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
49.6 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.40
Reason: strain 49.6 kcal/mol
strain ΔE 49.6 kcal/mol
4 protein-contact clashes
5 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (12/21 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 (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -9.57)
✓ Good H-bonds (3 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Extreme strain energy (49.6 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (11)
Score
-31.148
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-9.57
FQ (Leeson)
HAC
32
heavy atoms
MW
492
Da
LogP
2.75
cLogP
Final rank
1.4952
rank score
Inter norm
-0.821
normalised
Contacts
15
H-bonds 4
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 5
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
| 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 | 12 | Native recall | 0.57 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.40 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 647 | 1.1847930015500647 | -0.884942 | -49.0529 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 1.4951936856465549 | -0.821422 | -31.1479 | 4 | 15 | 12 | 0.57 | 0.40 | - | no | Current |
| 632 | 1.7612227019476687 | -0.793129 | -46.3282 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 3.075408860119218 | -0.786972 | -46.8966 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 3.178654702339341 | -0.732381 | -47.0997 | 5 | 13 | 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
-31.148kcal/mol
Ligand efficiency (LE)
-0.9734kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.572
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
491.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.75
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
49.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.18kcal/mol
Minimised FF energy
30.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
726.8Ų
Total solvent-accessible surface area of free ligand
BSA total
616.9Ų
Buried surface area upon binding
BSA apolar
447.8Ų
Hydrophobic contacts buried
BSA polar
169.1Ų
Polar contacts buried
Fraction buried
84.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1592.2Ų
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
599.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)