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
32.6 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.26, Jaccard 0.16, H-bond role recall 0.20
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.831 kcal/mol/HA)
✓ Good fit quality (FQ -8.44)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (32.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-29.902
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-8.44
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
4.36
cLogP
Interaction summary
HB 9
HY 24
PI 2
CLASH 5
Interaction summary
HB 9
HY 24
PI 2
CLASH 5
| Final rank | 4.213 | Score | -29.902 |
|---|---|---|---|
| Inter norm | -0.898 | Intra norm | 0.068 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 9 |
| Artifact reason | geometry warning; 18 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 32.6 | ||
| Residues |
ALA363
ALA365
ARG287
ASP327
CYS52
CYS57
GLY56
ILE199
LEU334
LYS60
NDP800
PHE182
PHE203
PHE367
PRO336
PRO435
SER14
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.16 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 230 | 2.982313699289413 | -0.9405 | -28.2532 | 8 | 22 | 8 | 0.30 | 0.20 | - | no | Open |
| 247 | 3.0372924803511148 | -0.807545 | -30.2799 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 3.069701690650272 | -0.813304 | -30.7805 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 4.2126177606212805 | -0.898385 | -29.9025 | 9 | 23 | 7 | 0.26 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.902kcal/mol
Ligand efficiency (LE)
-0.8306kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.442
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
482.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.36
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.73kcal/mol
Minimised FF energy
82.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
784.8Ų
Total solvent-accessible surface area of free ligand
BSA total
741.3Ų
Buried surface area upon binding
BSA apolar
594.2Ų
Hydrophobic contacts buried
BSA polar
147.1Ų
Polar contacts buried
Fraction buried
94.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3224.7Ų
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
1476.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)