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
27.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.83, Jaccard 0.62, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.910 kcal/mol/HA)
✓ Good fit quality (FQ -8.16)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (27.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-21.849
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-8.16
FQ (Leeson)
HAC
24
heavy atoms
MW
326
Da
LogP
1.84
cLogP
Interaction summary
HB 5
HY 22
PI 1
CLASH 3
Interaction summary
HB 5
HY 22
PI 1
CLASH 3
| Final rank | 4.188 | Score | -21.849 |
|---|---|---|---|
| Inter norm | -0.927 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 27.3 | ||
| Residues |
ALA365
ARG287
ARG331
ASP330
FAD501
GLY286
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 75 | 0.16084146293609375 | -1.54266 | -37.9275 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 0.534011300296592 | -1.62761 | -39.9852 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 1.790669485822701 | -0.992095 | -25.0548 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 57 | 2.235783854112483 | -1.10127 | -26.7452 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 2.264426210652542 | -1.14753 | -26.7069 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 2.461124243424092 | -1.0791 | -26.1127 | 8 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 71 | 3.1609815421158878 | -0.849646 | -20.0782 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 4.187711712922683 | -0.927428 | -21.8492 | 5 | 14 | 10 | 0.83 | 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
-21.849kcal/mol
Ligand efficiency (LE)
-0.9104kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.159
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.84
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-16.23kcal/mol
Minimised FF energy
-43.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.8Ų
Total solvent-accessible surface area of free ligand
BSA total
447.6Ų
Buried surface area upon binding
BSA apolar
377.0Ų
Hydrophobic contacts buried
BSA polar
70.6Ų
Polar contacts buried
Fraction buried
77.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6493.6Ų
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
2074.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)