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 mixed
SASA done
Strain ΔE
11.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.54, Jaccard 0.41
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.082 kcal/mol/HA)
✓ Good fit quality (FQ -10.21)
✓ Strong H-bond network (6 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (11.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-30.293
kcal/mol
LE
-1.082
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
28
heavy atoms
MW
395
Da
LogP
3.82
cLogP
Interaction summary
HB 6
HY 19
PI 3
CLASH 4
Interaction summary
HB 6
HY 19
PI 3
CLASH 4
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 | 3.108 | Score | -30.293 |
|---|---|---|---|
| Inter norm | -0.764 | Intra norm | -0.318 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
| ||
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.41 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 121 | 0.6480317823511264 | -1.09263 | -30.7137 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 128 | 0.704294296580414 | -0.82137 | -25.8407 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 123 | 2.0763430321148384 | -0.882629 | -31.3156 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 146 | 2.1987026073112794 | -1.06308 | -36.4462 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 91 | 2.235709846232026 | -0.978118 | -30.3416 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 102 | 2.3420725108936757 | -0.856611 | -30.5757 | 10 | 14 | 0 | 0.00 | - | - | no | Open |
| 152 | 2.882361998789424 | -1.01322 | -36.5034 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 138 | 3.107716007599668 | -0.763711 | -30.2928 | 6 | 11 | 7 | 0.54 | - | - | no | Current |
| 163 | 3.993422811367177 | -0.727878 | -30.4938 | 5 | 9 | 0 | 0.00 | - | - | no | Open |
| 100 | 4.39388549559622 | -0.956566 | -34.2918 | 15 | 18 | 0 | 0.00 | - | - | no | Open |
| 94 | 4.398591367272989 | -1.17212 | -40.5324 | 10 | 19 | 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
-30.293kcal/mol
Ligand efficiency (LE)
-1.0819kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.213
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.82
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-59.30kcal/mol
Minimised FF energy
-71.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
640.2Ų
Total solvent-accessible surface area of free ligand
BSA total
399.6Ų
Buried surface area upon binding
BSA apolar
261.9Ų
Hydrophobic contacts buried
BSA polar
137.7Ų
Polar contacts buried
Fraction buried
62.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3081.1Ų
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
1480.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)