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 strong
SASA done
Strain ΔE
19.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.38, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.912 kcal/mol/HA)
✓ Good fit quality (FQ -8.40)
✓ Good H-bonds (5 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (19.9 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (13)
Score
-23.707
kcal/mol
LE
-0.912
kcal/mol/HA
Fit Quality
-8.40
FQ (Leeson)
HAC
26
heavy atoms
MW
365
Da
LogP
2.13
cLogP
Interaction summary
HB 5
HY 19
PI 3
CLASH 2
Interaction summary
HB 5
HY 19
PI 3
CLASH 2
| Final rank | 1.465 | Score | -23.707 |
|---|---|---|---|
| Inter norm | -0.944 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 6 protein contact clashes | ||
| Residues |
ALA284
ARG228
GLY195
GLY196
GLY197
GLY229
GLY286
ILE199
ILE285
LEU227
LEU332
LEU334
PHE198
PHE230
SER364
TYR221
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 581 | 1.000264785721566 | -0.918966 | -22.4821 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 594 | 1.4646519661374353 | -0.944365 | -23.7072 | 5 | 17 | 8 | 0.67 | 0.00 | - | no | Current |
| 578 | 2.564509005169744 | -0.753638 | -20.2448 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 3.000529114437112 | -1.19895 | -30.0875 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 3.1093396187805626 | -1.14147 | -31.1887 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 3.516543969577786 | -0.922823 | -22.6476 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 3.8896490358075844 | -1.2635 | -33.1996 | 12 | 16 | 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
-23.707kcal/mol
Ligand efficiency (LE)
-0.9118kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.401
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
365.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
58.04kcal/mol
Minimised FF energy
38.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
574.7Ų
Total solvent-accessible surface area of free ligand
BSA total
473.2Ų
Buried surface area upon binding
BSA apolar
340.8Ų
Hydrophobic contacts buried
BSA polar
132.5Ų
Polar contacts buried
Fraction buried
82.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6406.3Ų
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
2060.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)