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 mixed
SASA done
Strain ΔE
20.3 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.24, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.256 kcal/mol/HA)
✓ Good fit quality (FQ -12.11)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (20.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (16)
Score
-37.668
kcal/mol
LE
-1.256
kcal/mol/HA
Fit Quality
-12.11
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Interaction summary
HB 7
HY 21
PI 2
CLASH 3
Interaction summary
HB 7
HY 21
PI 2
CLASH 3
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
| Final rank | 1.229 | Score | -37.668 |
|---|---|---|---|
| Inter norm | -1.050 | Intra norm | -0.205 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 3 protein contact clashes; 4 cofactor-context clashes; moderate strain Δ 20.3 | ||
| Residues |
ALA365
ARG287
ASP327
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
SER162
SER178
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.24 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 383 | 1.2287636357355942 | -1.0501 | -37.6676 | 7 | 20 | 9 | 0.33 | 0.40 | - | no | Current |
| 420 | 1.5304501302166158 | -0.780324 | -26.3523 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 2.785856035332341 | -0.980801 | -34.63 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 2.955093255524448 | -0.865923 | -27.6702 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 3.2491331708059237 | -0.794232 | -23.4452 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 4.004368900998721 | -0.799974 | -24.3755 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 4.4407993593659 | -1.07037 | -31.267 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 426 | 4.8004481778310115 | -0.756591 | -25.3759 | 10 | 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
-37.668kcal/mol
Ligand efficiency (LE)
-1.2556kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.112
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
112.88kcal/mol
Minimised FF energy
92.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
670.4Ų
Total solvent-accessible surface area of free ligand
BSA total
591.1Ų
Buried surface area upon binding
BSA apolar
477.6Ų
Hydrophobic contacts buried
BSA polar
113.5Ų
Polar contacts buried
Fraction buried
88.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3125.0Ų
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
1480.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)