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
17.8 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.33, Jaccard 0.23, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.759 kcal/mol/HA)
✓ Good fit quality (FQ -7.40)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.540
kcal/mol
LE
-0.759
kcal/mol/HA
Fit Quality
-7.40
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
cLogP
Interaction summary
HB 9
HY 20
PI 1
CLASH 5
Interaction summary
HB 9
HY 20
PI 1
CLASH 5
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
| Final rank | 2.637 | Score | -23.540 |
|---|---|---|---|
| Inter norm | -1.017 | Intra norm | 0.258 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 9 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA363
ALA365
ARG287
CYS52
CYS57
GLU202
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER178
SER364
THR335
THR51
VAL362
VAL55
| ||
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.23 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | 2.186616249521787 | -0.767138 | -19.682 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 2.4030765412283297 | -0.909145 | -25.0763 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 269 | 2.6372940514961205 | -1.01685 | -23.5396 | 9 | 22 | 9 | 0.33 | 0.00 | - | no | Current |
| 312 | 3.2393473524780756 | -0.83684 | -17.5204 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.272332131596446 | -0.77267 | -17.6481 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 3.6488397918246784 | -0.752019 | -16.7004 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 3.7498473298653865 | -0.798347 | -21.5987 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 4.113009301054676 | -0.859307 | -18.827 | 12 | 15 | 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
-23.540kcal/mol
Ligand efficiency (LE)
-0.7593kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.398
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.76kcal/mol
Minimised FF energy
32.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
711.1Ų
Total solvent-accessible surface area of free ligand
BSA total
664.9Ų
Buried surface area upon binding
BSA apolar
543.5Ų
Hydrophobic contacts buried
BSA polar
121.4Ų
Polar contacts buried
Fraction buried
93.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3175.0Ų
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
1473.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)