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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
78.2 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.60
Reason: strain 78.2 kcal/mol
strain ΔE 78.2 kcal/mol
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.124 kcal/mol/HA)
✓ Good fit quality (FQ -10.73)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Extreme strain energy (78.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-32.595
kcal/mol
LE
-1.124
kcal/mol/HA
Fit Quality
-10.73
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.66
cLogP
Interaction summary
HB 11
HY 17
PI 0
CLASH 2
Interaction summary
HB 11
HY 17
PI 0
CLASH 2
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 | 4.477 | Score | -32.595 |
|---|---|---|---|
| Inter norm | -1.090 | Intra norm | -0.034 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 11 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; 2 cofactor-context clashes; high strain Δ 78.2 | ||
| Residues |
ALA363
ALA365
ARG287
CYS52
CYS57
GLN439
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
SER364
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 | 8 | Native recall | 0.30 |
| Jaccard | 0.20 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 2 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 351 | 0.8650667078746962 | -0.850765 | -27.2287 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 1.6627027499769709 | -0.825865 | -25.326 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 3.2111062454516417 | -0.868648 | -28.173 | 14 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 3.951720802549187 | -0.94614 | -31.3901 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 407 | 4.076782527760934 | -0.988383 | -32.0049 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 4.476565184120372 | -1.08952 | -32.5951 | 11 | 21 | 8 | 0.30 | 0.60 | - | no | Current |
| 302 | 4.951550360652757 | -0.99337 | -28.826 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 327 | 5.675634801511128 | -1.13503 | -30.2464 | 12 | 24 | 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
-32.595kcal/mol
Ligand efficiency (LE)
-1.1240kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.729
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
78.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-31.89kcal/mol
Minimised FF energy
-110.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.0Ų
Total solvent-accessible surface area of free ligand
BSA total
609.2Ų
Buried surface area upon binding
BSA apolar
431.2Ų
Hydrophobic contacts buried
BSA polar
178.0Ų
Polar contacts buried
Fraction buried
93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3048.2Ų
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)