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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
108.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.83, Jaccard 0.40, H-bond role recall 0.00
Reason: strain 108.1 kcal/mol
strain ΔE 108.1 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (15/35 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.
✓ Good LE (-0.372 kcal/mol/HA)
✓ Good fit quality (FQ -3.97)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Extreme strain energy (108.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-16.359
kcal/mol
LE
-0.372
kcal/mol/HA
Fit Quality
-3.97
FQ (Leeson)
HAC
44
heavy atoms
MW
611
Da
LogP
-1.02
cLogP
Interaction summary
HB 8
HY 20
PI 2
CLASH 3
⚠ Exposure 42%
Interaction summary
HB 8
HY 20
PI 2
CLASH 3
⚠ Exposure 42%
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
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (15/35 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 35
Buried (contacted) 20
Exposed 15
LogP -1.02
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/4 atoms exposed)aliphatic chain/group (8 atoms exposed)
| Final rank | 5.271 | Score | -16.359 |
|---|---|---|---|
| Inter norm | -0.627 | Intra norm | 0.255 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; high strain Δ 108.0 | ||
| Residues |
ALA363
ALA365
ARG228
ARG361
CYS375
GLY197
GLY229
GLY286
GLY376
HIS359
HIS428
ILE285
LEU332
LEU334
LEU377
PHE198
PHE230
SER364
THR360
THR374
TYR221
VAL362
VAL366
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 10 | Native recall | 0.83 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 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 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 46 | 2.642224434708217 | -0.660802 | -27.1569 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 58 | 2.7881870811272145 | -0.63853 | -22.0415 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 2.8625249427168207 | -0.578951 | -22.2374 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 57 | 3.2584713736816546 | -0.57743 | -22.1226 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 56 | 5.270747018926702 | -0.627435 | -16.3586 | 8 | 23 | 10 | 0.83 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.359kcal/mol
Ligand efficiency (LE)
-0.3718kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.972
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
610.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.02
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
108.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.55kcal/mol
Minimised FF energy
-27.57kcal/mol
SASA & burial
✓ computed
SASA (unbound)
951.1Ų
Total solvent-accessible surface area of free ligand
BSA total
705.9Ų
Buried surface area upon binding
BSA apolar
650.5Ų
Hydrophobic contacts buried
BSA polar
55.4Ų
Polar contacts buried
Fraction buried
74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6913.7Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2038.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)