Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
58.2 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.33, Jaccard 0.28, H-bond role recall 0.60
Reason: strain 58.2 kcal/mol
strain ΔE 58.2 kcal/mol
1 protein-contact clashes
4 intramolecular clashes
48% of hydrophobic surface appears solvent-exposed (12/25 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 (-0.880 kcal/mol/HA)
✓ Good fit quality (FQ -8.95)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (58.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-31.697
kcal/mol
LE
-0.880
kcal/mol/HA
Fit Quality
-8.95
FQ (Leeson)
HAC
36
heavy atoms
MW
511
Da
LogP
-0.77
cLogP
Interaction summary
HB 12
HY 7
PI 0
CLASH 4
⚠ Exposure 48%
Interaction summary
HB 12
HY 7
PI 0
CLASH 4
⚠ Exposure 48%
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
48% of hydrophobic surface appears solvent-exposed (12/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 13
Exposed 12
LogP -0.77
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 4.136 | Score | -31.697 |
|---|---|---|---|
| Inter norm | -0.881 | Intra norm | 0.000 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 12 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes; 1 severe cofactor-context clash; high strain Δ 58.2 | ||
| Residues |
ARG222
ARG228
ARG287
ARG331
ASP330
GLN165
GLY229
GLY286
ILE285
ILE288
LEU227
LEU332
MET333
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 | 0.28 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 72 | 3.8594501751747776 | -0.827056 | -23.8656 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 4.135873877091396 | -0.880898 | -31.6966 | 12 | 14 | 9 | 0.33 | 0.60 | - | no | Current |
| 57 | 4.246759468271501 | -0.595939 | -22.8076 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 68 | 5.222560969371158 | -0.606925 | -19.6983 | 10 | 15 | 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
-31.697kcal/mol
Ligand efficiency (LE)
-0.8805kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.949
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
510.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.77
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
58.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
28.97kcal/mol
Minimised FF energy
-29.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.4Ų
Total solvent-accessible surface area of free ligand
BSA total
551.3Ų
Buried surface area upon binding
BSA apolar
437.7Ų
Hydrophobic contacts buried
BSA polar
113.6Ų
Polar contacts buried
Fraction buried
69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3182.2Ų
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
1530.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)