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
20.6 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.80
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.038 kcal/mol/HA)
✓ Good fit quality (FQ -10.01)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (20.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-31.138
kcal/mol
LE
-1.038
kcal/mol/HA
Fit Quality
-10.01
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
2.84
cLogP
Interaction summary
HB 5
HY 24
PI 4
CLASH 4
Interaction summary
HB 5
HY 24
PI 4
CLASH 4
| Final rank | 2.982 | Score | -31.138 |
|---|---|---|---|
| Inter norm | -1.124 | Intra norm | 0.086 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 19 clashes; 1 protein clash; 3 cofactor-context clashes; moderate strain Δ 20.6 | ||
| Residues |
ARG17
ASP232
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
SER111
SER112
TYR194
VAL230
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 15 | 2.183193883230364 | -1.11694 | -33.1782 | 5 | 12 | 12 | 0.63 | 0.80 | - | no | Open |
| 36 | 2.981557588522365 | -1.12397 | -31.1384 | 5 | 15 | 14 | 0.74 | 0.80 | - | no | Current |
| 12 | 3.33297460468041 | -0.731541 | -21.4791 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 5 | 3.5055674267181955 | -1.06865 | -30.3475 | 8 | 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
-31.138kcal/mol
Ligand efficiency (LE)
-1.0379kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.012
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
399.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.72kcal/mol
Minimised FF energy
37.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
658.9Ų
Total solvent-accessible surface area of free ligand
BSA total
529.2Ų
Buried surface area upon binding
BSA apolar
428.1Ų
Hydrophobic contacts buried
BSA polar
101.1Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1678.0Ų
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
1041.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)