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 medium
Native strong
SASA done
Strain ΔE
26.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.35
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 (-0.686 kcal/mol/HA)
✓ Good fit quality (FQ -6.68)
✓ Good H-bonds (5 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (26.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.270
kcal/mol
LE
-0.686
kcal/mol/HA
Fit Quality
-6.68
FQ (Leeson)
HAC
31
heavy atoms
MW
469
Da
LogP
6.28
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 3
Interaction summary
HB 5
HY 24
PI 1
CLASH 3
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 | 3.155 | Score | -21.270 |
|---|---|---|---|
| Inter norm | -0.719 | Intra norm | 0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 26.2 | ||
| Residues |
CYS52
CYS57
FAD501
GLU18
GLY13
ILE106
ILE339
LEU17
LYS60
LYS61
PHE367
PRO336
SER14
THR335
TRP21
TYR110
VAL53
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 594 | 1.3410706819170013 | -1.07491 | -32.7142 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 592 | 2.522743900294449 | -0.986254 | -30.4983 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 610 | 3.1552936204718893 | -0.718939 | -21.2695 | 5 | 18 | 8 | 0.62 | - | - | no | Current |
| 592 | 3.563539399678035 | -0.923231 | -29.0561 | 9 | 16 | 0 | 0.00 | - | - | no | Open |
| 605 | 3.7722593377195173 | -0.721287 | -21.7618 | 2 | 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
-21.270kcal/mol
Ligand efficiency (LE)
-0.6861kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.684
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
469.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.28
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.30kcal/mol
Minimised FF energy
70.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
730.5Ų
Total solvent-accessible surface area of free ligand
BSA total
506.7Ų
Buried surface area upon binding
BSA apolar
421.1Ų
Hydrophobic contacts buried
BSA polar
85.5Ų
Polar contacts buried
Fraction buried
69.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3183.2Ų
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
1512.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)