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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
61.9 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.00
Reason: strain 61.9 kcal/mol
strain ΔE 61.9 kcal/mol
2 protein-contact clashes
3 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.391 kcal/mol/HA)
✓ Good fit quality (FQ -12.81)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (61.9 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (12)
Score
-36.158
kcal/mol
LE
-1.391
kcal/mol/HA
Fit Quality
-12.81
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
5.63
cLogP
Interaction summary
HB 2
HY 23
PI 2
CLASH 3
⚠ Exposure 35%
Interaction summary
HB 2
HY 23
PI 2
CLASH 3
⚠ Exposure 35%
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
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 5.63
H-bonds 2
Exposed fragments:
phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 0.870 | Score | -36.158 |
|---|---|---|---|
| Inter norm | -1.212 | Intra norm | -0.178 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 12 clashes; 4 protein contact clashes; 1 cofactor-context clash; high strain Δ 61.9 | ||
| Residues |
ARG287
ASP327
CYS57
GLU202
GLY56
ILE199
ILE206
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
SER162
SER178
THR335
THR51
VAL55
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 2WOV | Contacts | 27 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA284
ALA365
ARG222
ARG228
ARG287
ASN223
ASN254
GLN165
GLU202
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
LEU334
LYS60
MET333
NDP800
PHE198
PHE367
PRO167
SER200
TYR221
VAL194
VAL366
| ||
| Current overlap | 8 | Native recall | 0.30 |
| Jaccard | 0.21 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
493 residues
| Protein target | T19 | Atoms | 7541 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221 | ||
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
C:NDP800
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 515 | 0.8702289118380384 | -1.21221 | -36.1577 | 2 | 19 | 8 | 0.30 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-36.158kcal/mol
Ligand efficiency (LE)
-1.3907kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.813
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
402.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.63
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
61.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.06kcal/mol
Minimised FF energy
67.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
629.1Ų
Total solvent-accessible surface area of free ligand
BSA total
596.3Ų
Buried surface area upon binding
BSA apolar
515.0Ų
Hydrophobic contacts buried
BSA polar
81.3Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3147.2Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1465.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)