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
31.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.47
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.450 kcal/mol/HA)
✓ Good fit quality (FQ -4.73)
✓ Good H-bonds (3 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Very high strain energy (31.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (24)
Score
-18.458
kcal/mol
LE
-0.450
kcal/mol/HA
Fit Quality
-4.73
FQ (Leeson)
HAC
41
heavy atoms
MW
541
Da
LogP
5.65
cLogP
Interaction summary
HB 3
HY 24
PI 0
CLASH 2
Interaction summary
HB 3
HY 24
PI 0
CLASH 2
| Final rank | 3.553 | Score | -18.458 |
|---|---|---|---|
| Inter norm | -0.563 | Intra norm | 0.113 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 24 clashes; 1 protein clash; high strain Δ 31.1 | ||
| Residues |
ALA209
ALA90
ARG74
ASN91
LEU73
LYS211
LYS89
LYS93
MET70
PHE83
PRO187
PRO212
PRO213
TRP92
TYR210
VAL88
| ||
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
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 77 | 2.0118570697338822 | -0.680695 | -22.2353 | 1 | 17 | 1 | 0.08 | - | - | no | Open |
| 72 | 2.042884377801323 | -0.641846 | -24.1189 | 0 | 20 | 0 | 0.00 | - | - | no | Open |
| 61 | 2.1949413175310615 | -0.507118 | -15.2226 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 47 | 3.552709512306892 | -0.563454 | -18.4579 | 3 | 16 | 9 | 0.75 | - | - | no | Current |
| 72 | 4.036056587384694 | -0.600365 | -23.7922 | 4 | 21 | 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
-18.458kcal/mol
Ligand efficiency (LE)
-0.4502kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.730
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
540.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.65
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.01kcal/mol
Minimised FF energy
76.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
851.5Ų
Total solvent-accessible surface area of free ligand
BSA total
599.5Ų
Buried surface area upon binding
BSA apolar
548.5Ų
Hydrophobic contacts buried
BSA polar
51.1Ų
Polar contacts buried
Fraction buried
70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3370.1Ų
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
1479.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)