Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
38.0 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.58, Jaccard 0.41
Reason: 13 internal clashes
13 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.522 kcal/mol/HA)
✓ Good fit quality (FQ -5.27)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-18.288
kcal/mol
LE
-0.522
kcal/mol/HA
Fit Quality
-5.27
FQ (Leeson)
HAC
35
heavy atoms
MW
537
Da
LogP
3.10
cLogP
Interaction summary
HB 2
HY 23
PI 0
CLASH 0
⚠ Exposure 37%
Interaction summary
HB 2
HY 23
PI 0
CLASH 0
⚠ Exposure 37%
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
CLASH · Clashes
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 17
Exposed 10
LogP 3.1
H-bonds 2
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.157 | Score | -18.288 |
|---|---|---|---|
| Inter norm | -0.654 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; high strain Δ 38.0 | ||
| Residues |
ALA209
ALA90
ASN208
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
SER86
TYR210
VAL88
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 7 | Native recall | 0.58 |
| Jaccard | 0.41 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
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:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 58 | 1.1223741488018864 | -0.801293 | -25.4071 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 45 | 1.1281698153493345 | -0.771609 | -24.2502 | 1 | 22 | 1 | 0.08 | - | - | no | Open |
| 31 | 2.1571437553685304 | -0.654367 | -18.2875 | 2 | 12 | 7 | 0.58 | - | - | no | Current |
| 42 | 2.4303185099117717 | -0.721238 | -22.4793 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 48 | 3.0872957566922725 | -0.778345 | -30.7053 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 39 | 4.7604810903429815 | -0.766988 | -27.1536 | 4 | 17 | 0 | 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
-18.288kcal/mol
Ligand efficiency (LE)
-0.5225kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.270
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
537.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.10
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
225.32kcal/mol
Minimised FF energy
187.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
774.5Ų
Total solvent-accessible surface area of free ligand
BSA total
462.4Ų
Buried surface area upon binding
BSA apolar
427.7Ų
Hydrophobic contacts buried
BSA polar
34.7Ų
Polar contacts buried
Fraction buried
59.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3263.9Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1511.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)