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
30.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.56, Jaccard 0.50, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
58% of hydrophobic surface appears solvent-exposed (7/12 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 (-1.246 kcal/mol/HA)
✓ Good fit quality (FQ -10.82)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Very high strain energy (30.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.411
kcal/mol
LE
-1.246
kcal/mol/HA
Fit Quality
-10.82
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
0.85
cLogP
Interaction summary
HB 10
HY 3
PI 2
CLASH 2
⚠ Exposure 58%
Interaction summary
HB 10
HY 3
PI 2
CLASH 2
⚠ Exposure 58%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (7/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 5
Exposed 7
LogP 0.85
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.566 | Score | -27.411 |
|---|---|---|---|
| Inter norm | -1.224 | Intra norm | -0.022 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; high strain Δ 30.7 | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
TYR97
ARG116
ARG46
ASP13
GLY73
HIS14
ILE15
| ||
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 | 9 | Native recall | 0.56 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 317 | 1.5601098518676115 | -0.979351 | -23.9959 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 348 | 1.8122616068789374 | -1.31829 | -31.2362 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 2.4145491483460817 | -1.32008 | -28.8892 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 367 | 2.623864518054188 | -1.26054 | -27.9304 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 386 | 2.7976856271821577 | -1.0561 | -23.1357 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 3.091715337324087 | -1.24823 | -26.7494 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 3.1767117400164997 | -1.1623 | -28.2979 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 3.255674010577603 | -1.16586 | -27.0009 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 261 | 3.5655398357745285 | -1.22387 | -27.4107 | 10 | 11 | 9 | 0.56 | 0.50 | - | no | Current |
| 260 | 3.8051734407824642 | -1.2978 | -28.8576 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 3.870022958916809 | -1.15097 | -25.1072 | 11 | 13 | 5 | 0.31 | 0.20 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.411kcal/mol
Ligand efficiency (LE)
-1.2459kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.85
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-53.92kcal/mol
Minimised FF energy
-84.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
538.1Ų
Total solvent-accessible surface area of free ligand
BSA total
366.9Ų
Buried surface area upon binding
BSA apolar
239.5Ų
Hydrophobic contacts buried
BSA polar
127.5Ų
Polar contacts buried
Fraction buried
68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2052.6Ų
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
777.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)