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
24.6 kcal/mol
Protein clashes
2
Internal clashes
8
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.20
Reason: 8 internal clashes
2 protein-contact clashes
8 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.820 kcal/mol/HA)
✓ Good fit quality (FQ -16.07)
✓ Good H-bonds (3 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (8)
Score
-41.870
kcal/mol
LE
-1.820
kcal/mol/HA
Fit Quality
-16.07
FQ (Leeson)
HAC
23
heavy atoms
MW
331
Da
LogP
2.93
cLogP
Interaction summary
HB 3
HY 21
PI 5
CLASH 0
Interaction summary
HB 3
HY 21
PI 5
CLASH 0
| Final rank | 0.056 | Score | -41.870 |
|---|---|---|---|
| Inter norm | -1.356 | Intra norm | -0.464 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 3 |
| Artifact reason | geometry warning; 8 clashes; 2 protein contact clashes; 1 cofactor-context clash; very favorable intra outlier; moderate strain Δ 24.6 | ||
| Residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
SER111
SER227
TYR191
TYR194
| ||
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 | 0.63 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 533 | 0.05601415744938339 | -1.35636 | -41.8697 | 3 | 12 | 12 | 0.63 | 0.20 | - | no | Current |
| 524 | 4.127316334406169 | -1.49003 | -41.4757 | 11 | 19 | 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
-41.870kcal/mol
Ligand efficiency (LE)
-1.8204kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-16.067
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
331.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.93
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.09kcal/mol
Minimised FF energy
59.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
556.4Ų
Total solvent-accessible surface area of free ligand
BSA total
469.1Ų
Buried surface area upon binding
BSA apolar
315.8Ų
Hydrophobic contacts buried
BSA polar
153.3Ų
Polar contacts buried
Fraction buried
84.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1523.5Ų
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
1024.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)