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
46.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.87, H-bond role recall 0.78
Reason: strain 46.1 kcal/mol
strain ΔE 46.1 kcal/mol
2 protein-contact clashes
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.205 kcal/mol/HA)
✓ Good fit quality (FQ -10.80)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (68% SASA buried)
✗ Extreme strain energy (46.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.922
kcal/mol
LE
-1.205
kcal/mol/HA
Fit Quality
-10.80
FQ (Leeson)
HAC
24
heavy atoms
MW
371
Da
LogP
-0.09
cLogP
Interaction summary
HB 16
HY 1
PI 2
CLASH 2
⚠ Exposure 58%
Interaction summary
HB 16
HY 1
PI 2
CLASH 2
⚠ Exposure 58%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 5
Exposed 7
LogP -0.09
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.529 | Score | -28.922 |
|---|---|---|---|
| Inter norm | -1.100 | Intra norm | -0.105 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 16 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 46.1 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER71
| ||
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.87 | RMSD | - |
| HB strict | 9 | Strict recall | 0.75 |
| HB same residue+role | 7 | HB role recall | 0.78 |
| HB same residue | 6 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 292 | 1.7946739624493355 | -1.19096 | -30.682 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 1.924012194694617 | -1.22878 | -31.9908 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 371 | 2.860721822836255 | -1.13963 | -23.8328 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 2.967120976705636 | -1.02603 | -27.0223 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 321 | 3.3317421160485563 | -1.00101 | -23.3908 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 3.4743736314794007 | -0.96628 | -26.6162 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 3.529383570256196 | -1.09969 | -28.9223 | 16 | 14 | 13 | 0.93 | 0.78 | - | no | Current |
| 374 | 3.8228138562848994 | -1.15583 | -29.9842 | 8 | 15 | 0 | 0.00 | 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
-28.922kcal/mol
Ligand efficiency (LE)
-1.2051kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.800
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.09
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-15.79kcal/mol
Minimised FF energy
-61.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.2Ų
Total solvent-accessible surface area of free ligand
BSA total
395.1Ų
Buried surface area upon binding
BSA apolar
212.4Ų
Hydrophobic contacts buried
BSA polar
182.6Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
53.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2064.1Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
761.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)