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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
30.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (14/25 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 (-0.624 kcal/mol/HA)
✓ Good fit quality (FQ -6.30)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (30.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-21.851
kcal/mol
LE
-0.624
kcal/mol/HA
Fit Quality
-6.30
FQ (Leeson)
HAC
35
heavy atoms
MW
512
Da
LogP
4.13
cLogP
Interaction summary
HB 8
HY 14
PI 2
CLASH 2
⚠ Exposure 56%
Interaction summary
HB 8
HY 14
PI 2
CLASH 2
⚠ Exposure 56%
Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (14/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 11
Exposed 14
LogP 4.13
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.720 | Score | -21.851 |
|---|---|---|---|
| Inter norm | -0.674 | Intra norm | 0.050 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; high strain Δ 30.2 | ||
| Residues |
ALA365
ARG228
ARG331
CYS375
GLY229
GLY376
HIS428
ILE378
LEU332
LEU334
LEU377
MET333
PHE198
PHE230
SER364
THR374
VAL362
VAL366
| ||
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
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 | 12 | Native recall | 1.00 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 403 | 1.8056888399198356 | -0.719953 | -20.1535 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 2.1013551352678435 | -0.777468 | -25.9952 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 4.183505542941841 | -0.585981 | -16.2516 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 4.720481022983788 | -0.674248 | -21.8514 | 8 | 18 | 12 | 1.00 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.851kcal/mol
Ligand efficiency (LE)
-0.6243kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.297
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
512.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.11kcal/mol
Minimised FF energy
-3.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
782.2Ų
Total solvent-accessible surface area of free ligand
BSA total
570.0Ų
Buried surface area upon binding
BSA apolar
410.2Ų
Hydrophobic contacts buried
BSA polar
159.8Ų
Polar contacts buried
Fraction buried
72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6528.4Ų
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
2151.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)