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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.606 kcal/mol/HA)
✓ Good fit quality (FQ -5.85)
✓ Good H-bonds (3 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (13)
Score
-18.189
kcal/mol
LE
-0.606
kcal/mol/HA
Fit Quality
-5.85
FQ (Leeson)
HAC
30
heavy atoms
MW
423
Da
LogP
3.86
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
| Final rank | 1.598 | Score | -18.189 |
|---|---|---|---|
| Inter norm | -0.710 | Intra norm | 0.103 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 5 protein contact clashes; moderate strain Δ 24.5 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
GLY50
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.53 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 464 | 0.4451516956311664 | -1.02208 | -26.2076 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 488 | 0.6322481432378098 | -1.09663 | -30.4758 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 522 | 1.5979843433875394 | -0.709612 | -18.1885 | 3 | 16 | 10 | 0.77 | - | - | no | Current |
| 497 | 3.4551430426968652 | -0.714979 | -22.6991 | 5 | 11 | 0 | 0.00 | - | - | no | Open |
| 509 | 4.137784089387699 | -0.990097 | -31.83 | 7 | 16 | 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
-18.189kcal/mol
Ligand efficiency (LE)
-0.6063kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.848
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
422.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.01kcal/mol
Minimised FF energy
54.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
668.6Ų
Total solvent-accessible surface area of free ligand
BSA total
477.1Ų
Buried surface area upon binding
BSA apolar
359.0Ų
Hydrophobic contacts buried
BSA polar
118.1Ų
Polar contacts buried
Fraction buried
71.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3117.7Ų
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
1475.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)