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 mixed
SASA done
Strain ΔE
23.9 kcal/mol
Protein clashes
2
Internal clashes
7
Native overlap
contact recall 0.47, Jaccard 0.47, H-bond role recall 0.40
Reason: 7 internal clashes
2 protein-contact clashes
7 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.124 kcal/mol/HA)
✓ Good fit quality (FQ -10.07)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ High strain energy (23.9 kcal/mol)
✗ Geometry warnings
Score
-26.980
kcal/mol
LE
-1.124
kcal/mol/HA
Fit Quality
-10.07
FQ (Leeson)
HAC
24
heavy atoms
MW
354
Da
LogP
2.94
cLogP
Final rank
1.0759
rank score
Inter norm
-1.172
normalised
Contacts
9
H-bonds 3
Interaction summary
HBA 2
PC 1
HY 3
PI 4
CLASH 7
Interaction summary
HBA 2
PC 1
HY 3
PI 4
CLASH 7
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 9 | Native recall | 0.47 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 474 | 1.0759279908145714 | -1.17192 | -26.9797 | 3 | 9 | 9 | 0.47 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.980kcal/mol
Ligand efficiency (LE)
-1.1242kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.075
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
354.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.94
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
34.24kcal/mol
Minimised FF energy
10.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
526.6Ų
Total solvent-accessible surface area of free ligand
BSA total
399.6Ų
Buried surface area upon binding
BSA apolar
248.9Ų
Hydrophobic contacts buried
BSA polar
150.7Ų
Polar contacts buried
Fraction buried
75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1485.2Ų
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
1046.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)