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
63.3 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.33, Jaccard 0.23, H-bond role recall 0.40
Reason: 12 internal clashes, strain 63.3 kcal/mol
strain ΔE 63.3 kcal/mol
12 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.142 kcal/mol/HA)
✓ Good fit quality (FQ -10.90)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Extreme strain energy (63.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-33.127
kcal/mol
LE
-1.142
kcal/mol/HA
Fit Quality
-10.90
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.49
cLogP
Interaction summary
HB 8
HY 16
PI 0
CLASH 0
Interaction summary
HB 8
HY 16
PI 0
CLASH 0
| Final rank | 2.840 | Score | -33.127 |
|---|---|---|---|
| Inter norm | -1.181 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 63.3 | ||
| Residues |
ALA363
ALA365
ARG287
CYS52
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
SER364
THR335
THR51
VAL55
| ||
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
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.23 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 1 | HB residue recall | 0.25 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.8052625623810137 | -0.956826 | -26.5786 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 1.329263884816044 | -0.859526 | -24.8294 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 2.453092962966273 | -0.93103 | -26.9955 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 2.4975808499608676 | -0.967058 | -25.9968 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.750322901945091 | -1.0068 | -27.2349 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 286 | 2.8402209002504564 | -1.18094 | -33.1271 | 8 | 21 | 9 | 0.33 | 0.40 | - | no | Current |
| 340 | 3.0348573502876355 | -0.845126 | -25.451 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 307 | 3.364737405609164 | -1.16289 | -34.6979 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.6446324022786087 | -0.978854 | -27.1972 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 4.744139486087101 | -0.827695 | -24.2166 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 5.145683840208263 | -1.07823 | -23.7962 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 6.264571217814828 | -0.9861 | -22.256 | 10 | 23 | 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
-33.127kcal/mol
Ligand efficiency (LE)
-1.1423kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.904
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
63.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-31.84kcal/mol
Minimised FF energy
-95.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
643.8Ų
Total solvent-accessible surface area of free ligand
BSA total
594.9Ų
Buried surface area upon binding
BSA apolar
380.9Ų
Hydrophobic contacts buried
BSA polar
214.0Ų
Polar contacts buried
Fraction buried
92.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3003.6Ų
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
1469.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)