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
Reject
No SASA yet
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA missing
Strain ΔE
29.7 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.68, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.910 kcal/mol/HA)
✓ Good fit quality (FQ -9.25)
✗ High strain energy (29.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (16)
ℹ SASA not computed
Score
-32.754
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-9.25
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
5.06
cLogP
Interaction summary
HB 2
HY 24
PI 4
CLASH 4
Interaction summary
HB 2
HY 24
PI 4
CLASH 4
| Final rank | 5.879 | Score | -32.754 |
|---|---|---|---|
| Inter norm | -0.796 | Intra norm | -0.114 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 1 |
| Artifact reason | geometry warning; 16 clashes; 7 protein contact clashes; high strain Δ 32.3 | ||
| Residues |
ARG14
ASP161
LEU208
LEU209
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
TRP221
TYR174
TYR98
| ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| 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 | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2184 | 4.614540518243182 | -0.818501 | -26.2491 | 2 | 17 | 14 | 0.74 | 0.00 | - | no | Open |
| 2183 | 4.68727944917791 | -0.690042 | -22.7785 | 0 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 3165 | 5.335877589857202 | -0.707983 | -27.7628 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2186 | 5.879476557389142 | -0.795684 | -32.7539 | 1 | 13 | 13 | 0.68 | 0.00 | - | no | Current |
| 3160 | 7.490407099445143 | -0.580747 | -17.3863 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3161 | 7.882129821552622 | -0.72906 | -17.4267 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2187 | 6.585916680181024 | -0.695498 | -23.5563 | 0 | 14 | 13 | 0.68 | 0.00 | - | yes | Open |
| 2188 | 6.638558359145298 | -0.782849 | -29.2739 | 0 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2185 | 8.632533309205227 | -0.784229 | -32.4514 | 5 | 16 | 12 | 0.63 | 0.20 | - | yes | Open |
| 3163 | 9.230738807532372 | -0.704018 | -30.3141 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3164 | 12.54575112579421 | -0.692076 | -22.3496 | 3 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3162 | 13.238925520518073 | -0.678001 | -25.0814 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.754kcal/mol
Ligand efficiency (LE)
-0.9098kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.247
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
481.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.06
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.55kcal/mol
Minimised FF energy
111.83kcal/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.