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 strong
SASA done
Strain ΔE
27.6 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.799 kcal/mol/HA)
✓ Good fit quality (FQ -8.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (91% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (27.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-28.759
kcal/mol
LE
-0.799
kcal/mol/HA
Fit Quality
-8.12
FQ (Leeson)
HAC
36
heavy atoms
MW
483
Da
LogP
0.88
cLogP
Interaction summary
HB 6
HY 24
PI 1
CLASH 3
Interaction summary
HB 6
HY 24
PI 1
CLASH 3
| Final rank | 3.853 | Score | -28.759 |
|---|---|---|---|
| Inter norm | -0.868 | Intra norm | 0.065 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 6 |
| Artifact reason | geometry warning; 19 clashes; 2 protein clashes; 2 cofactor-context clashes; moderate strain Δ 27.6 | ||
| Residues |
ALA338
ARG287
ASP327
CYS52
CYS57
GLU202
GLY161
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER162
SER178
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 | 0.20 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 2 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 609 | 3.0641401779374218 | -0.771676 | -25.6514 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 613 | 3.706288720740278 | -0.792109 | -28.0575 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 602 | 3.8525293786513526 | -0.867928 | -28.7592 | 6 | 22 | 8 | 0.30 | 0.60 | - | no | Current |
| 610 | 3.987352034276114 | -0.623204 | -20.5309 | 7 | 21 | 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
-28.759kcal/mol
Ligand efficiency (LE)
-0.7989kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.119
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
482.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.88
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-79.08kcal/mol
Minimised FF energy
-106.67kcal/mol
SASA & burial
✓ computed
SASA (unbound)
768.3Ų
Total solvent-accessible surface area of free ligand
BSA total
696.5Ų
Buried surface area upon binding
BSA apolar
606.6Ų
Hydrophobic contacts buried
BSA polar
89.8Ų
Polar contacts buried
Fraction buried
90.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3260.2Ų
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
1478.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)