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 medium
Native mixed
SASA done
Strain ΔE
33.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.40
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -8.25)
✓ Good H-bonds (5 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (33.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-25.064
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-8.25
FQ (Leeson)
HAC
29
heavy atoms
MW
389
Da
LogP
2.67
cLogP
Final rank
2.9786
rank score
Inter norm
-1.109
normalised
Contacts
21
H-bonds 13
Interaction summary
HBA 5
PC 1
HY 8
PI 1
CLASH 5
Interaction summary
HBA 5
PC 1
HY 8
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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: permissive.
| 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 | 8 | Native recall | 0.30 |
| Jaccard | 0.20 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 677 | 1.107016484399169 | -0.881351 | -23.185 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 1.6158736970212109 | -0.87175 | -24.6014 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 1.6972869032612417 | -0.806037 | -16.4517 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.616838790837006 | -0.943091 | -25.2687 | 12 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 2.978630292673607 | -1.10931 | -25.0643 | 13 | 21 | 8 | 0.30 | 0.40 | - | no | Current |
| 675 | 3.095613666400984 | -0.872994 | -23.3912 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 3.1137994545420247 | -0.761658 | -20.7865 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 3.3031328082286535 | -1.22786 | -33.4802 | 13 | 16 | 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
-25.064kcal/mol
Ligand efficiency (LE)
-0.8643kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.250
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
389.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.67
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.04kcal/mol
Minimised FF energy
7.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
666.0Ų
Total solvent-accessible surface area of free ligand
BSA total
623.5Ų
Buried surface area upon binding
BSA apolar
470.4Ų
Hydrophobic contacts buried
BSA polar
153.1Ų
Polar contacts buried
Fraction buried
93.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3092.9Ų
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
1481.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)