Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
7.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.70, Jaccard 0.58, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.8 kcal/mol)
✓ Excellent LE (-1.175 kcal/mol/HA)
✓ Good fit quality (FQ -10.37)
✓ Good H-bonds (3 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-27.015
kcal/mol
LE
-1.175
kcal/mol/HA
Fit Quality
-10.37
FQ (Leeson)
HAC
23
heavy atoms
MW
528
Da
LogP
4.23
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 2
Interaction summary
HB 3
HY 24
PI 1
CLASH 2
| Final rank | 1.462 | Score | -27.015 |
|---|---|---|---|
| Inter norm | -1.205 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA32
ARG48
ASP52
GLY157
ILE45
LEU94
NDP301
PHE56
SER44
SER86
THR180
THR83
TRP47
TYR162
VAL156
VAL30
VAL31
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 | 14 | Native recall | 0.70 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.08932108552118626 | -1.53139 | -33.7137 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 1.4623494220460063 | -1.20535 | -27.015 | 3 | 18 | 14 | 0.70 | 0.20 | - | no | Current |
| 670 | 1.4838971022548233 | -1.01085 | -19.596 | 1 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 660 | 1.5296363297884992 | -1.24398 | -27.7842 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 1.6127658204479765 | -1.16325 | -26.2443 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 1.813401811970726 | -1.08305 | -23.0344 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.618099765994593 | -1.24331 | -24.7088 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 2.650135671650861 | -0.972587 | -21.0295 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 2.7068022141827996 | -1.03337 | -23.1766 | 3 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 670 | 3.068566625982152 | -1.0102 | -22.9013 | 4 | 16 | 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
-27.015kcal/mol
Ligand efficiency (LE)
-1.1746kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.366
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
528.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.23
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.27kcal/mol
Minimised FF energy
47.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
592.9Ų
Total solvent-accessible surface area of free ligand
BSA total
546.6Ų
Buried surface area upon binding
BSA apolar
532.0Ų
Hydrophobic contacts buried
BSA polar
14.7Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1572.0Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
826.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)