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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
27.0 kcal/mol
Protein clashes
2
Internal clashes
6
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.00
Reason: 6 internal clashes
2 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.463 kcal/mol/HA)
✓ Good fit quality (FQ -4.56)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (27.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (10)
Score
-14.826
kcal/mol
LE
-0.463
kcal/mol/HA
Fit Quality
-4.56
FQ (Leeson)
HAC
32
heavy atoms
MW
494
Da
LogP
3.50
cLogP
Interaction summary
HB 2
HY 20
PI 3
CLASH 6
Interaction summary
HB 2
HY 20
PI 3
CLASH 6
| Final rank | 0.661 | Score | -14.826 |
|---|---|---|---|
| Inter norm | -0.748 | Intra norm | 0.285 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 2 |
| Artifact reason | geometry warning; 10 clashes; 2 protein contact clashes; 4 cofactor-context clashes; moderate strain Δ 27.0 | ||
| Residues |
ARG17
ASP232
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
VAL237
ARG287
| ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 523 | 0.6607101623108528 | -0.747814 | -14.8258 | 2 | 14 | 12 | 0.63 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-14.826kcal/mol
Ligand efficiency (LE)
-0.4633kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.556
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
494.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.50
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
28.59kcal/mol
Minimised FF energy
1.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
777.4Ų
Total solvent-accessible surface area of free ligand
BSA total
565.1Ų
Buried surface area upon binding
BSA apolar
437.6Ų
Hydrophobic contacts buried
BSA polar
127.5Ų
Polar contacts buried
Fraction buried
72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1727.4Ų
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
1036.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)