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 medium
Native strong
SASA missing
Strain ΔE
36.2 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.40
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.056 kcal/mol/HA)
✓ Good fit quality (FQ -10.38)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (36.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-33.776
kcal/mol
LE
-1.056
kcal/mol/HA
Fit Quality
-10.38
FQ (Leeson)
HAC
32
heavy atoms
MW
434
Da
LogP
4.07
cLogP
Interaction summary
HB 9
HY 24
PI 5
CLASH 1
Interaction summary
HB 9
HY 24
PI 5
CLASH 1
| Final rank | 7.811 | Score | -33.776 |
|---|---|---|---|
| Inter norm | -0.936 | Intra norm | -0.119 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 17 clashes; 1 protein clash; high strain Δ 43.0 | ||
| Residues |
ALA170
ARG14
ASP161
CYS168
GLU217
LEU208
LEU209
LYS178
LYS220
MET169
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
TRP221
TYR174
| ||
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1406 | 4.597080988345055 | -0.985915 | -22.99 | 7 | 15 | 11 | 0.58 | 0.60 | - | no | Open |
| 1404 | 4.661917681470836 | -0.82314 | -23.9565 | 4 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 3499 | 4.710478616573362 | -0.670633 | -22.313 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2131 | 5.97113929719616 | -0.575467 | -14.5233 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2132 | 6.5542935964349205 | -0.68026 | -22.1842 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2123 | 6.672741907279237 | -0.590838 | -21.5145 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2127 | 7.717351609018184 | -0.652045 | -19.1483 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2125 | 7.750248059263065 | -0.640842 | -22.5904 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3504 | 8.229408185792026 | -0.859572 | -33.8612 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3503 | 8.706219372901863 | -0.665477 | -26.3443 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1405 | 5.7479251539054985 | -0.785898 | -30.7464 | 4 | 16 | 16 | 0.84 | 0.40 | - | yes | Open |
| 3497 | 7.0204175697363596 | -0.649422 | -18.5732 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3506 | 7.184725648542509 | -0.720953 | -21.8427 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1413 | 7.1859422124202785 | -0.966079 | -21.9788 | 7 | 18 | 13 | 0.68 | 0.60 | - | yes | Open |
| 3505 | 7.738642189576931 | -0.619665 | -19.6418 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1408 | 7.810830650880446 | -0.936013 | -33.7764 | 5 | 18 | 14 | 0.74 | 0.40 | - | yes | Current |
| 3507 | 8.321725388643328 | -0.61981 | -20.6343 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1412 | 8.422852477168364 | -0.886485 | -23.4202 | 7 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2124 | 8.515970032523061 | -0.748819 | -21.3543 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2129 | 8.632322088371021 | -0.684813 | -15.2213 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1411 | 8.785940220908063 | -0.735865 | -24.2711 | 5 | 12 | 11 | 0.58 | 0.60 | - | yes | Open |
| 3498 | 9.258651404018638 | -0.702783 | -19.1563 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1409 | 9.669341810718509 | -1.02054 | -36.6574 | 8 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1414 | 9.757141253879212 | -0.94632 | -24.0378 | 9 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2126 | 9.90165099956009 | -0.628696 | -26.6578 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3502 | 10.196185795286425 | -0.713848 | -25.5859 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2121 | 10.331879163539698 | -0.650216 | -11.4523 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1407 | 56.35447134801713 | -0.855775 | -21.4011 | 8 | 15 | 12 | 0.63 | 0.60 | - | yes | Open |
| 3508 | 59.44618331896669 | -0.658809 | -18.4045 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3501 | 59.72221200964438 | -0.661087 | -21.9454 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2122 | 60.0408513723887 | -0.640144 | -23.4261 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2128 | 60.084965041717744 | -0.657502 | -24.2603 | 10 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3500 | 60.142599288718245 | -0.685896 | -21.2838 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2130 | 60.62519173416365 | -0.658992 | -22.3718 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1410 | 61.20997923312359 | -0.953088 | -24.7181 | 9 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1415 | 61.25658247783677 | -0.918798 | -21.2035 | 8 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-33.776kcal/mol
Ligand efficiency (LE)
-1.0555kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.380
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
434.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.07
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
131.88kcal/mol
Minimised FF energy
95.66kcal/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.