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
52.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.88, H-bond role recall 0.60
Reason: strain 52.7 kcal/mol
strain ΔE 52.7 kcal/mol
1 protein-contact clashes
62% of hydrophobic surface is solvent-exposed (10/16 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.138 kcal/mol/HA)
✓ Good fit quality (FQ -10.48)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Extreme strain energy (52.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-29.589
kcal/mol
LE
-1.138
kcal/mol/HA
Fit Quality
-10.48
FQ (Leeson)
HAC
26
heavy atoms
MW
378
Da
LogP
0.79
cLogP
Interaction summary
HB 14
HY 3
PI 3
CLASH 1
⚠ Exposure 62%
Interaction summary
HB 14
HY 3
PI 3
CLASH 1
⚠ Exposure 62%
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (10/16 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 16
Buried (contacted) 6
Exposed 10
LogP 0.79
H-bonds 14
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.180 | Score | -29.589 |
|---|---|---|---|
| Inter norm | -1.147 | Intra norm | 0.009 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; high strain Δ 52.5 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
SER74
TYR49
| ||
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 14 | Native recall | 0.88 |
| Jaccard | 0.88 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 538 | 1.6890420589433734 | -0.876062 | -18.5492 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 1.7455832875701298 | -1.04513 | -22.1499 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 1.7724214234298203 | -1.01549 | -23.1894 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 1.7783840791674765 | -1.0041 | -24.7592 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 2.1801023352322155 | -1.14702 | -29.589 | 14 | 14 | 14 | 0.88 | 0.60 | - | no | Current |
| 578 | 2.2950088551183443 | -0.939152 | -19.4559 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 572 | 2.4866872836960074 | -1.07884 | -24.8429 | 11 | 15 | 1 | 0.06 | 0.10 | - | no | Open |
| 573 | 3.847742802334122 | -0.869936 | -20.868 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 564 | 4.090578712367698 | -0.991863 | -19.9768 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 4.424815777537417 | -0.904088 | -20.6734 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 4.437704091940646 | -1.08851 | -28.813 | 14 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 4.53216170732747 | -1.11454 | -27.9889 | 13 | 18 | 5 | 0.31 | 0.30 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.589kcal/mol
Ligand efficiency (LE)
-1.1380kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.485
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
378.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.79
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
52.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
145.25kcal/mol
Minimised FF energy
92.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.9Ų
Total solvent-accessible surface area of free ligand
BSA total
437.6Ų
Buried surface area upon binding
BSA apolar
283.7Ų
Hydrophobic contacts buried
BSA polar
154.0Ų
Polar contacts buried
Fraction buried
67.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2131.9Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
765.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)