Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
56.6 kcal/mol
Protein clashes
3
Internal clashes
17
Native overlap
contact recall 0.86, Jaccard 0.72, H-bond role recall 0.33
Reason: 17 internal clashes, strain 56.6 kcal/mol
strain ΔE 56.6 kcal/mol
3 protein-contact clashes
17 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.582 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Extreme strain energy (56.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (17)
Score
-19.789
kcal/mol
LE
-0.582
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
3.08
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 0
Interaction summary
HB 7
HY 24
PI 2
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 1.682 | Score | -19.789 |
|---|---|---|---|
| Inter norm | -0.780 | Intra norm | 0.198 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 7 |
| Artifact reason | geometry warning; 17 clashes; 3 protein contact clashes; high strain Δ 56.6 | ||
| Residues |
NDP301
ALA32
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO50
PRO88
THR180
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
VAL87
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 18 | Native recall | 0.86 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.33 |
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 427 | 1.3468576735481605 | -0.808417 | -18.675 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 1.6823460811845725 | -0.78016 | -19.7888 | 7 | 22 | 18 | 0.86 | 0.33 | - | no | Current |
| 411 | 2.2104857339584942 | -0.669199 | -19.1927 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 444 | 2.4534108204004426 | -0.764614 | -17.3765 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 3.765478119320939 | -0.643558 | -19.7646 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 5.369926118840396 | -0.895866 | -25.0991 | 15 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 5.56934551442081 | -0.761521 | -17.001 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.789kcal/mol
Ligand efficiency (LE)
-0.5820kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.824
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
56.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.64kcal/mol
Minimised FF energy
69.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
772.5Ų
Total solvent-accessible surface area of free ligand
BSA total
664.5Ų
Buried surface area upon binding
BSA apolar
533.3Ų
Hydrophobic contacts buried
BSA polar
131.2Ų
Polar contacts buried
Fraction buried
86.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3392.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1662.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)