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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
25.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.931 kcal/mol/HA)
✓ Good fit quality (FQ -8.69)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (25.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-25.137
kcal/mol
LE
-0.931
kcal/mol/HA
Fit Quality
-8.69
FQ (Leeson)
HAC
27
heavy atoms
MW
384
Da
LogP
-0.23
cLogP
Interaction summary
HB 8
HY 24
PI 2
CLASH 1
Interaction summary
HB 8
HY 24
PI 2
CLASH 1
| Final rank | 3.259 | Score | -25.137 |
|---|---|---|---|
| Inter norm | -1.048 | Intra norm | 0.117 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 25.5 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
GLY157
ILE45
MET53
PHE56
PRO50
PRO88
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
VAL87
| ||
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
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 | 13 | Native recall | 0.62 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 257 | 0.4011332948469937 | -1.24877 | -30.4063 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 0.7112098443834395 | -0.942986 | -19.0186 | 3 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 360 | 1.143412050685196 | -0.90019 | -21.6461 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 317 | 2.1564064725732535 | -1.03355 | -25.1287 | 8 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 260 | 2.4809595684265946 | -1.00326 | -27.3155 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 280 | 2.986032798063189 | -0.883222 | -24.6464 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 3.2589755731920693 | -1.0482 | -25.1368 | 8 | 17 | 13 | 0.62 | 0.50 | - | no | Current |
| 223 | 3.6714800169018886 | -1.23796 | -31.5102 | 12 | 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
-25.137kcal/mol
Ligand efficiency (LE)
-0.9310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.686
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
384.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.23
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.29kcal/mol
Minimised FF energy
33.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.9Ų
Total solvent-accessible surface area of free ligand
BSA total
559.2Ų
Buried surface area upon binding
BSA apolar
411.2Ų
Hydrophobic contacts buried
BSA polar
148.0Ų
Polar contacts buried
Fraction buried
89.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3236.2Ų
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
1662.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)