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 strong
SASA done
Strain ΔE
29.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.70
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.704 kcal/mol/HA)
✓ Good fit quality (FQ -7.10)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (29.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-24.648
kcal/mol
LE
-0.704
kcal/mol/HA
Fit Quality
-7.10
FQ (Leeson)
HAC
35
heavy atoms
MW
472
Da
LogP
1.90
cLogP
Interaction summary
HB 10
HY 15
PI 3
CLASH 3
Interaction summary
HB 10
HY 15
PI 3
CLASH 3
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 | 5.846 | Score | -24.648 |
|---|---|---|---|
| Inter norm | -0.801 | Intra norm | 0.097 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 19 clashes; 3 protein clashes; moderate strain Δ 29.7 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
SER74
TYR49
| ||
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 7 | HB role recall | 0.70 |
| HB same residue | 8 | HB residue recall | 0.80 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 329 | 5.846201648225675 | -0.801466 | -24.6479 | 10 | 18 | 15 | 0.94 | 0.70 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.648kcal/mol
Ligand efficiency (LE)
-0.7042kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.103
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
471.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.90
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
186.53kcal/mol
Minimised FF energy
156.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
747.0Ų
Total solvent-accessible surface area of free ligand
BSA total
547.9Ų
Buried surface area upon binding
BSA apolar
466.8Ų
Hydrophobic contacts buried
BSA polar
81.2Ų
Polar contacts buried
Fraction buried
73.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2310.4Ų
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
794.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)