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
19.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.42
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.246 kcal/mol/HA)
✓ Good fit quality (FQ -11.76)
✓ Strong H-bond network (7 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-34.891
kcal/mol
LE
-1.246
kcal/mol/HA
Fit Quality
-11.76
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
2.60
cLogP
Interaction summary
HB 7
HY 22
PI 3
CLASH 1
Interaction summary
HB 7
HY 22
PI 3
CLASH 1
| Final rank | 2.208 | Score | -34.891 |
|---|---|---|---|
| Inter norm | -0.743 | Intra norm | -0.503 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; very favorable intra outlier | ||
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 451 | 2.2077759887268074 | -0.743449 | -34.8909 | 7 | 14 | 8 | 0.62 | - | - | no | Current |
| 400 | 4.846685112785981 | -1.12303 | -27.3764 | 15 | 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
-34.891kcal/mol
Ligand efficiency (LE)
-1.2461kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.764
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.60
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.16kcal/mol
Minimised FF energy
15.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
681.8Ų
Total solvent-accessible surface area of free ligand
BSA total
425.0Ų
Buried surface area upon binding
BSA apolar
275.6Ų
Hydrophobic contacts buried
BSA polar
149.5Ų
Polar contacts buried
Fraction buried
62.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3108.8Ų
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
1467.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)