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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
32.2 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.48, Jaccard 0.43, H-bond role recall 0.20
Reason: 16 internal clashes
16 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.916 kcal/mol/HA)
✓ Good fit quality (FQ -9.09)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-30.246
kcal/mol
LE
-0.916
kcal/mol/HA
Fit Quality
-9.09
FQ (Leeson)
HAC
33
heavy atoms
MW
455
Da
LogP
2.76
cLogP
Interaction summary
HB 8
HY 11
PI 0
CLASH 0
⚠ Exposure 48%
Interaction summary
HB 8
HY 11
PI 0
CLASH 0
⚠ 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
No clash · clashes detected for this pose.
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 2.76
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.377 | Score | -30.246 |
|---|---|---|---|
| Inter norm | -0.964 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes; 2 cofactor-context clashes; moderate strain Δ 22.3 | ||
| Residues |
ARG222
ARG228
ARG287
GLN165
GLY196
GLY197
GLY229
GLY286
ILE285
LEU227
LEU332
LEU334
MET333
NDP800
PHE198
PHE230
| ||
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 | 13 | Native recall | 0.48 |
| Jaccard | 0.43 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 296 | 1.2094497069229952 | -0.798718 | -24.0361 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 246 | 1.5777109956035995 | -1.02348 | -27.0051 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 217 | 2.907166553436376 | -0.828931 | -26.0142 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 272 | 2.937604839504376 | -0.709141 | -16.628 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 3.3766176770969594 | -0.963848 | -30.2461 | 8 | 16 | 13 | 0.48 | 0.20 | - | no | Current |
| 195 | 3.764082353800593 | -0.885488 | -30.0305 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 253 | 5.228683162267013 | -0.827143 | -20.3337 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 5.457047523773753 | -0.802528 | -20.4234 | 6 | 18 | 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
-30.246kcal/mol
Ligand efficiency (LE)
-0.9165kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.094
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.81kcal/mol
Minimised FF energy
20.63kcal/mol
SASA & burial
✓ computed
SASA (unbound)
710.9Ų
Total solvent-accessible surface area of free ligand
BSA total
537.3Ų
Buried surface area upon binding
BSA apolar
441.9Ų
Hydrophobic contacts buried
BSA polar
95.5Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3144.1Ų
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
1511.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)