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 mixed
SASA done
Strain ΔE
29.0 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.866 kcal/mol/HA)
✓ Good fit quality (FQ -8.73)
✓ Good H-bonds (5 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (29.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-30.309
kcal/mol
LE
-0.866
kcal/mol/HA
Fit Quality
-8.73
FQ (Leeson)
HAC
35
heavy atoms
MW
490
Da
LogP
3.21
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 5
Interaction summary
HB 5
HY 24
PI 2
CLASH 5
| Final rank | 4.413 | Score | -30.309 |
|---|---|---|---|
| Inter norm | -0.988 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 3 protein clashes; 2 cofactor-context clashes; moderate strain Δ 29.0 | ||
| Residues |
ALA363
ALA365
ASP327
CYS52
CYS57
GLN439
GLY56
ILE199
LEU334
LYS60
MET333
NDP800
PHE182
PHE203
PHE367
PRO336
SER14
SER178
SER364
THR335
THR51
VAL55
| ||
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 | 0.17 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 528 | 2.1387138988154137 | -0.609177 | -24.6017 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 554 | 3.0340948021098755 | -0.676873 | -24.202 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 502 | 4.044125737962072 | -0.738563 | -24.401 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 501 | 4.125457344917445 | -0.9198 | -33.5948 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 481 | 4.413251044837232 | -0.98789 | -30.3095 | 5 | 22 | 7 | 0.26 | 0.20 | - | no | Current |
| 500 | 4.744143382506253 | -0.613518 | -18.2226 | 5 | 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
-30.309kcal/mol
Ligand efficiency (LE)
-0.8660kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.735
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
489.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
46.76kcal/mol
Minimised FF energy
17.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
770.6Ų
Total solvent-accessible surface area of free ligand
BSA total
708.6Ų
Buried surface area upon binding
BSA apolar
558.9Ų
Hydrophobic contacts buried
BSA polar
149.7Ų
Polar contacts buried
Fraction buried
92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3198.8Ų
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
1469.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)