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
33.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.22, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.787 kcal/mol/HA)
✓ Good fit quality (FQ -8.00)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (33.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-28.339
kcal/mol
LE
-0.787
kcal/mol/HA
Fit Quality
-8.00
FQ (Leeson)
HAC
36
heavy atoms
MW
526
Da
LogP
5.89
cLogP
Interaction summary
HB 6
HY 24
PI 4
CLASH 2
Interaction summary
HB 6
HY 24
PI 4
CLASH 2
| Final rank | 2.732 | Score | -28.339 |
|---|---|---|---|
| Inter norm | -0.884 | Intra norm | 0.097 |
| Top1000 | no | Excluded | no |
| Contacts | 23 | H-bonds | 6 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 33.5 | ||
| Residues |
ALA363
ALA365
ARG287
ASP327
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
PRO435
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.22 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 518 | 1.5317635819657096 | -0.88026 | -24.6218 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 1.7074599916409356 | -0.665198 | -16.9126 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 2.7039259759344065 | -0.701134 | -19.8874 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 2.732464516163644 | -0.883815 | -28.3394 | 6 | 23 | 9 | 0.33 | 0.00 | - | no | Current |
| 478 | 2.7730499915817934 | -0.576088 | -17.2298 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 3.5890135434641097 | -0.656405 | -20.7614 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 511 | 4.286679271760215 | -0.659078 | -20.8376 | 8 | 22 | 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
-28.339kcal/mol
Ligand efficiency (LE)
-0.7872kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.001
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
526.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.08kcal/mol
Minimised FF energy
36.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
778.4Ų
Total solvent-accessible surface area of free ligand
BSA total
700.0Ų
Buried surface area upon binding
BSA apolar
554.9Ų
Hydrophobic contacts buried
BSA polar
145.1Ų
Polar contacts buried
Fraction buried
89.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3210.2Ų
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
1476.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)