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
26.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.65
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.371 kcal/mol/HA)
✓ Good fit quality (FQ -3.90)
✓ Good H-bonds (3 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ High strain energy (26.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (22)
Score
-15.223
kcal/mol
LE
-0.371
kcal/mol/HA
Fit Quality
-3.90
FQ (Leeson)
HAC
41
heavy atoms
MW
541
Da
LogP
5.65
cLogP
Interaction summary
HB 3
HY 24
PI 3
CLASH 1
Interaction summary
HB 3
HY 24
PI 3
CLASH 1
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
| Final rank | 2.195 | Score | -15.223 |
|---|---|---|---|
| Inter norm | -0.507 | Intra norm | 0.136 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 22 clashes; 2 protein contact clashes; moderate strain Δ 26.4 | ||
| Residues |
ASP116
CYS52
GLU18
GLY112
ILE339
LEU17
MET113
PRO336
SER109
SER14
THR117
THR335
TRP21
TYR110
VAL58
| ||
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.65 | 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 | 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
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 | 0 | 0.00 | - | - | 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 | 11 | 0.85 | - | - | no | Current |
| 47 | 3.552709512306892 | -0.563454 | -18.4579 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 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
-15.223kcal/mol
Ligand efficiency (LE)
-0.3713kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.901
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)
26.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.61kcal/mol
Minimised FF energy
80.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
871.0Ų
Total solvent-accessible surface area of free ligand
BSA total
529.4Ų
Buried surface area upon binding
BSA apolar
491.1Ų
Hydrophobic contacts buried
BSA polar
38.3Ų
Polar contacts buried
Fraction buried
60.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3336.5Ų
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
1527.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)