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 strong
SASA done
Strain ΔE
39.8 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.831 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✓ Good H-bonds (5 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (39.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-29.081
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
35
heavy atoms
MW
479
Da
LogP
2.03
cLogP
Final rank
2.3921
rank score
Inter norm
-0.985
normalised
Contacts
16
H-bonds 7
Interaction summary
HBD 3
HBA 2
HY 7
PI 4
CLASH 2
Interaction summary
HBD 3
HBA 2
HY 7
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.83 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 14 | 2.3921481588111457 | -0.9847 | -29.0807 | 7 | 16 | 14 | 0.74 | 0.80 | - | no | Current |
| 16 | 2.663819250670003 | -0.807209 | -20.3115 | 5 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.081kcal/mol
Ligand efficiency (LE)
-0.8309kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.381
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
478.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.20kcal/mol
Minimised FF energy
-14.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
790.4Ų
Total solvent-accessible surface area of free ligand
BSA total
594.5Ų
Buried surface area upon binding
BSA apolar
474.2Ų
Hydrophobic contacts buried
BSA polar
120.2Ų
Polar contacts buried
Fraction buried
75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1798.9Ų
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
1025.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)