Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA missing
Strain ΔE
10.2 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.267 kcal/mol/HA)
✓ Good fit quality (FQ -10.15)
✗ Moderate strain (10.2 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
ℹ SASA not computed
Score
-22.802
kcal/mol
LE
-1.267
kcal/mol/HA
Fit Quality
-10.15
FQ (Leeson)
HAC
18
heavy atoms
MW
258
Da
LogP
3.00
cLogP
Interaction summary
HB 2
HY 14
PI 3
CLASH 2
Interaction summary
HB 2
HY 14
PI 3
CLASH 2
| Final rank | 1.498 | Score | -22.802 |
|---|---|---|---|
| Inter norm | -1.305 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 1 |
| Artifact reason | geometry warning; 3 clashes; 6 protein contact clashes | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
TYR191
TYR194
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: 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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1379 | 1.4983702612961016 | -1.30538 | -22.8022 | 1 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.802kcal/mol
Ligand efficiency (LE)
-1.2668kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.152
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
258.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-6.76kcal/mol
Minimised FF energy
-16.92kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.