Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
No SASA yet
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA missing
Strain ΔE
38.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.54, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.635 kcal/mol/HA)
✓ Good fit quality (FQ -6.35)
✗ Very high strain energy (38.8 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (12)
✗ Many internal clashes (18)
ℹ SASA not computed
Score
-21.586
kcal/mol
LE
-0.635
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
34
heavy atoms
MW
465
Da
LogP
1.20
cLogP
Interaction summary
HB 1
HY 24
PI 2
CLASH 3
Interaction summary
HB 1
HY 24
PI 2
CLASH 3
| Final rank | 56.764 | Score | -21.586 |
|---|---|---|---|
| Inter norm | -0.681 | Intra norm | 0.046 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 18 clashes; 12 protein contact clashes | ||
| Residues |
ALA32
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
PHE56
PHE91
PRO88
SER44
SER86
THR54
TRP47
VAL49
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 | ||
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:NDP301
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 | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.65 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
HB · H-bonds
Mode: strict. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 980 | 4.2667967127332425 | -0.647076 | -18.8906 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 964 | 4.4375082130399335 | -0.666507 | -20.7389 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 963 | 4.8283277279898265 | -0.818882 | -26.4773 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 976 | 4.861076246789533 | -0.717485 | -23.0849 | 3 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 1020 | 5.608822815282937 | -0.559562 | -18.2789 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 975 | 5.658661119979025 | -0.72701 | -19.9178 | 3 | 16 | 15 | 0.75 | 0.60 | - | no | Open |
| 972 | 5.872917234042555 | -0.66726 | -10.5276 | 2 | 16 | 12 | 0.60 | 0.20 | - | no | Open |
| 1017 | 5.943411109675365 | -0.558633 | -16.3741 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1013 | 6.307109152626905 | -0.591976 | -22.2418 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 998 | 6.617839771151886 | -0.692384 | -24.2271 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1005 | 7.263428324635448 | -0.598723 | -20.9956 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1001 | 8.518952245362764 | -0.512154 | -10.4528 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 965 | 54.268108346420284 | -0.680293 | -21.6517 | 1 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 969 | 54.730108154157584 | -0.83792 | -26.6193 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 966 | 54.90998971603653 | -0.681929 | -20.9942 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 974 | 55.25225600517029 | -0.712966 | -21.7259 | 2 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 957 | 55.33920843725555 | -0.601959 | -15.7833 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 961 | 55.34723382073465 | -0.695261 | -21.8508 | 1 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 1018 | 55.577770402172845 | -0.615158 | -14.106 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 970 | 56.763655045820364 | -0.680825 | -21.5861 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Current |
| 1015 | 55.7401178962693 | -0.644859 | -23.9105 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 979 | 56.22693303779636 | -0.793334 | -24.9168 | 1 | 22 | 18 | 0.90 | 0.20 | - | yes | Open |
| 959 | 56.22887233234621 | -0.657743 | -14.235 | 6 | 18 | 15 | 0.75 | 0.60 | - | yes | Open |
| 971 | 56.25495307434291 | -0.857331 | -26.9352 | 1 | 21 | 18 | 0.90 | 0.20 | - | yes | Open |
| 1014 | 56.3140252935371 | -0.690966 | -20.8452 | 2 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 999 | 56.37188078468921 | -0.631895 | -19.5435 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 973 | 56.56725214004422 | -0.623201 | -24.1552 | 1 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 968 | 56.7475004943868 | -0.581465 | -19.5245 | 6 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 967 | 56.759649217372015 | -0.676006 | -18.7339 | 3 | 20 | 17 | 0.85 | 0.40 | - | yes | Open |
| 978 | 57.32083151732589 | -0.712682 | -25.1394 | 4 | 20 | 18 | 0.90 | 0.60 | - | yes | Open |
| 997 | 57.3249242113801 | -0.604676 | -18.5954 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1009 | 57.394715812575434 | -0.52356 | -11.3693 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1002 | 57.4808605706708 | -0.617815 | -16.9265 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1000 | 57.625401861715766 | -0.674365 | -18.6906 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1019 | 57.800249436248784 | -0.723992 | -26.6835 | 1 | 24 | 0 | 0.00 | 0.00 | - | yes | Open |
| 958 | 57.93847770081955 | -0.710876 | -22.6368 | 2 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1003 | 58.20546004129062 | -0.675781 | -24.2705 | 2 | 24 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1006 | 58.38086441393017 | -0.693607 | -24.2081 | 5 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 977 | 58.49646276358023 | -0.732312 | -24.1209 | 2 | 15 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1012 | 58.925483999481 | -0.743273 | -20.6742 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1016 | 59.78910891302541 | -0.540698 | -18.6917 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1011 | 59.83248892398216 | -0.718821 | -24.3108 | 3 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1004 | 59.87167927601356 | -0.603058 | -21.4062 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 962 | 59.872548927288754 | -0.784707 | -24.1046 | 2 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1008 | 60.23140483524128 | -0.615151 | -10.199 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1007 | 60.38065659113832 | -0.565567 | -15.815 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1010 | 60.75011301860987 | -0.623404 | -16.21 | 1 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 960 | 62.283215330865104 | -0.611563 | -6.28831 | 4 | 22 | 15 | 0.75 | 0.20 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.586kcal/mol
Ligand efficiency (LE)
-0.6349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.353
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
464.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.20
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.14kcal/mol
Minimised FF energy
86.33kcal/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.