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
30.3 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.30, Jaccard 0.27, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (10/24 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 (-0.886 kcal/mol/HA)
✓ Good fit quality (FQ -8.63)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (30.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (16)
Score
-27.466
kcal/mol
LE
-0.886
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
31
heavy atoms
MW
430
Da
LogP
4.70
cLogP
Interaction summary
HB 7
HY 13
PI 1
CLASH 3
⚠ Exposure 41%
Interaction summary
HB 7
HY 13
PI 1
CLASH 3
⚠ Exposure 41%
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
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (10/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 14
Exposed 10
LogP 4.7
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.277 | Score | -27.466 |
|---|---|---|---|
| Inter norm | -1.038 | Intra norm | 0.152 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 3 protein contact clashes; 2 severe cofactor-context clashes; high strain Δ 30.3 | ||
| Residues |
ARG228
ARG287
ASP330
GLY197
GLY286
LEU227
LEU332
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 | 8 | Native recall | 0.30 |
| Jaccard | 0.27 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 430 | 1.123128311050852 | -1.09943 | -35.0127 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 426 | 1.276767181328564 | -1.03765 | -27.4665 | 7 | 11 | 8 | 0.30 | 0.20 | - | no | Current |
| 461 | 1.476372703816213 | -0.919152 | -22.5547 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 2.272725915955015 | -0.896059 | -31.1212 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 412 | 2.595705842520432 | -0.930582 | -22.1691 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 2.7191745516353594 | -0.998852 | -30.5149 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.7494314954702257 | -0.737507 | -24.9974 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 2.7843928705051484 | -0.713014 | -21.158 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 2.791217765151704 | -0.947142 | -35.2818 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 2.8617363901087467 | -0.750125 | -25.1003 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 2.90635541192479 | -0.798773 | -25.6886 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.9238440516247857 | -0.997616 | -30.3793 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 3.20302513162988 | -0.824135 | -23.5686 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 457 | 3.6279625865993608 | -1.05901 | -33.3892 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 498 | 4.00190802340201 | -0.862379 | -25.6577 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 5.080933656035169 | -0.767574 | -22.0757 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 458 | 5.444083752190545 | -1.06966 | -30.8753 | 11 | 29 | 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
-27.466kcal/mol
Ligand efficiency (LE)
-0.8860kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.632
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.36kcal/mol
Minimised FF energy
108.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
630.3Ų
Total solvent-accessible surface area of free ligand
BSA total
482.2Ų
Buried surface area upon binding
BSA apolar
350.0Ų
Hydrophobic contacts buried
BSA polar
132.2Ų
Polar contacts buried
Fraction buried
76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3023.9Ų
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
1516.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)