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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.4 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.41, Jaccard 0.38, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
4 intramolecular clashes
46% of hydrophobic surface appears solvent-exposed (13/28 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 (-0.882 kcal/mol/HA)
✓ Good fit quality (FQ -9.03)
✓ Strong H-bond network (7 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (31.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (19)
Score
-32.639
kcal/mol
LE
-0.882
kcal/mol/HA
Fit Quality
-9.03
FQ (Leeson)
HAC
37
heavy atoms
MW
510
Da
LogP
4.78
cLogP
Interaction summary
HB 7
HY 13
PI 1
CLASH 4
⚠ Exposure 46%
Interaction summary
HB 7
HY 13
PI 1
CLASH 4
⚠ Exposure 46%
Partial hydrophobic solvent exposure
46% of hydrophobic surface appears solvent-exposed (13/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 15
Exposed 13
LogP 4.78
H-bonds 7
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.913 | Score | -32.639 |
|---|---|---|---|
| Inter norm | -0.920 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 19 clashes; 4 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 31.4 | ||
| Residues |
ARG222
ARG228
GLN165
GLY196
GLY197
GLY286
ILE285
LEU227
LEU332
MET333
NDP800
PHE198
PHE230
| ||
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 | 11 | Native recall | 0.41 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 2 | Strict recall | 0.17 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 2 | HB residue recall | 0.50 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 600 | 1.7891122435833013 | -0.850133 | -27.6099 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 1.8854541359846666 | -0.744048 | -18.7794 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 1.912824126418511 | -0.919529 | -32.6385 | 7 | 13 | 11 | 0.41 | 0.60 | - | no | Current |
| 595 | 2.3928452038013317 | -0.722626 | -24.9806 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 588 | 2.9213174943752986 | -0.78739 | -27.4334 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 3.4725507700301645 | -0.556151 | -19.3613 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 585 | 3.5413949258232296 | -0.711709 | -22.3977 | 8 | 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
-32.639kcal/mol
Ligand efficiency (LE)
-0.8821kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.031
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
509.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.78
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-11.52kcal/mol
Minimised FF energy
-42.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
842.6Ų
Total solvent-accessible surface area of free ligand
BSA total
504.0Ų
Buried surface area upon binding
BSA apolar
433.4Ų
Hydrophobic contacts buried
BSA polar
70.6Ų
Polar contacts buried
Fraction buried
59.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3200.1Ų
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
1581.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)