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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.141 kcal/mol/HA)
✓ Good fit quality (FQ -9.73)
✗ High strain energy (15.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.958
kcal/mol
LE
-1.141
kcal/mol/HA
Fit Quality
-9.73
FQ (Leeson)
HAC
21
heavy atoms
MW
288
Da
LogP
-0.67
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 15.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 21
π–π 1
Clashes 6
Severe clashes 0
| Final rank | 52.64861941163747 | Score | -23.958 |
|---|---|---|---|
| Inter norm | -1.13461 | Intra norm | -0.00624754 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 2 |
| Artifact reason | geometry warning; 8 clashes; 6 protein contact clashes | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU209;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER207;A:TRP221;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 | 11 | Native recall | 0.58 |
| Jaccard | 0.58 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 16 | 1.7560141062214014 | -1.20663 | -25.5475 | 1 | 13 | 13 | 0.68 | 0.00 | - | no | Open |
| 10 | 1.888172377929454 | -1.02472 | -22.0146 | 1 | 12 | 12 | 0.63 | 0.00 | - | no | Open |
| 26 | 2.0971161853979896 | -0.987236 | -20.8219 | 1 | 13 | 12 | 0.63 | 0.00 | - | no | Open |
| 22 | 2.3059671867532634 | -0.793874 | -17.0018 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 24 | 2.719865414046415 | -0.885439 | -18.4534 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 2.720342691899464 | -0.998332 | -21.0876 | 0 | 11 | 11 | 0.58 | 0.00 | - | no | Open |
| 44 | 2.776218763839954 | -1.13179 | -23.7886 | 3 | 13 | 12 | 0.63 | 0.20 | - | no | Open |
| 23 | 2.7925734656953995 | -0.850217 | -18.2791 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 2.824599960540031 | -0.934707 | -19.7402 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 39 | 3.0358277480960867 | -1.15845 | -24.4342 | 1 | 10 | 10 | 0.53 | 0.00 | - | no | Open |
| 39 | 3.2466134400556075 | -0.874566 | -18.4155 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 4.215436318075171 | -1.08393 | -22.8918 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 52.26417434047719 | -1.19576 | -25.2364 | 4 | 13 | 12 | 0.63 | 0.40 | - | no | Open |
| 19 | 52.58415827640906 | -1.12439 | -23.7074 | 0 | 14 | 13 | 0.68 | 0.00 | - | no | Open |
| 33 | 52.64861941163747 | -1.13461 | -23.958 | 2 | 11 | 11 | 0.58 | 0.20 | - | no | Current |
| 16 | 52.69845691933538 | -0.889031 | -18.9359 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 19 | 52.72717374331903 | -0.841579 | -17.6051 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 22 | 52.76032570906284 | -1.21454 | -25.2705 | 6 | 13 | 12 | 0.63 | 0.40 | - | no | Open |
| 44 | 52.77588432662359 | -0.896991 | -19.1527 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 35 | 52.805144278223956 | -1.2672 | -26.8236 | 1 | 14 | 13 | 0.68 | 0.00 | - | no | Open |
| 27 | 52.83680157601255 | -1.27807 | -27.3117 | 1 | 13 | 13 | 0.68 | 0.00 | - | no | Open |
| 28 | 52.87468656523788 | -0.899015 | -18.7025 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 53.13206041892625 | -1.02499 | -21.6205 | 5 | 13 | 12 | 0.63 | 0.20 | - | no | Open |
| 33 | 53.27094344215489 | -0.768857 | -16.7147 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 27 | 53.37976920300719 | -0.852124 | -17.8965 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 53.462242195449626 | -1.17254 | -22.9983 | 7 | 12 | 11 | 0.58 | 0.40 | - | no | Open |
| 21 | 53.48614102642408 | -0.952122 | -20.1812 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 43 | 53.549751793027625 | -0.979847 | -20.9789 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 25 | 53.59769501294243 | -0.926057 | -19.7788 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 53.6469381599786 | -1.03807 | -22.2103 | 6 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 40 | 53.706935309317146 | -1.00825 | -21.3763 | 5 | 13 | 12 | 0.63 | 0.20 | - | no | Open |
| 21 | 53.75030056218244 | -1.10562 | -22.8594 | 7 | 12 | 11 | 0.58 | 0.40 | - | no | Open |
| 34 | 53.76049903062781 | -0.968239 | -20.3316 | 5 | 14 | 14 | 0.74 | 0.20 | - | no | Open |
