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
33.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.89, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.837 kcal/mol/HA)
✓ Good fit quality (FQ -8.51)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Very high strain energy (33.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-30.127
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-8.51
FQ (Leeson)
HAC
36
heavy atoms
MW
480
Da
LogP
2.23
cLogP
Interaction summary
HB 12
HY 9
PI 5
CLASH 2
Interaction summary
HB 12
HY 9
PI 5
CLASH 2
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 | 4.005 | Score | -30.127 |
|---|---|---|---|
| Inter norm | -0.808 | Intra norm | -0.029 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 19 clashes; 1 protein clash; high strain Δ 33.5 | ||
| Residues |
ARG140
ARG144
ASN106
GLN104
GLU138
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
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 | 16 | Native recall | 1.00 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 6 | HB role recall | 0.60 |
| HB same residue | 7 | HB residue recall | 0.70 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 448 | 2.1753586768424085 | -0.759862 | -27.2521 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 327 | 2.196257409577572 | -1.12511 | -44.4786 | 6 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 2.263257935292505 | -0.673764 | -26.8912 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 365 | 2.78635018813914 | -0.932024 | -31.3948 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 3.556867624173379 | -0.572201 | -20.9021 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 358 | 4.004585156869844 | -0.808049 | -30.127 | 12 | 18 | 16 | 1.00 | 0.60 | - | no | Current |
| 391 | 5.477055042660596 | -0.684733 | -29.5647 | 7 | 20 | 1 | 0.06 | 0.10 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.127kcal/mol
Ligand efficiency (LE)
-0.8369kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.506
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-26.28kcal/mol
Minimised FF energy
-59.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
737.7Ų
Total solvent-accessible surface area of free ligand
BSA total
514.1Ų
Buried surface area upon binding
BSA apolar
379.3Ų
Hydrophobic contacts buried
BSA polar
134.8Ų
Polar contacts buried
Fraction buried
69.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2232.9Ų
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
807.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)