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
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.26, Jaccard 0.25, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (5/10 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 (-1.509 kcal/mol/HA)
✓ Good fit quality (FQ -12.37)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ High strain energy (23.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
Score
-28.670
kcal/mol
LE
-1.509
kcal/mol/HA
Fit Quality
-12.37
FQ (Leeson)
HAC
19
heavy atoms
MW
268
Da
LogP
-2.20
cLogP
Interaction summary
HB 12
HY 4
PI 0
CLASH 1
⚠ Exposure 50%
Interaction summary
HB 12
HY 4
PI 0
CLASH 1
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (5/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 10
Buried (contacted) 5
Exposed 5
LogP -2.2
H-bonds 12
Exposed fragments:
aromatic ring (3/5 atoms exposed)aromatic ring (4/6 atoms exposed)
| Final rank | -0.588 | Score | -28.670 |
|---|---|---|---|
| Inter norm | -1.637 | Intra norm | 0.128 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 12 |
| Artifact reason | geometry warning; 3 clashes; 3 protein contact clashes; 3 severe cofactor-context clashes; moderate strain Δ 23.1 | ||
| Residues |
ARG222
ARG228
GLY197
LEU227
NDP800
PHE198
PHE230
TYR221
| ||
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 | 0.25 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 126 | -0.5879377610528022 | -1.63674 | -28.6704 | 12 | 8 | 7 | 0.26 | 0.20 | - | no | Current |
| 120 | 0.9041903580328218 | -1.78179 | -33.7757 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 84 | 1.3951132055642954 | -1.31974 | -22.3982 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 183 | 1.6114407945426672 | -0.996377 | -18.1312 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 1.8405702221899884 | -1.63635 | -29.0274 | 16 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 117 | 3.98837453237915 | -1.40899 | -25.9622 | 10 | 12 | 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
-28.670kcal/mol
Ligand efficiency (LE)
-1.5090kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.369
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
268.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.20
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.72kcal/mol
Minimised FF energy
32.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
448.0Ų
Total solvent-accessible surface area of free ligand
BSA total
333.4Ų
Buried surface area upon binding
BSA apolar
201.7Ų
Hydrophobic contacts buried
BSA polar
131.7Ų
Polar contacts buried
Fraction buried
74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2809.3Ų
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
1510.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)