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
14.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.024 kcal/mol/HA)
✓ Good fit quality (FQ -9.88)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (9)
✗ Many internal clashes (10)
Score
-30.717
kcal/mol
LE
-1.024
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
30
heavy atoms
MW
419
Da
LogP
5.28
cLogP
Interaction summary
HB 6
HY 19
PI 0
CLASH 5
Interaction summary
HB 6
HY 19
PI 0
CLASH 5
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 | 1.519 | Score | -30.717 |
|---|---|---|---|
| Inter norm | -1.070 | Intra norm | 0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 6 |
| Artifact reason | geometry warning; 10 clashes; 9 protein contact clashes | ||
| Residues |
ALA338
ALA365
ASP327
CYS52
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
NDP800
PHE182
PHE203
PHE367
PRO336
PRO435
SER14
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.17 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 504 | 1.5190146538650384 | -1.06968 | -30.7167 | 6 | 22 | 7 | 0.26 | 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
-30.717kcal/mol
Ligand efficiency (LE)
-1.0239kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.877
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.28
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.81kcal/mol
Minimised FF energy
3.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
725.4Ų
Total solvent-accessible surface area of free ligand
BSA total
659.1Ų
Buried surface area upon binding
BSA apolar
562.3Ų
Hydrophobic contacts buried
BSA polar
96.8Ų
Polar contacts buried
Fraction buried
90.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3220.9Ų
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
1470.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)