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
25.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.40
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 (-1.425 kcal/mol/HA)
✓ Good fit quality (FQ -11.42)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
Score
-25.649
kcal/mol
LE
-1.425
kcal/mol/HA
Fit Quality
-11.42
FQ (Leeson)
HAC
18
heavy atoms
MW
294
Da
LogP
3.38
cLogP
Interaction summary
HB 10
HY 11
PI 4
CLASH 3
Interaction summary
HB 10
HY 11
PI 4
CLASH 3
| Final rank | 1.962 | Score | -25.649 |
|---|---|---|---|
| Inter norm | -1.516 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 3 clashes; 2 protein clashes; moderate strain Δ 25.5 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
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 | 16 | Native recall | 1.00 |
| Jaccard | 1.00 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 416 | -0.02197705513071642 | -1.35055 | -24.9974 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 398 | 0.4756929644349943 | -1.47357 | -25.319 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 424 | 0.5658076263964957 | -1.25601 | -20.4768 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 0.9142477678312333 | -1.41951 | -23.8348 | 7 | 17 | 5 | 0.31 | 0.20 | - | no | Open |
| 383 | 1.962238201095857 | -1.51574 | -25.6489 | 10 | 16 | 16 | 1.00 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.649kcal/mol
Ligand efficiency (LE)
-1.4249kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.420
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
294.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.38
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
39.26kcal/mol
Minimised FF energy
13.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
497.4Ų
Total solvent-accessible surface area of free ligand
BSA total
421.8Ų
Buried surface area upon binding
BSA apolar
269.8Ų
Hydrophobic contacts buried
BSA polar
152.1Ų
Polar contacts buried
Fraction buried
84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2009.3Ų
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
757.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)