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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
50.7 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.30, Jaccard 0.22, H-bond role recall 0.40
Reason: 6 internal clashes, strain 50.7 kcal/mol
strain ΔE 50.7 kcal/mol
5 protein-contact clashes
6 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.087 kcal/mol/HA)
✓ Good fit quality (FQ -10.69)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (50.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-34.777
kcal/mol
LE
-1.087
kcal/mol/HA
Fit Quality
-10.69
FQ (Leeson)
HAC
32
heavy atoms
MW
426
Da
LogP
0.88
cLogP
Interaction summary
HB 8
HY 24
PI 0
CLASH 6
Interaction summary
HB 8
HY 24
PI 0
CLASH 6
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 3.081 | Score | -34.777 |
|---|---|---|---|
| Inter norm | -1.039 | Intra norm | -0.048 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 8 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 50.1 | ||
| Residues |
ALA363
ALA365
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE367
PRO336
SER364
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 | 0.22 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 624 | 3.0807991426272445 | -1.03895 | -34.7769 | 8 | 18 | 8 | 0.30 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.777kcal/mol
Ligand efficiency (LE)
-1.0868kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.687
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
426.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.88
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-65.82kcal/mol
Minimised FF energy
-116.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
675.2Ų
Total solvent-accessible surface area of free ligand
BSA total
631.3Ų
Buried surface area upon binding
BSA apolar
543.1Ų
Hydrophobic contacts buried
BSA polar
88.2Ų
Polar contacts buried
Fraction buried
93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3167.6Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1476.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)