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
17.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.42, Jaccard 0.26
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.765 kcal/mol/HA)
✓ Good fit quality (FQ -7.38)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.940
kcal/mol
LE
-0.765
kcal/mol/HA
Fit Quality
-7.38
FQ (Leeson)
HAC
30
heavy atoms
MW
410
Da
LogP
4.14
cLogP
Interaction summary
HB 7
HY 18
PI 0
CLASH 2
Interaction summary
HB 7
HY 18
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.650 | Score | -22.940 |
|---|---|---|---|
| Inter norm | -0.802 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
LYS93
PRO187
PRO212
PRO213
TRP92
VAL88
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 5 | Native recall | 0.42 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 328 | 1.335472556434909 | -0.869741 | -22.1507 | 6 | 21 | 0 | 0.00 | - | - | no | Open |
| 314 | 1.6238841746355366 | -1.05294 | -27.7493 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 248 | 1.931387223919564 | -0.842261 | -21.7943 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 278 | 2.3547857195395823 | -0.830967 | -19.5975 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 192 | 2.6379962648860182 | -0.981534 | -26.8051 | 9 | 17 | 0 | 0.00 | - | - | no | Open |
| 358 | 2.6496229478126923 | -0.801915 | -22.94 | 7 | 12 | 5 | 0.42 | - | - | no | Current |
| 216 | 3.8647520879309516 | -1.0093 | -26.7027 | 11 | 19 | 0 | 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
-22.940kcal/mol
Ligand efficiency (LE)
-0.7647kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.376
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.14
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.00kcal/mol
Minimised FF energy
49.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
686.4Ų
Total solvent-accessible surface area of free ligand
BSA total
489.7Ų
Buried surface area upon binding
BSA apolar
403.9Ų
Hydrophobic contacts buried
BSA polar
85.8Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3180.0Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1472.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)