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 high
Native mixed
SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.25, Jaccard 0.12, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.713 kcal/mol/HA)
✓ Good fit quality (FQ -6.57)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ High strain energy (22.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-18.545
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-6.57
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
2.33
cLogP
Interaction summary
HB 6
HY 12
PI 1
CLASH 1
Interaction summary
HB 6
HY 12
PI 1
CLASH 1
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
| Final rank | 4.332 | Score | -18.545 |
|---|---|---|---|
| Inter norm | -0.886 | Intra norm | 0.165 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 22.8 | ||
| Residues |
ALA284
ARG228
ARG287
ASN223
ASP330
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
MET333
PHE198
TYR221
| ||
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 | 3 | Native recall | 0.25 |
| Jaccard | 0.12 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 132 | 0.6034787560662435 | -0.986253 | -17.9228 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 138 | 1.4476132232114785 | -1.32116 | -31.3906 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 1.8348160871656356 | -1.07441 | -21.076 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 3.5037539024917495 | -1.26397 | -32.0923 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 61 | 3.9546360904873596 | -0.94287 | -20.9441 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 123 | 4.331751406084817 | -0.886047 | -18.545 | 6 | 15 | 3 | 0.25 | 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
-18.545kcal/mol
Ligand efficiency (LE)
-0.7133kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.572
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-55.66kcal/mol
Minimised FF energy
-78.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
608.9Ų
Total solvent-accessible surface area of free ligand
BSA total
458.9Ų
Buried surface area upon binding
BSA apolar
312.7Ų
Hydrophobic contacts buried
BSA polar
146.2Ų
Polar contacts buried
Fraction buried
75.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6405.2Ų
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
2100.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)