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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
34.5 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.67, Jaccard 0.40
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.765 kcal/mol/HA)
✓ Good fit quality (FQ -7.99)
✓ Strong H-bond network (7 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (34.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (21)
Score
-30.592
kcal/mol
LE
-0.765
kcal/mol/HA
Fit Quality
-7.99
FQ (Leeson)
HAC
40
heavy atoms
MW
538
Da
LogP
5.13
cLogP
Final rank
6.2609
rank score
Inter norm
-0.803
normalised
Contacts
16
H-bonds 10
Interaction summary
HBD 3
HBA 4
HY 5
PI 0
CLASH 7
Interaction summary
HBD 3
HBA 4
HY 5
PI 0
CLASH 7
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 8 | Native recall | 0.67 |
| Jaccard | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 34 | 2.037464332345491 | -0.816862 | -31.8466 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 25 | 2.378437056644811 | -0.79296 | -25.1786 | 11 | 20 | 0 | 0.00 | - | - | no | Open |
| 28 | 3.1939535201530846 | -0.720039 | -24.3367 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 12 | 3.2679598625087527 | -0.927293 | -34.1568 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 20 | 3.495100387591973 | -0.687709 | -25.9631 | 8 | 13 | 0 | 0.00 | - | - | no | Open |
| 26 | 3.6318101855931193 | -0.794213 | -29.5742 | 8 | 21 | 1 | 0.08 | - | - | no | Open |
| 25 | 3.6473712664434346 | -0.864399 | -31.0091 | 12 | 17 | 0 | 0.00 | - | - | no | Open |
| 11 | 3.756350175949824 | -0.818637 | -30.0821 | 11 | 18 | 0 | 0.00 | - | - | no | Open |
| 36 | 4.328059027755822 | -0.664103 | -25.5651 | 8 | 12 | 0 | 0.00 | - | - | no | Open |
| 13 | 4.367243655754057 | -0.718582 | -25.2048 | 10 | 15 | 0 | 0.00 | - | - | no | Open |
| 30 | 4.3947619074725255 | -0.797581 | -32.0325 | 7 | 21 | 0 | 0.00 | - | - | no | Open |
| 27 | 4.675590440132758 | -0.575435 | -21.4762 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 18 | 4.709489958919522 | -0.661154 | -21.8688 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 26 | 4.853888287172083 | -0.702973 | -26.167 | 8 | 19 | 0 | 0.00 | - | - | no | Open |
| 25 | 5.0046255959625645 | -0.602508 | -21.2208 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 20 | 5.305300875417073 | -0.744562 | -26.4698 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 17 | 5.662829045447725 | -0.771959 | -29.8084 | 10 | 17 | 0 | 0.00 | - | - | no | Open |
| 12 | 6.260876601403174 | -0.803018 | -30.5918 | 10 | 16 | 8 | 0.67 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.592kcal/mol
Ligand efficiency (LE)
-0.7648kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.987
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.13
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
149.43kcal/mol
Minimised FF energy
114.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
730.1Ų
Total solvent-accessible surface area of free ligand
BSA total
471.4Ų
Buried surface area upon binding
BSA apolar
345.1Ų
Hydrophobic contacts buried
BSA polar
126.3Ų
Polar contacts buried
Fraction buried
64.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3083.3Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1499.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)