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
35.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.68, H-bond role recall 0.50
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.724 kcal/mol/HA)
✓ Good fit quality (FQ -7.19)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (35.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.905
kcal/mol
LE
-0.724
kcal/mol/HA
Fit Quality
-7.19
FQ (Leeson)
HAC
33
heavy atoms
MW
477
Da
LogP
1.81
cLogP
Interaction summary
HB 10
HY 16
PI 3
CLASH 4
⚠ Exposure 37%
Interaction summary
HB 10
HY 16
PI 3
CLASH 4
⚠ Exposure 37%
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 15
Exposed 9
LogP 1.81
H-bonds 10
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (3/3 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.335 | Score | -23.905 |
|---|---|---|---|
| Inter norm | -0.812 | Intra norm | 0.069 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 35.1 | ||
| Residues |
ARG140
ARG144
ASN106
GLN104
GLU138
HIS105
HIS141
MET101
TYR97
ARG116
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
MET78
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 99 | 1.520175150280541 | -0.838175 | -25.9773 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 140 | 1.796135031564517 | -0.839245 | -27.1798 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 3.334748612110413 | -0.812088 | -23.905 | 10 | 21 | 15 | 0.94 | 0.50 | - | no | Current |
| 112 | 3.6154002439715773 | -0.674333 | -20.3464 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 5.923421607085572 | -0.832714 | -26.2276 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.905kcal/mol
Ligand efficiency (LE)
-0.7244kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.187
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
476.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.22kcal/mol
Minimised FF energy
8.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
761.6Ų
Total solvent-accessible surface area of free ligand
BSA total
561.4Ų
Buried surface area upon binding
BSA apolar
484.2Ų
Hydrophobic contacts buried
BSA polar
77.2Ų
Polar contacts buried
Fraction buried
73.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2337.1Ų
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
774.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)