Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
24.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.25
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 (-0.614 kcal/mol/HA)
✓ Good fit quality (FQ -6.19)
✓ Good H-bonds (5 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-21.492
kcal/mol
LE
-0.614
kcal/mol/HA
Fit Quality
-6.19
FQ (Leeson)
HAC
35
heavy atoms
MW
484
Da
LogP
5.23
cLogP
Interaction summary
HB 5
HY 17
PI 0
CLASH 3
Interaction summary
HB 5
HY 17
PI 0
CLASH 3
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 | 3.114 | Score | -21.492 |
|---|---|---|---|
| Inter norm | -0.662 | Intra norm | 0.048 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; moderate strain Δ 24.6 | ||
| Residues |
ALA209
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
LYS93
MET70
PRO187
PRO212
PRO213
TRP92
| ||
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 | 0.25 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 415 | 1.5938133996310813 | -0.665402 | -21.432 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 428 | 2.4464746181095354 | -0.842361 | -29.7104 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 474 | 3.113919791182743 | -0.6619 | -21.4925 | 5 | 13 | 5 | 0.42 | - | - | no | Current |
| 407 | 4.078275200580851 | -0.611683 | -22.9727 | 4 | 10 | 0 | 0.00 | - | - | no | Open |
| 382 | 4.463328460122904 | -0.916375 | -30.2807 | 9 | 20 | 0 | 0.00 | - | - | no | Open |
| 376 | 5.640170233863105 | -0.842318 | -22.9166 | 9 | 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
-21.492kcal/mol
Ligand efficiency (LE)
-0.6141kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.194
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
483.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.23
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-30.60kcal/mol
Minimised FF energy
-55.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
806.6Ų
Total solvent-accessible surface area of free ligand
BSA total
484.9Ų
Buried surface area upon binding
BSA apolar
386.1Ų
Hydrophobic contacts buried
BSA polar
98.7Ų
Polar contacts buried
Fraction buried
60.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3238.1Ų
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
1512.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)