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 high
Native mixed
SASA done
Strain ΔE
27.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.30, Jaccard 0.21, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.480 kcal/mol/HA)
✓ Good fit quality (FQ -14.13)
✓ Good H-bonds (4 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (27.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-42.919
kcal/mol
LE
-1.480
kcal/mol/HA
Fit Quality
-14.13
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.81
cLogP
Interaction summary
HB 4
HY 21
PI 0
CLASH 1
Interaction summary
HB 4
HY 21
PI 0
CLASH 1
| Final rank | 3.913 | Score | -42.919 |
|---|---|---|---|
| Inter norm | -1.230 | Intra norm | -0.250 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 3 protein clashes; moderate strain Δ 27.7 | ||
| Residues |
ALA363
ALA365
ARG287
CYS57
GLU202
GLY56
ILE199
ILE438
LEU334
LYS60
NDP800
PHE182
PHE203
PHE367
PRO336
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 | 8 | Native recall | 0.30 |
| Jaccard | 0.21 | 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 654 | 3.91281635502643 | -1.22988 | -42.9192 | 4 | 20 | 8 | 0.30 | 0.00 | - | no | Current |
| 656 | 4.358848948961455 | -0.925626 | -25.7441 | 4 | 20 | 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
-42.919kcal/mol
Ligand efficiency (LE)
-1.4800kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.127
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.81
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-3.69kcal/mol
Minimised FF energy
-31.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
699.3Ų
Total solvent-accessible surface area of free ligand
BSA total
663.1Ų
Buried surface area upon binding
BSA apolar
506.6Ų
Hydrophobic contacts buried
BSA polar
156.5Ų
Polar contacts buried
Fraction buried
94.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3119.2Ų
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
1478.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)