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
64.3 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.27, H-bond role recall 0.60
Reason: strain 64.3 kcal/mol
strain ΔE 64.3 kcal/mol
57% of hydrophobic surface appears solvent-exposed (17/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.749 kcal/mol/HA)
✓ Good fit quality (FQ -7.87)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (64.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-30.711
kcal/mol
LE
-0.749
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
41
heavy atoms
MW
573
Da
LogP
0.41
cLogP
Interaction summary
HB 12
HY 9
PI 0
CLASH 2
⚠ Exposure 56%
Interaction summary
HB 12
HY 9
PI 0
CLASH 2
⚠ Exposure 56%
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
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (17/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 13
Exposed 17
LogP 0.41
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.762 | Score | -30.711 |
|---|---|---|---|
| Inter norm | -0.830 | Intra norm | 0.081 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; 5 cofactor-context clashes; high strain Δ 58.2 | ||
| Residues |
ARG222
ARG228
ARG287
ARG331
ASP330
GLN165
GLY229
GLY286
ILE285
ILE288
LEU227
LEU332
MET333
NDP800
PRO289
| ||
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 | 0.27 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 58 | 4.229715209788138 | -0.532983 | -17.6581 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 41 | 4.761501954767904 | -0.830286 | -30.711 | 12 | 15 | 9 | 0.33 | 0.60 | - | no | Current |
| 68 | 4.8272040167623 | -0.568842 | -22.4135 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 5.446949228940074 | -0.700223 | -18.4291 | 13 | 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
-30.711kcal/mol
Ligand efficiency (LE)
-0.7490kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.871
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
572.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.41
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
64.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.27kcal/mol
Minimised FF energy
-2.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
894.8Ų
Total solvent-accessible surface area of free ligand
BSA total
592.4Ų
Buried surface area upon binding
BSA apolar
468.2Ų
Hydrophobic contacts buried
BSA polar
124.2Ų
Polar contacts buried
Fraction buried
66.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3243.5Ų
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
1568.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)