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
21.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.80
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.890 kcal/mol/HA)
✓ Good fit quality (FQ -8.41)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (21.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.935
kcal/mol
LE
-0.890
kcal/mol/HA
Fit Quality
-8.41
FQ (Leeson)
HAC
28
heavy atoms
MW
407
Da
LogP
1.50
cLogP
Interaction summary
HB 11
HY 11
PI 4
CLASH 4
Interaction summary
HB 11
HY 11
PI 4
CLASH 4
| Final rank | 4.498 | Score | -24.935 |
|---|---|---|---|
| Inter norm | -1.004 | Intra norm | 0.113 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; moderate strain Δ 21.9 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
CYS72
GLY73
GLY77
HIS14
ILE15
ILE76
SER74
| ||
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 | 13 | Native recall | 0.81 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 8 | HB role recall | 0.80 |
| HB same residue | 8 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 459 | 0.6501375225651361 | -1.14926 | -31.4886 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 442 | 4.498195063356032 | -1.00399 | -24.935 | 11 | 16 | 13 | 0.81 | 0.80 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.935kcal/mol
Ligand efficiency (LE)
-0.8905kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.407
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.50
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-9.80kcal/mol
Minimised FF energy
-31.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
679.7Ų
Total solvent-accessible surface area of free ligand
BSA total
499.4Ų
Buried surface area upon binding
BSA apolar
374.8Ų
Hydrophobic contacts buried
BSA polar
124.6Ų
Polar contacts buried
Fraction buried
73.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2231.7Ų
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
769.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)