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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
17.3 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.75, Jaccard 0.36, H-bond role recall 0.00
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.708 kcal/mol/HA)
✓ Good fit quality (FQ -6.61)
✓ Good H-bonds (4 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Moderate strain (17.3 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Internal clashes (9)
Score
-19.122
kcal/mol
LE
-0.708
kcal/mol/HA
Fit Quality
-6.61
FQ (Leeson)
HAC
27
heavy atoms
MW
426
Da
LogP
3.34
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 10
Interaction summary
HB 4
HY 24
PI 2
CLASH 10
| Final rank | 1.871 | Score | -19.122 |
|---|---|---|---|
| Inter norm | -0.825 | Intra norm | 0.116 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 10 protein contact clashes | ||
| Residues |
ALA363
ALA365
ARG287
ARG331
ASP330
FAD501
GLU202
GLY286
ILE199
LEU332
LEU334
LYS60
MET333
PHE198
PHE230
PHE367
PRO336
SER364
VAL366
GLY459
HIS461
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 | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 112 | 1.0237228161835357 | -0.921618 | -20.3586 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 112 | 1.1484773859344817 | -0.881947 | -22.294 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 1.5906811673286758 | -1.13802 | -30.2193 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 1.7368687972028278 | -0.939455 | -24.4564 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 1.8705548783515578 | -0.824677 | -19.122 | 4 | 22 | 9 | 0.75 | 0.00 | - | no | Current |
| 111 | 1.9567266273999773 | -0.941489 | -19.4943 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 148 | 2.1545192277817584 | -0.83535 | -23.2836 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 134 | 2.3450479455114124 | -0.937703 | -23.0809 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 2.657445309836105 | -1.16369 | -27.7545 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 2.796280609468839 | -1.05791 | -24.8275 | 7 | 12 | 0 | 0.00 | 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
-19.122kcal/mol
Ligand efficiency (LE)
-0.7082kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.607
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
426.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.34
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
9.73kcal/mol
Minimised FF energy
-7.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
668.0Ų
Total solvent-accessible surface area of free ligand
BSA total
581.4Ų
Buried surface area upon binding
BSA apolar
533.5Ų
Hydrophobic contacts buried
BSA polar
47.9Ų
Polar contacts buried
Fraction buried
87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6599.5Ų
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
2075.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)