| 24 | 53.94138138425924 | -1.00732 | -20.9877 | 2 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 38 | 53.28621482057616 | -1.28509 | -26.5306 | 6 | 10 | 10 | 0.53 | 0.40 | - | yes | Open |
| 15 | 53.37899721963296 | -0.924536 | -19.6857 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 37 | 53.41914277155535 | -1.5352 | -32.2935 | 6 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 39 | 53.54989418798989 | -0.890216 | -19.0501 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 8 | 53.64400949393495 | -1.26802 | -26.1285 | 6 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 22 | 53.650480652086905 | -0.912603 | -19.8481 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 38 | 53.66326954672378 | -0.904199 | -19.1306 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 6 | 53.69425420051818 | -1.52723 | -32.1329 | 7 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 31 | 53.73114069396836 | -0.74637 | -16.2757 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 14 | 53.784145888715294 | -0.923804 | -19.8637 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 36 | 53.79571093022694 | -0.971543 | -20.8064 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 29 | 53.91210198945252 | -0.984496 | -20.8161 | 3 | 14 | 13 | 0.68 | 0.20 | - | yes | Open |
| 28 | 53.998680886361726 | -1.37702 | -29.5134 | 5 | 11 | 10 | 0.53 | 0.40 | - | yes | Open |
| 30 | 54.03758036711071 | -0.927113 | -19.6165 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 17 | 54.145119277616416 | -0.844835 | -18.2477 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 36 | 54.36174901373821 | -1.34554 | -27.5203 | 7 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 42 | 54.410595272526315 | -0.833651 | -17.7547 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 9 | 54.53920127476467 | -1.1452 | -24.235 | 2 | 10 | 10 | 0.53 | 0.20 | - | yes | Open |
| 48 | 54.56665987471909 | -1.41094 | -30.0909 | 5 | 11 | 10 | 0.53 | 0.40 | - | yes | Open |
| 26 | 54.58354594644788 | -0.917636 | -19.7573 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 18 | 54.588578873450686 | -0.826281 | -17.5692 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 29 | 54.60442916440621 | -1.10663 | -23.17 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 37 | 54.69564411766596 | -1.0421 | -21.953 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 52 | 54.91200480920365 | -1.39577 | -29.3336 | 7 | 11 | 10 | 0.53 | 0.40 | - | yes | Open |
| 42 | 54.95176444371878 | -1.18138 | -24.6405 | 1 | 14 | 14 | 0.74 | 0.00 | - | yes | Open |
| 20 | 55.00709281260365 | -1.26243 | -26.2758 | 13 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 15 | 55.028144702503816 | -0.894835 | -18.2001 | 1 | 13 | 12 | 0.63 | 0.00 | - | yes | Open |
| 35 | 55.15056366108062 | -0.944746 | -20.0766 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 11 | 55.1517158582631 | -1.09833 | -23.012 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 37 | 55.19935192456473 | -0.949471 | -20.419 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 29 | 55.2006519318776 | -0.935121 | -20.1249 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 42 | 55.235468046944995 | -1.05979 | -19.4561 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 34 | 55.2866860802012 | -0.878742 | -18.8771 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 13 | 55.32220505572965 | -0.988989 | -20.9711 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 5 | 55.385222193391996 | -1.33666 | -27.756 | 7 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 25 | 55.46201919274124 | -1.14812 | -24.2354 | 4 | 13 | 13 | 0.68 | 0.20 | - | yes | Open |
| 30 | 55.467221947777986 | -1.09381 | -22.6652 | 4 | 13 | 12 | 0.63 | 0.20 | - | yes | Open |
