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
31.0 kcal/mol
Protein clashes
6
Internal clashes
8
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.40
Reason: 8 internal clashes
6 protein-contact clashes
8 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.730 kcal/mol/HA)
✓ Good fit quality (FQ -7.24)
✓ Good H-bonds (5 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (31.0 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (15)
Score
-24.074
kcal/mol
LE
-0.730
kcal/mol/HA
Fit Quality
-7.24
FQ (Leeson)
HAC
33
heavy atoms
MW
505
Da
LogP
6.04
cLogP
Interaction summary
HB 5
HY 20
PI 1
CLASH 8
Interaction summary
HB 5
HY 20
PI 1
CLASH 8
| Final rank | 1.810 | Score | -24.074 |
|---|---|---|---|
| Inter norm | -0.945 | Intra norm | 0.216 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 7 protein contact clashes; 3 cofactor-context clashes; high strain Δ 31.0 | ||
| Residues |
ALA365
ARG287
ASP327
CYS57
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER162
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 | 8 | Native recall | 0.30 |
| Jaccard | 0.21 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 497 | 1.8101435960865835 | -0.94533 | -24.074 | 5 | 20 | 8 | 0.30 | 0.40 | - | no | Current |
| 519 | 3.2260856282522616 | -0.73506 | -21.3289 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 528 | 3.2656347244432626 | -0.806697 | -23.8344 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 514 | 3.5202537042303303 | -0.593741 | -18.1016 | 5 | 12 | 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
-24.074kcal/mol
Ligand efficiency (LE)
-0.7295kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.238
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
505.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.04
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
5.46kcal/mol
Minimised FF energy
-25.58kcal/mol
SASA & burial
✓ computed
SASA (unbound)
741.7Ų
Total solvent-accessible surface area of free ligand
BSA total
691.1Ų
Buried surface area upon binding
BSA apolar
608.2Ų
Hydrophobic contacts buried
BSA polar
82.9Ų
Polar contacts buried
Fraction buried
93.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3225.3Ų
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
1498.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)