Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
45.2 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.56
Reason: 7 internal clashes, strain 45.2 kcal/mol
strain ΔE 45.2 kcal/mol
7 protein-contact clashes
7 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.557 kcal/mol/HA)
✓ Good fit quality (FQ -5.92)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Extreme strain energy (45.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (21)
Score
-23.939
kcal/mol
LE
-0.557
kcal/mol/HA
Fit Quality
-5.92
FQ (Leeson)
HAC
43
heavy atoms
MW
654
Da
LogP
7.33
cLogP
Interaction summary
HB 6
HY 10
PI 5
CLASH 7
Interaction summary
HB 6
HY 10
PI 5
CLASH 7
| Final rank | 4.441 | Score | -23.939 |
|---|---|---|---|
| Inter norm | -0.647 | Intra norm | 0.090 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 21 clashes; 1 protein clash; high strain Δ 45.1 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 14 | Native recall | 1.00 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 26 | 2.1688970873774895 | -0.58667 | -27.5364 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 2.3190570076294623 | -0.603254 | -21.9181 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 2.872325018187148 | -0.635792 | -24.439 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.3402080092915787 | -0.686468 | -26.5185 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.9691236791986175 | -0.521697 | -21.5427 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 4.4414998865683915 | -0.646675 | -23.9393 | 6 | 18 | 14 | 1.00 | 0.56 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.939kcal/mol
Ligand efficiency (LE)
-0.5567kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.917
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
654.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.33
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
45.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
295.70kcal/mol
Minimised FF energy
250.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
796.4Ų
Total solvent-accessible surface area of free ligand
BSA total
548.0Ų
Buried surface area upon binding
BSA apolar
499.1Ų
Hydrophobic contacts buried
BSA polar
48.9Ų
Polar contacts buried
Fraction buried
68.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2367.2Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
862.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)