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 (-0.528 kcal/mol/HA)
✓ Good fit quality (FQ -4.87)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (42.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-13.737
kcal/mol
LE
-0.528
kcal/mol/HA
Fit Quality
-4.87
FQ (Leeson)
HAC
26
heavy atoms
MW
391
Da
LogP
2.82
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 42.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 5
Clashes 20
Severe clashes 2
| Final rank | 59.04500853296573 | Score | -13.7367 |
|---|---|---|---|
| Inter norm | -0.815942 | Intra norm | 0.287533 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 7 clashes; 2 protein clashes | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A: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 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1842 | 3.1133321991395055 | -0.87433 | -22.5365 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1841 | 4.3490622664198515 | -0.470213 | -13.1094 | 11 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 1440 | 4.908627513339317 | -1.28266 | -29.5944 | 12 | 18 | 15 | 0.79 | 0.80 | - | no | Open |
| 1844 | 5.0999335004630515 | -0.596796 | -18.3255 | 11 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1849 | 5.300776758589868 | -0.54038 | -15.6086 | 8 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1424 | 5.386715977883529 | -1.15004 | -21.6135 | 8 | 19 | 14 | 0.74 | 0.40 | - | no | Open |
| 1435 | 5.401482304974276 | -1.16516 | -25.2961 | 5 | 15 | 15 | 0.79 | 0.40 | - | no | Open |
| 1432 | 5.433666787232679 | -1.02471 | -21.8436 | 11 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 1425 | 5.4535910914822985 | -1.21892 | -25.3501 | 11 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 1416 | 5.576299776040164 | -1.26701 | -28.7135 | 9 | 16 | 12 | 0.63 | 0.40 | - | no | Open |
| 1433 | 5.759974328077087 | -1.07854 | -24.6109 | 10 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 1845 | 5.883909322814641 | -0.507212 | -16.5237 | 9 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 1428 | 6.209186179378377 | -1.17626 | -27.2084 | 9 | 18 | 14 | 0.74 | 0.40 | - | no | Open |
| 1823 | 5.1035358440697784 | -0.773741 | -20.5905 | 11 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1436 | 5.119286506811955 | -1.34529 | -30.3633 | 11 | 18 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1826 | 5.126648438580764 | -0.918548 | -22.6557 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1441 | 5.192300988836735 | -1.11339 | -28.2854 | 7 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1437 | 5.678936619115596 | -1.11262 | -28.8242 | 9 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1827 | 5.941639692641504 | -0.757272 | -16.4924 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1438 | 6.019794952602811 | -0.980844 | -26.2515 | 0 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1419 | 6.154678538083644 | -1.09421 | -30.9786 | 5 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1837 | 6.3700717800428 | -0.592518 | -15.6972 | 10 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1838 | 6.4853101464288025 | -0.895912 | -26.9883 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1830 | 6.578306443856781 | -0.943457 | -24.174 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1429 | 6.685470217730337 | -1.10933 | -24.016 | 10 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1442 | 6.786206373340011 | -0.900521 | -20.8384 | 3 | 18 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1846 | 6.83833503712086 | -0.788871 | -22.0966 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1421 | 7.146378835262468 | -1.27843 | -31.3904 | 7 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1825 | 7.354250639560291 | -0.66482 | -21.7701 | 12 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1829 | 7.357053210822859 | -0.726553 | -21.3484 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1833 | 7.387698361779618 | -0.428123 | -13.4339 | 7 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1835 | 7.504673721089589 | -0.654332 | -17.3787 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1847 | 7.57869342299191 | -0.677278 | -14.0309 | 13 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1832 | 7.901613241869535 | -0.820647 | -13.5796 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1423 | 8.079073671006576 | -0.908927 | -27.0417 | 1 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1834 | 8.883682836452696 | -0.851486 | -25.5961 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1417 | 8.973487742216555 | -1.10363 | -24.3159 | 9 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1824 | 9.016688398733075 | -0.793776 | -21.204 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1840 | 9.051065618289286 | -0.730282 | -18.324 | 13 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1430 | 9.20595737004045 | -1.09881 | -24.7765 | 8 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 1422 | 9.520085128769104 | -0.987988 | -14.5666 | 8 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1426 | 9.718393045779345 | -0.944885 | -24.0518 | 8 | 18 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1843 | 55.086316148686095 | -0.65112 | -12.7529 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1828 | 56.11678798918629 | -0.669467 | -10.7767 | 12 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1831 | 56.48667498271498 | -0.568472 | -18.2965 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1443 | 57.3690345187781 | -1.03474 | -27.0637 | 10 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1420 | 57.56334374756213 | -1.4697 | -25.327 | 13 | 18 | 14 | 0.74 | 0.80 | - | yes | Open |
| 1434 | 59.04500853296573 | -0.815942 | -13.7367 | 5 | 14 | 12 | 0.63 | 0.60 | - | yes | Current |
| 1418 | 59.67422971378323 | -1.17873 | -32.0992 | 10 | 18 | 16 | 0.84 | 0.60 | - | yes | Open |
| 1836 | 59.68810708578806 | -0.946597 | -25.3515 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1848 | 59.86731240161714 | -0.538505 | -15.278 | 13 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1822 | 60.17223480225931 | -0.960557 | -18.1922 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1431 | 62.18673615564879 | -0.781756 | -22.6074 | 2 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1427 | 62.350440283932656 | -0.945761 | -24.9819 | 3 | 19 | 15 | 0.79 | 0.00 | - | yes | Open |
| 1439 | 62.71052188688268 | -0.487396 | -5.12753 | 5 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1839 | 64.17637494874273 | -0.823076 | -19.3358 | 11 | 20 | 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
-13.737kcal/mol
Ligand efficiency (LE)
-0.5283kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.868
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
391.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.82
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.92kcal/mol
Minimised FF energy
81.76kcal/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.