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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
21.2 kcal/mol
Protein clashes
4
Internal clashes
6
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.20
Reason: 6 internal clashes
4 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.740 kcal/mol/HA)
✓ Good fit quality (FQ -7.14)
✓ Good H-bonds (4 bonds)
✗ High strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-22.196
kcal/mol
LE
-0.740
kcal/mol/HA
Fit Quality
-7.14
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
4.83
cLogP
Interaction summary
HB 4
HY 24
PI 5
CLASH 6
Interaction summary
HB 4
HY 24
PI 5
CLASH 6
| Final rank | 61.027 | Score | -22.196 |
|---|---|---|---|
| Inter norm | -0.982 | Intra norm | 0.242 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 18 clashes; 3 protein clashes | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
GLY205
LEU208
LEU209
MET163
MET213
NAP301
PHE171
PHE97
PRO167
PRO210
SER207
TRP221
TYR174
VAL164
VAL206
| ||
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 | 0.65 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 662 | 3.645310442279257 | -0.620809 | -20.1903 | 2 | 11 | 10 | 0.53 | 0.20 | - | no | Open |
| 658 | 5.946912658772893 | -0.964374 | -28.5484 | 1 | 17 | 12 | 0.63 | 0.00 | - | no | Open |
| 656 | 5.3022857083799275 | -1.02366 | -29.3388 | 1 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 661 | 6.918944324914556 | -0.784578 | -22.4662 | 2 | 11 | 8 | 0.42 | 0.20 | - | yes | Open |
| 651 | 7.106490681562764 | -0.625911 | -18.0071 | 1 | 11 | 9 | 0.47 | 0.20 | - | yes | Open |
| 650 | 7.775682514053509 | -0.925604 | -16.2869 | 2 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 654 | 7.915336387760832 | -0.890753 | -20.5344 | 2 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 652 | 8.585268445025196 | -0.945524 | -24.3242 | 1 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 655 | 9.2475841540719 | -0.651262 | -17.5338 | 1 | 11 | 9 | 0.47 | 0.20 | - | yes | Open |
| 663 | 56.74400776727596 | -1.03735 | -29.4712 | 1 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 657 | 56.95628912620001 | -0.968237 | -20.6844 | 2 | 21 | 15 | 0.79 | 0.20 | - | yes | Open |
| 659 | 57.212325907207735 | -0.962844 | -25.4027 | 3 | 19 | 14 | 0.74 | 0.20 | - | yes | Open |
| 660 | 57.45071296749822 | -0.878981 | -18.4367 | 1 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 664 | 58.16650395574976 | -0.900094 | -23.646 | 1 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 649 | 58.27317098965996 | -1.07291 | -26.1517 | 2 | 19 | 15 | 0.79 | 0.00 | - | yes | Open |
| 653 | 61.02652196241503 | -0.982144 | -22.1956 | 3 | 19 | 15 | 0.79 | 0.20 | - | yes | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.196kcal/mol
Ligand efficiency (LE)
-0.7399kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.137
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
397.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.83
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.02kcal/mol
Minimised FF energy
83.83kcal/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.