Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.802 kcal/mol/HA)
✓ Good fit quality (FQ -7.73)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (28.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.053
kcal/mol
LE
-0.802
kcal/mol/HA
Fit Quality
-7.73
FQ (Leeson)
HAC
30
heavy atoms
MW
403
Da
LogP
3.03
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 28.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 0
| Final rank | 6.341676698106401 | Score | -24.053 |
|---|---|---|---|
| Inter norm | -1.02007 | Intra norm | 0.2183 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 16 clashes; 9 protein contact clashes; high strain Δ 32.2 | ||
| Residues | A:ALA170;A:ALA96;A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:LYS178;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.68 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2448 | 4.43025476137173 | -0.724578 | -17.3777 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2446 | 4.811263535841935 | -0.838167 | -22.8722 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1190 | 5.188799712693009 | -0.989104 | -28.8589 | 11 | 16 | 10 | 0.53 | 0.40 | - | no | Open |
| 2443 | 5.391074974530297 | -0.757442 | -18.1365 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2445 | 5.858421286376118 | -0.717704 | -17.3808 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3154 | 5.881722433582309 | -0.600199 | -16.5515 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1187 | 5.896663796908923 | -1.03069 | -24.8004 | 6 | 18 | 12 | 0.63 | 0.40 | - | no | Open |
| 944 | 6.341676698106401 | -1.02007 | -24.053 | 9 | 18 | 15 | 0.79 | 0.60 | - | no | Current |
| 1269 | 6.616379416893809 | -1.04489 | -25.9132 | 11 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 1426 | 7.684934071764042 | -0.644513 | -17.1447 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1427 | 7.72103723091868 | -0.725593 | -19.9932 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1658 | 8.319479369242973 | -0.859931 | -21.9247 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1271 | 8.762677921882279 | -0.767846 | -15.3776 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 3155 | 6.280535576007522 | -0.803675 | -22.5539 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1185 | 7.004903273740248 | -1.06544 | -29.1684 | 8 | 18 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1423 | 7.137169865838878 | -0.81878 | -19.5886 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 945 | 7.473452391652232 | -0.862383 | -17.5648 | 10 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 947 | 7.525586097632106 | -0.937799 | -23.5309 | 7 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 3156 | 7.566879764507743 | -0.671574 | -14.0023 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1659 | 7.581017482944879 | -0.782979 | -18.653 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3153 | 7.731428286409812 | -0.70986 | -17.5169 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1273 | 7.997819842706005 | -0.787361 | -16.7088 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1656 | 8.75904607583594 | -0.819234 | -16.5479 | 14 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1270 | 8.799021362722794 | -0.926116 | -20.2082 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1274 | 8.807534272336433 | -0.919791 | -28.4259 | 13 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 948 | 8.842389381576252 | -0.751559 | -21.4708 | 11 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1657 | 8.924955649897983 | -0.782984 | -15.3845 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 943 | 8.943002869404996 | -0.912966 | -29.3966 | 10 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1188 | 9.835762576659484 | -1.01183 | -25.6227 | 9 | 16 | 11 | 0.58 | 0.60 | - | yes | Open |
| 3157 | 10.030458887014385 | -0.647889 | -14.807 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1660 | 10.117558515744099 | -0.888167 | -19.7996 | 13 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3152 | 10.18413460686104 | -0.741307 | -15.0785 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1424 | 10.495114906518236 | -0.758356 | -13.5057 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1422 | 10.978468598909217 | -0.892376 | -24.7512 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 946 | 11.128849113051963 | -0.748415 | -15.9143 | 4 | 16 | 12 | 0.63 | 0.00 | - | yes | Open |
| 1272 | 12.868686833401883 | -0.93907 | -20.147 | 15 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1189 | 13.23969207115157 | -1.12038 | -30.2922 | 6 | 18 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1186 | 14.338220256165153 | -0.942833 | -20.5796 | 6 | 17 | 10 | 0.53 | 0.20 | - | yes | Open |
| 2444 | 14.339589112904978 | -0.840555 | -18.1266 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1425 | 14.464209250979884 | -0.827027 | -23.8307 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1655 | 14.737981827982527 | -0.953864 | -21.2357 | 13 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2447 | 14.780817739108691 | -0.828759 | -22.1668 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.053kcal/mol
Ligand efficiency (LE)
-0.8018kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.734
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
403.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.03
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.59kcal/mol
Minimised FF energy
68.98kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.