| 47 | 55.57946463664375 | -1.01958 | -21.2147 | 2 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 35 | 55.617760955107556 | -0.990163 | -20.546 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 46 | 55.69221114155544 | -1.0317 | -21.7306 | 6 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 41 | 55.80107234560119 | -1.09861 | -23.378 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 32 | 55.846774171323666 | -1.12188 | -23.738 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 40 | 55.963552519495025 | -0.969057 | -20.7058 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 13 | 55.98892683665186 | -1.25038 | -26.6135 | 9 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 50 | 56.04549935196316 | -1.31584 | -27.4031 | 6 | 17 | 14 | 0.74 | 0.60 | - | yes | Open |
| 23 | 56.15757848681047 | -1.19707 | -25.4276 | 5 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 16 | 56.183903444781606 | -1.02049 | -21.7965 | 12 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 17 | 56.240180015864325 | -1.01651 | -21.52 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 25 | 56.25300248382341 | -1.00391 | -21.1675 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 33 | 56.25857546118402 | -1.0745 | -23.2704 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 15 | 56.36722555700875 | -1.08569 | -23.3267 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 14 | 56.40397003375172 | -1.38796 | -28.4136 | 9 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 23 | 56.40698898604623 | -1.07561 | -23.0374 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 41 | 56.41735339438745 | -1.41437 | -28.8529 | 9 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 11 | 56.487487393655 | -1.27641 | -27.0019 | 3 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
| 32 | 56.577108395603126 | -1.32999 | -28.2955 | 7 | 17 | 14 | 0.74 | 0.60 | - | yes | Open |
| 30 | 56.598044270859596 | -0.811125 | -17.2005 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 19 | 56.60635018785296 | -1.12653 | -21.1297 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 21 | 56.66724244667868 | -0.838974 | -17.4467 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 28 | 56.784849550759446 | -1.00856 | -20.9607 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 14 | 56.7998328973748 | -0.834001 | -17.814 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 12 | 56.99671884141425 | -1.07444 | -22.1978 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 7 | 57.18365220240859 | -0.767566 | -15.6338 | 2 | 14 | 12 | 0.63 | 0.20 | - | yes | Open |
| 34 | 57.23510661455563 | -1.04449 | -21.8342 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 31 | 57.251613643566316 | -0.937705 | -19.9232 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 38 | 57.32801367218756 | -0.962826 | -20.3055 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 31 | 57.46251885364829 | -1.21302 | -25.9728 | 10 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 43 | 57.87133951436225 | -0.948598 | -19.8894 | 0 | 12 | 12 | 0.63 | 0.00 | - | yes | Open |
| 49 | 58.075512616438495 | -1.02246 | -21.1921 | 4 | 14 | 13 | 0.68 | 0.20 | - | yes | Open |
| 17 | 58.24690058891521 | -0.908155 | -18.7471 | 1 | 12 | 12 | 0.63 | 0.00 | - | yes | Open |
| 32 | 58.61523045284797 | -0.829511 | -17.8164 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 40 | 58.61559147573556 | -0.828558 | -17.6854 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 24 | 58.78507323108733 | -0.94474 | -20.3446 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 41 | 58.88667461864863 | -0.895601 | -18.7272 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 27 | 59.04685444691613 | -0.990546 | -21.0607 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 13 | 59.6351791078979 | -0.815067 | -16.8026 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 18 | 63.3464280799657 | -1.09942 | -22.5372 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 26 | 63.39848281625264 | -0.94836 | -19.8108 | 7 | 16 | 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
-23.958kcal/mol
Ligand efficiency (LE)
-1.1409kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.731
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
288.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.67
Lipinski: ≤ 5
Rotatable bonds
0
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.46kcal/mol
Minimised FF energy
59.40kcal/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.