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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
30.6 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.20
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.593 kcal/mol/HA)
✓ Good fit quality (FQ -6.19)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (30.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-23.721
kcal/mol
LE
-0.593
kcal/mol/HA
Fit Quality
-6.19
FQ (Leeson)
HAC
40
heavy atoms
MW
540
Da
LogP
5.07
cLogP
Interaction summary
HB 12
HY 24
PI 3
CLASH 10
Interaction summary
HB 12
HY 24
PI 3
CLASH 10
| Final rank | 5.779 | Score | -23.721 |
|---|---|---|---|
| Inter norm | -0.677 | Intra norm | 0.084 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 20 clashes; 2 protein clashes; high strain Δ 30.6 | ||
| Residues |
ALA10
GLU31
ILE61
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
SER60
THR137
THR57
TRP25
TRP58
TYR122
VAL116
VAL9
| ||
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
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 | 0.56 | RMSD | - |
| HB strict | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 23 | 2.085904116821016 | -0.689121 | -27.2607 | 6 | 19 | 16 | 0.76 | 0.20 | - | no | Open |
| 23 | 2.1701300817805826 | -0.675101 | -25.5028 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 22 | 3.4612009219277655 | -0.699987 | -23.8891 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.8141245244208646 | -0.630551 | -23.742 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 3.842246669612219 | -0.815955 | -30.8126 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 23 | 4.243877337445351 | -0.580358 | -22.9581 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 4.9090251791855755 | -0.835688 | -32.1088 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 5.00112541062026 | -0.513565 | -18.5786 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 5.122166298635419 | -0.789091 | -27.5249 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 24 | 5.182612819385439 | -0.664602 | -23.5725 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 25 | 5.220830016407855 | -0.703529 | -25.5734 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 5.522584583539993 | -0.672093 | -28.6314 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 28 | 5.779053666691942 | -0.677449 | -23.7205 | 12 | 18 | 14 | 0.67 | 0.20 | - | no | Current |
| 10 | 6.104412655989357 | -0.702536 | -24.6488 | 9 | 24 | 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
-23.721kcal/mol
Ligand efficiency (LE)
-0.5930kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.193
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
40HA
Physicochemical properties
Molecular weight
540.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.07
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.62kcal/mol
Minimised FF energy
110.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
787.8Ų
Total solvent-accessible surface area of free ligand
BSA total
627.0Ų
Buried surface area upon binding
BSA apolar
439.0Ų
Hydrophobic contacts buried
BSA polar
187.9Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1640.3Ų
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
606.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)