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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
6
Internal clashes
7
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.00
Reason: 7 internal clashes
6 protein-contact clashes
7 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (6/17 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 (-1.357 kcal/mol/HA)
✓ Good fit quality (FQ -12.51)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-35.295
kcal/mol
LE
-1.357
kcal/mol/HA
Fit Quality
-12.51
FQ (Leeson)
HAC
26
heavy atoms
MW
377
Da
LogP
2.13
cLogP
Interaction summary
HB 10
HY 12
PI 0
CLASH 7
⚠ Exposure 35%
Interaction summary
HB 10
HY 12
PI 0
CLASH 7
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 2.13
H-bonds 10
Exposed fragments:
pyrrolyl (6/6 atoms exposed)
| Final rank | 4.826 | Score | -35.295 |
|---|---|---|---|
| Inter norm | -1.289 | Intra norm | -0.089 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 10 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; 1 cofactor-context clash | ||
| Residues |
ARG287
ASP327
CYS52
CYS57
GLU202
GLY161
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PRO336
SER14
SER162
SER178
THR335
THR51
VAL55
| ||
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
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 | 7 | Native recall | 0.26 |
| Jaccard | 0.17 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 55 | 0.5243665770310006 | -0.920154 | -21.7702 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 93 | 1.53189922327258 | -0.953717 | -25.0514 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.2728827443071546 | -0.991054 | -25.8828 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 4.82559950042143 | -1.28946 | -35.2953 | 10 | 21 | 7 | 0.26 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-35.295kcal/mol
Ligand efficiency (LE)
-1.3575kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.507
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
376.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-93.92kcal/mol
Minimised FF energy
-109.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.0Ų
Total solvent-accessible surface area of free ligand
BSA total
580.7Ų
Buried surface area upon binding
BSA apolar
485.2Ų
Hydrophobic contacts buried
BSA polar
95.5Ų
Polar contacts buried
Fraction buried
97.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3101.6Ų
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
1465.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)