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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
66.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.43, Jaccard 0.33, H-bond role recall 0.17
Reason: strain 66.9 kcal/mol
strain ΔE 66.9 kcal/mol
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (11/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.435 kcal/mol/HA)
✓ Good fit quality (FQ -4.65)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (66.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-19.139
kcal/mol
LE
-0.435
kcal/mol/HA
Fit Quality
-4.65
FQ (Leeson)
HAC
44
heavy atoms
MW
625
Da
LogP
-1.02
cLogP
Final rank
5.0796
rank score
Inter norm
-0.579
normalised
Contacts
15
H-bonds 8
Interaction summary
HBD 3
HBA 3
HY 6
PI 0
CLASH 2
Interaction summary
HBD 3
HBA 3
HY 6
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 9 | Native recall | 0.43 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 1 | HB residue recall | 0.17 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 8 | 3.2033408266422643 | -0.573234 | -28.8529 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 4.9161042670389214 | -0.511687 | -20.0147 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 5.079561609865208 | -0.57923 | -19.1388 | 8 | 15 | 9 | 0.43 | 0.17 | - | no | Current |
| 8 | 5.452691758188365 | -0.552019 | -21.2818 | 14 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 5.52295819363822 | -0.667573 | -20.4746 | 16 | 21 | 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
-19.139kcal/mol
Ligand efficiency (LE)
-0.4350kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.648
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
624.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.02
Lipinski: ≤ 5
Rotatable bonds
19
Conformational strain (MMFF94s)
Strain energy (ΔE)
66.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
211.79kcal/mol
Minimised FF energy
144.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
914.7Ų
Total solvent-accessible surface area of free ligand
BSA total
670.1Ų
Buried surface area upon binding
BSA apolar
470.1Ų
Hydrophobic contacts buried
BSA polar
200.0Ų
Polar contacts buried
Fraction buried
73.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3355.4Ų
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
1706.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)