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
35.5 kcal/mol
Protein clashes
12
Internal clashes
14
Native overlap
contact recall 0.75, Jaccard 0.36, H-bond role recall 1.00
Reason: 1 severe internal clashes, 12 protein-contact clashes, 14 internal clashes
1 severe internal clashes
12 protein-contact clashes
14 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.662 kcal/mol/HA)
✓ Good fit quality (FQ -6.25)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (35.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-18.526
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.25
FQ (Leeson)
HAC
28
heavy atoms
MW
462
Da
LogP
3.91
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 14
Severe 1
Interaction summary
HB 2
HY 24
PI 2
CLASH 14
Severe 1
| Final rank | 4.889 | Score | -18.526 |
|---|---|---|---|
| Inter norm | -0.836 | Intra norm | 0.175 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 2 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; 2 cofactor-context clashes; high strain Δ 35.5 | ||
| Residues |
ALA284
ALA365
ARG287
ARG331
FAD501
GLU202
GLY286
ILE199
ILE285
LEU332
LEU334
LYS60
MET333
PHE198
PHE230
PHE367
SER364
VAL366
HIS461
PRO462
THR463
VAL460
| ||
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.36 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 471 | 1.5395518164582227 | -0.908136 | -23.753 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 477 | 2.5964271622007544 | -0.861558 | -24.8902 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 470 | 3.628058194338564 | -1.19186 | -22.4542 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 4.711687193998053 | -1.1026 | -23.5647 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 4.889442986114997 | -0.8363 | -18.5261 | 2 | 22 | 9 | 0.75 | 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
-18.526kcal/mol
Ligand efficiency (LE)
-0.6616kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.246
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
462.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
5.20kcal/mol
Minimised FF energy
-30.32kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.2Ų
Total solvent-accessible surface area of free ligand
BSA total
606.5Ų
Buried surface area upon binding
BSA apolar
469.8Ų
Hydrophobic contacts buried
BSA polar
136.7Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6540.9Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2068.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)