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
17.4 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.023 kcal/mol/HA)
✓ Good fit quality (FQ -9.97)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (17)
Score
-31.715
kcal/mol
LE
-1.023
kcal/mol/HA
Fit Quality
-9.97
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
6.15
cLogP
Interaction summary
HB 2
HY 24
PI 0
CLASH 4
Interaction summary
HB 2
HY 24
PI 0
CLASH 4
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 | 1.171 | Score | -31.715 |
|---|---|---|---|
| Inter norm | -1.043 | Intra norm | -0.056 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 2 |
| Artifact reason | geometry warning; 17 clashes; 2 protein contact clashes; 4 cofactor-context clashes | ||
| Residues |
ALA338
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER14
SER178
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 | 1 | Strict recall | 0.08 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 141 | 1.1706970081307735 | -1.04318 | -31.7149 | 2 | 20 | 7 | 0.26 | 0.40 | - | no | Current |
| 296 | 1.7709278570270426 | -0.762985 | -26.8287 | 4 | 16 | 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
-31.715kcal/mol
Ligand efficiency (LE)
-1.0231kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.967
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
500.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.15
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.79kcal/mol
Minimised FF energy
77.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
709.5Ų
Total solvent-accessible surface area of free ligand
BSA total
672.7Ų
Buried surface area upon binding
BSA apolar
660.7Ų
Hydrophobic contacts buried
BSA polar
12.0Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3273.8Ų
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
1488.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)