Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
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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 medium
Native strong
SASA missing
Strain ΔE
14.8 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.75, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.058 kcal/mol/HA)
✓ Good fit quality (FQ -9.74)
✓ Strong H-bond network (13 bonds)
✗ Moderate strain (14.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Internal clashes (5)
ℹ SASA not computed
Score
-27.500
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
26
heavy atoms
MW
368
Da
LogP
3.48
cLogP
Interaction summary
HB 13
HY 22
PI 4
CLASH 3
Interaction summary
HB 13
HY 22
PI 4
CLASH 3
| Final rank | 2.889 | Score | -27.500 |
|---|---|---|---|
| Inter norm | -1.200 | Intra norm | 0.142 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 5 clashes; 8 protein contact clashes; moderate strain Δ 15.8 | ||
| Residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE97
PRO210
SER95
TRP221
TYR174
VAL206
VAL211
| ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
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:NAP301
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 367 | 2.889302566751153 | -1.20007 | -27.4996 | 6 | 16 | 15 | 0.79 | 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
-27.500kcal/mol
Ligand efficiency (LE)
-1.0577kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.745
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
368.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.48
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.90kcal/mol
Minimised FF energy
37.06kcal/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.