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 high
Native mixed
SASA done
Strain ΔE
16.9 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.19, Jaccard 0.14, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.213 kcal/mol/HA)
✓ Good fit quality (FQ -11.18)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (16.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-31.541
kcal/mol
LE
-1.213
kcal/mol/HA
Fit Quality
-11.18
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
4.45
cLogP
Interaction summary
HB 7
HY 24
PI 0
CLASH 2
Interaction summary
HB 7
HY 24
PI 0
CLASH 2
| Final rank | 2.009 | Score | -31.541 |
|---|---|---|---|
| Inter norm | -1.224 | Intra norm | 0.011 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash | ||
| Residues |
ALA363
ALA365
ASP327
CYS52
CYS57
GLY56
LEU334
LYS60
NDP800
PHE367
PRO336
SER14
SER364
THR335
THR51
| ||
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 | 5 | Native recall | 0.19 |
| Jaccard | 0.14 | 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 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 526 | 0.6409395339681533 | -1.2315 | -30.6716 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 2.0089429246725263 | -1.22432 | -31.5412 | 7 | 15 | 5 | 0.19 | 0.40 | - | no | Current |
| 583 | 2.028788667769846 | -0.89851 | -17.9649 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 558 | 3.035354955052957 | -0.855052 | -14.8555 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 3.145909239658254 | -1.06862 | -21.7447 | 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
-31.541kcal/mol
Ligand efficiency (LE)
-1.2131kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.177
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.45
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.02kcal/mol
Minimised FF energy
101.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.0Ų
Total solvent-accessible surface area of free ligand
BSA total
541.2Ų
Buried surface area upon binding
BSA apolar
474.8Ų
Hydrophobic contacts buried
BSA polar
66.5Ų
Polar contacts buried
Fraction buried
90.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3098.3Ų
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
1496.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)