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 strong
SASA done
Strain ΔE
53.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.64, H-bond role recall 0.20
Reason: strain 53.3 kcal/mol
strain ΔE 53.3 kcal/mol
1 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (10/20 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 (-0.621 kcal/mol/HA)
✓ Good fit quality (FQ -6.21)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Extreme strain energy (53.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-21.102
kcal/mol
LE
-0.621
kcal/mol/HA
Fit Quality
-6.21
FQ (Leeson)
HAC
34
heavy atoms
MW
475
Da
LogP
0.55
cLogP
Final rank
3.0719
rank score
Inter norm
-0.852
normalised
Contacts
15
H-bonds 6
Interaction summary
HBD 2
HBA 4
HY 7
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 4
HY 7
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 14 | Native recall | 0.67 |
| Jaccard | 0.64 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
200 residues
| Protein target | T01 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 377 | 1.8841664189840277 | -0.769525 | -21.2201 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 448 | 3.071887405802105 | -0.852423 | -21.1023 | 6 | 15 | 14 | 0.67 | 0.20 | - | no | Current |
| 364 | 3.133688206135927 | -1.02712 | -22.5304 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 453 | 4.086047927141944 | -0.700167 | -14.205 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 4.52394464358143 | -1.02112 | -24.6335 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 478 | 5.104203299647547 | -0.685287 | -16.0435 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 345 | 5.2886042849095505 | -0.850662 | -20.1556 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 5.993348980737754 | -0.738643 | -19.1252 | 12 | 19 | 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
-21.102kcal/mol
Ligand efficiency (LE)
-0.6207kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.210
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
475.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.55
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
204.90kcal/mol
Minimised FF energy
151.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
720.7Ų
Total solvent-accessible surface area of free ligand
BSA total
588.4Ų
Buried surface area upon binding
BSA apolar
476.2Ų
Hydrophobic contacts buried
BSA polar
112.1Ų
Polar contacts buried
Fraction buried
81.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1625.2Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
620.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)