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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.2 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.94, Jaccard 0.79, H-bond role recall 0.50
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (10/28 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 (-0.940 kcal/mol/HA)
✓ Good fit quality (FQ -9.55)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (30.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-33.835
kcal/mol
LE
-0.940
kcal/mol/HA
Fit Quality
-9.55
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
5.06
cLogP
Interaction summary
HB 10
HY 16
PI 2
CLASH 7
⚠ Exposure 35%
Interaction summary
HB 10
HY 16
PI 2
CLASH 7
⚠ Exposure 35%
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 18
Exposed 10
LogP 5.06
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.230 | Score | -33.835 |
|---|---|---|---|
| Inter norm | -0.787 | Intra norm | -0.153 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 17 clashes; 1 protein clash; high strain Δ 30.2 | ||
| Residues |
ARG140
ARG144
ASN106
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
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 | 15 | Native recall | 0.94 |
| Jaccard | 0.79 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 604 | 2.391433960054099 | -0.72906 | -17.4267 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 3.1727607344736213 | -0.598552 | -19.2757 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 3.398860628331752 | -0.818739 | -26.296 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 4.123937815695857 | -0.730944 | -28.0767 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 608 | 4.229730232478214 | -0.787302 | -33.8349 | 10 | 18 | 15 | 0.94 | 0.50 | - | no | Current |
| 636 | 5.9796918661171885 | -0.85151 | -28.2644 | 7 | 26 | 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
-33.835kcal/mol
Ligand efficiency (LE)
-0.9399kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.552
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
481.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.06
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
136.49kcal/mol
Minimised FF energy
106.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.0Ų
Total solvent-accessible surface area of free ligand
BSA total
535.9Ų
Buried surface area upon binding
BSA apolar
441.6Ų
Hydrophobic contacts buried
BSA polar
94.3Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2233.9Ų
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
787.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)