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 mixed
SASA done
Strain ΔE
57.9 kcal/mol
Protein clashes
5
Internal clashes
6
Native overlap
contact recall 0.44, Jaccard 0.40, H-bond role recall 0.20
Reason: 6 internal clashes, strain 57.9 kcal/mol
strain ΔE 57.9 kcal/mol
5 protein-contact clashes
6 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (13/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.966 kcal/mol/HA)
✓ Good fit quality (FQ -9.22)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Extreme strain energy (57.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-28.001
kcal/mol
LE
-0.966
kcal/mol/HA
Fit Quality
-9.22
FQ (Leeson)
HAC
29
heavy atoms
MW
421
Da
LogP
2.01
cLogP
Final rank
2.5268
rank score
Inter norm
-1.106
normalised
Contacts
15
H-bonds 7
Interaction summary
HBD 3
HBA 3
HY 6
PI 2
CLASH 6
Interaction summary
HBD 3
HBA 3
HY 6
PI 2
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 12 | Native recall | 0.44 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 46 | 1.3061135800995796 | -0.833631 | -15.0981 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 2.5267981267085653 | -1.1057 | -28.001 | 7 | 15 | 12 | 0.44 | 0.20 | - | no | Current |
| 39 | 2.984454236444561 | -0.957658 | -27.8854 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 3.3433164112676046 | -0.879147 | -23.3489 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 3.842845825095622 | -0.729544 | -17.075 | 6 | 14 | 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
-28.001kcal/mol
Ligand efficiency (LE)
-0.9656kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.217
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
420.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.01
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
57.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
73.56kcal/mol
Minimised FF energy
15.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
675.1Ų
Total solvent-accessible surface area of free ligand
BSA total
546.5Ų
Buried surface area upon binding
BSA apolar
420.4Ų
Hydrophobic contacts buried
BSA polar
126.1Ų
Polar contacts buried
Fraction buried
80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3077.9Ų
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
1516.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)