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
34.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.50, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.833 kcal/mol/HA)
✓ Good fit quality (FQ -8.26)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (34.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (10)
Score
-27.480
kcal/mol
LE
-0.833
kcal/mol/HA
Fit Quality
-8.26
FQ (Leeson)
HAC
33
heavy atoms
MW
483
Da
LogP
3.01
cLogP
Interaction summary
HB 1
HY 23
PI 2
CLASH 3
Interaction summary
HB 1
HY 23
PI 2
CLASH 3
| Final rank | 0.887 | Score | -27.480 |
|---|---|---|---|
| Inter norm | -0.774 | Intra norm | -0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 1 |
| Artifact reason | geometry warning; 10 clashes; 3 protein contact clashes; 1 cofactor-context clash; high strain Δ 34.0 | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
TYR191
TYR194
VAL237
| ||
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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
A:NDP302
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 10 | Native recall | 0.53 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 423 | 0.5779680781020033 | -0.879258 | -25.5601 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 0.8866961236497148 | -0.774494 | -27.4796 | 1 | 11 | 10 | 0.53 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.480kcal/mol
Ligand efficiency (LE)
-0.8327kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.262
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
482.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-24.78kcal/mol
Minimised FF energy
-58.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
736.6Ų
Total solvent-accessible surface area of free ligand
BSA total
552.8Ų
Buried surface area upon binding
BSA apolar
396.9Ų
Hydrophobic contacts buried
BSA polar
155.9Ų
Polar contacts buried
Fraction buried
75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1705.9Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1017.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)