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.
✓ Good LE (-0.354 kcal/mol/HA)
✓ Good fit quality (FQ -3.62)
✗ Very high strain energy (55.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-13.082
kcal/mol
LE
-0.354
kcal/mol/HA
Fit Quality
-3.62
FQ (Leeson)
HAC
37
heavy atoms
MW
504
Da
LogP
1.03
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 55.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 0
Clashes 8
Severe clashes 1
| Final rank | 56.65342978202953 | Score | -13.0818 |
|---|---|---|---|
| Inter norm | -0.616097 | Intra norm | 0.262536 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 17 clashes; 1 protein clash | ||
| Residues | A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:VAL156;A:VAL49;A:VAL87 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 13 | Native recall | 0.65 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1982 | 4.096259971016183 | -0.572995 | -20.2156 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1980 | 4.158249591625412 | -0.641065 | -22.7849 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1989 | 4.360020024950123 | -0.503326 | -17.0968 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1991 | 4.637679115752923 | -0.530664 | -19.1092 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1995 | 4.681642512188212 | -0.549548 | -19.566 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2007 | 4.728917301729567 | -0.522515 | -18.905 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1564 | 4.751021351776478 | -0.608635 | -20.3641 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1988 | 5.215160003345578 | -0.647752 | -22.4615 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 995 | 5.219422446519349 | -0.405309 | -12.2782 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1997 | 5.28694492462732 | -0.61169 | -21.1481 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2005 | 5.536329650338111 | -0.501747 | -15.8265 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1573 | 5.569455912754119 | -0.598456 | -19.9988 | 1 | 18 | 13 | 0.65 | 0.20 | - | no | Open |
| 2008 | 5.595525679020442 | -0.482142 | -17.7102 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2011 | 5.7750846501833735 | -0.784897 | -24.5686 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1572 | 5.7945423896701245 | -0.63738 | -23.3911 | 2 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 996 | 5.810609518220929 | -0.386828 | -13.7685 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1571 | 5.8810155507853565 | -0.689462 | -24.1981 | 2 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1558 | 5.945572642860268 | -0.657335 | -23.4504 | 1 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 1549 | 6.005282614407176 | -0.722507 | -22.778 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 1556 | 6.013149890304173 | -0.686235 | -24.2541 | 2 | 18 | 18 | 0.90 | 0.20 | - | no | Open |
| 2002 | 6.107744975399211 | -0.559521 | -18.8946 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1545 | 6.11777221370727 | -0.542402 | -16.5689 | 1 | 11 | 10 | 0.50 | 0.00 | - | no | Open |
| 1983 | 6.159101112080368 | -0.546611 | -18.126 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1548 | 6.259073668104662 | -0.7054 | -21.3948 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1555 | 6.299798675604545 | -0.628249 | -22.0899 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 1565 | 6.452837692677551 | -0.627657 | -20.0804 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 2009 | 6.463014201239348 | -0.697549 | -24.0513 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1994 | 6.594878570292005 | -0.560484 | -17.9487 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1563 | 6.637403061038889 | -0.623184 | -18.9155 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 999 | 6.905448035310564 | -0.440955 | -14.8641 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1987 | 54.09786479047063 | -0.570002 | -19.0007 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 997 | 54.18218672431736 | -0.486661 | -14.2956 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2003 | 54.25294961820678 | -0.723951 | -25.816 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 993 | 54.304458356107205 | -0.529664 | -18.9152 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1984 | 54.436201706773154 | -0.622936 | -22.6373 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1561 | 54.47965933788253 | -0.585923 | -18.3256 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1569 | 54.55756551657956 | -0.619853 | -19.5582 | 2 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1570 | 54.608118765129404 | -0.619901 | -19.6765 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 994 | 54.682384852141176 | -0.381592 | -12.3033 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1986 | 54.73932406985215 | -0.491774 | -17.1184 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1576 | 54.74476402566062 | -0.628727 | -18.0065 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 1547 | 54.841400359034566 | -0.602312 | -17.2037 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1985 | 54.84649941750429 | -0.50762 | -13.4629 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1562 | 55.09807263404506 | -0.5379 | -16.0877 | 2 | 18 | 18 | 0.90 | 0.20 | - | no | Open |
| 1550 | 55.2516414641922 | -0.64553 | -20.12 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1552 | 55.252108829680054 | -0.680654 | -20.1834 | 1 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1546 | 55.25514050599857 | -0.543414 | -21.7406 | 1 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 2004 | 55.34155556395291 | -0.527064 | -18.7573 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1981 | 55.45541501422659 | -0.615658 | -25.8126 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1559 | 55.58329648944083 | -0.692946 | -21.2217 | 1 | 16 | 14 | 0.70 | 0.20 | - | no | Open |
| 2000 | 55.63817344882523 | -0.476478 | -16.3522 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1575 | 55.96471653637596 | -0.727994 | -20.9738 | 2 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 1567 | 56.77731985642442 | -0.661411 | -20.0134 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 1553 | 56.82553773746523 | -0.555292 | -14.4536 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 2012 | 56.90373105904995 | -0.543908 | -16.6172 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2015 | 55.07754897802556 | -0.527916 | -17.9933 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2006 | 55.42605143595837 | -0.487338 | -19.1369 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 992 | 55.45961957900708 | -0.548704 | -20.4534 | 1 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1560 | 55.67401635625515 | -0.691498 | -17.8294 | 1 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 998 | 55.770518992034255 | -0.435576 | -16.8519 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1551 | 55.83491794408026 | -0.645372 | -22.1622 | 0 | 21 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1998 | 55.96494228781032 | -0.529681 | -19.5652 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2013 | 56.02728392909035 | -0.532941 | -16.8002 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1557 | 56.1276426361327 | -0.587268 | -20.5965 | 0 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 2014 | 56.2760765542486 | -0.570324 | -19.9009 | 2 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1566 | 56.46968964377703 | -0.67603 | -21.8869 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 2010 | 56.47000001669766 | -0.613575 | -21.3112 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1992 | 56.54976176385149 | -0.576141 | -19.258 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1568 | 56.65342978202953 | -0.616097 | -13.0818 | 1 | 18 | 13 | 0.65 | 0.20 | - | yes | Current |
| 1574 | 56.70797254718726 | -0.664694 | -23.5368 | 2 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1999 | 56.85020317883867 | -0.575675 | -14.4061 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1990 | 57.04129653309247 | -0.500095 | -15.1238 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1996 | 57.11671253080415 | -0.51482 | -19.1376 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1993 | 57.284041369937206 | -0.4983 | -18.316 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1554 | 57.75403018180653 | -0.667119 | -20.8835 | 2 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2001 | 59.72185820392242 | -0.509006 | -17.3642 | 2 | 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
-13.082kcal/mol
Ligand efficiency (LE)
-0.3536kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.620
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
503.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
327.21kcal/mol
Minimised FF energy
272.21kcal/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.