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 strong
SASA done
Strain ΔE
26.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.42
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.786 kcal/mol/HA)
✓ Good fit quality (FQ -7.14)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (26.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-19.646
kcal/mol
LE
-0.786
kcal/mol/HA
Fit Quality
-7.14
FQ (Leeson)
HAC
25
heavy atoms
MW
404
Da
LogP
0.56
cLogP
Interaction summary
HB 4
HY 20
PI 2
CLASH 2
Interaction summary
HB 4
HY 20
PI 2
CLASH 2
| Final rank | 1.767 | Score | -19.646 |
|---|---|---|---|
| Inter norm | -0.828 | Intra norm | 0.042 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 26.7 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 501 | 1.406540502809502 | -0.776521 | -15.751 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 531 | 1.7669910686618124 | -0.828226 | -19.6464 | 4 | 14 | 8 | 0.62 | - | - | no | Current |
| 555 | 2.019091271852642 | -0.95225 | -18.4019 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 473 | 4.144549198167141 | -1.23926 | -27.7812 | 10 | 16 | 0 | 0.00 | - | - | no | Open |
| 504 | 4.245746357076541 | -1.0618 | -22.9763 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 533 | 4.7802568935273655 | -0.954752 | -21.8921 | 11 | 19 | 0 | 0.00 | - | - | no | Open |
| 487 | 6.7556041603467545 | -1.17079 | -25.4634 | 13 | 18 | 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
-19.646kcal/mol
Ligand efficiency (LE)
-0.7859kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
403.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-184.84kcal/mol
Minimised FF energy
-211.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
620.6Ų
Total solvent-accessible surface area of free ligand
BSA total
442.1Ų
Buried surface area upon binding
BSA apolar
295.5Ų
Hydrophobic contacts buried
BSA polar
146.6Ų
Polar contacts buried
Fraction buried
71.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2996.2Ų
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
1482.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)