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
84.4 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.83, Jaccard 0.62
Reason: 18 internal clashes, strain 84.4 kcal/mol
strain ΔE 84.4 kcal/mol
18 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Acceptable LE (-0.253 kcal/mol/HA)
✓ Good fit quality (FQ -2.81)
✓ Strong H-bond network (6 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ Extreme strain energy (84.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-13.173
kcal/mol
LE
-0.253
kcal/mol/HA
Fit Quality
-2.81
FQ (Leeson)
HAC
52
heavy atoms
MW
707
Da
LogP
-1.96
cLogP
Interaction summary
HB 6
HY 21
PI 0
CLASH 0
⚠ Exposure 35%
Interaction summary
HB 6
HY 21
PI 0
CLASH 0
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 40
Buried (contacted) 26
Exposed 14
LogP -1.96
H-bonds 6
Exposed fragments:
phenyl (8/12 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.890 | Score | -13.173 |
|---|---|---|---|
| Inter norm | -0.512 | Intra norm | 0.259 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; high raw intra; high strain Δ 84.3 | ||
| Residues |
ALA209
ALA90
ARG74
LEU73
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
SER86
SER87
TYR210
VAL88
| ||
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
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 78 | 1.9477987273075534 | -0.613897 | -22.6904 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 90 | 2.0174935328161827 | -0.500364 | -20.9277 | 5 | 21 | 0 | 0.00 | - | - | no | Open |
| 109 | 2.297692817419667 | -0.691616 | -29.5067 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 81 | 3.0444813778977284 | -0.598468 | -25.8901 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 75 | 3.1272769283568476 | -0.501173 | -13.329 | 4 | 20 | 0 | 0.00 | - | - | no | Open |
| 109 | 3.426055917331537 | -0.363483 | -18.9274 | 4 | 12 | 0 | 0.00 | - | - | no | Open |
| 109 | 3.59237430105183 | -0.558946 | -19.384 | 3 | 20 | 0 | 0.00 | - | - | no | Open |
| 67 | 3.8897517609389602 | -0.512355 | -13.1727 | 6 | 14 | 10 | 0.83 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-13.173kcal/mol
Ligand efficiency (LE)
-0.2533kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-2.806
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
52HA
Physicochemical properties
Molecular weight
707.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.96
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
84.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
531.06kcal/mol
Minimised FF energy
446.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1118.2Ų
Total solvent-accessible surface area of free ligand
BSA total
556.8Ų
Buried surface area upon binding
BSA apolar
520.5Ų
Hydrophobic contacts buried
BSA polar
36.4Ų
Polar contacts buried
Fraction buried
49.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3642.6Ų
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
1510.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)