF energy
111.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.4Ų
Total solvent-accessible surface area of free ligand
BSA total
665.6Ų
Buried surface area upon binding
BSA apolar
463.8Ų
Hydrophobic contacts buried
BSA polar
201.8Ų
Polar contacts buried
Fraction buried
87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1412.5Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
514.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)