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
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
10.2 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.88, Jaccard 0.74, H-bond role recall 0.50
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.233 kcal/mol/HA)
✓ Good fit quality (FQ -10.71)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (10.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-27.130
kcal/mol
LE
-1.233
kcal/mol/HA
Fit Quality
-10.71
FQ (Leeson)
HAC
22
heavy atoms
MW
288
Da
LogP
2.66
cLogP
Interaction summary
HB 11
HY 7
PI 3
CLASH 10
Interaction summary
HB 11
HY 7
PI 3
CLASH 10
| Final rank | 3.619 | Score | -27.130 |
|---|---|---|---|
| Inter norm | -1.258 | Intra norm | 0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
ARG46
ASP13
ASP48
CYS72
GLY73
GLY77
HIS14
ILE15
SER74
TYR49
VAL47
| ||
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 | 0.74 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 5 | HB role recall | 0.50 |
| HB same residue | 5 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 91 | 3.6194887458232743 | -1.25823 | -27.1304 | 11 | 17 | 14 | 0.88 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.130kcal/mol
Ligand efficiency (LE)
-1.2332kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.707
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
288.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-74.23kcal/mol
Minimised FF energy
-84.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
525.9Ų
Total solvent-accessible surface area of free ligand
BSA total
431.8Ų
Buried surface area upon binding
BSA apolar
346.7Ų
Hydrophobic contacts buried
BSA polar
85.1Ų
Polar contacts buried
Fraction buried
82.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2132.4Ų
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
762.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)