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
26.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.397 kcal/mol/HA)
✓ Good fit quality (FQ -11.92)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ High strain energy (26.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.341
kcal/mol
LE
-1.397
kcal/mol/HA
Fit Quality
-11.92
FQ (Leeson)
HAC
21
heavy atoms
MW
327
Da
LogP
0.46
cLogP
Interaction summary
HB 8
HY 20
PI 2
CLASH 1
Interaction summary
HB 8
HY 20
PI 2
CLASH 1
| Final rank | 2.684 | Score | -29.341 |
|---|---|---|---|
| Inter norm | -1.366 | Intra norm | -0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 26.1 | ||
| Residues |
ALA10
ARG29
GLU31
GLY117
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
TRP25
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 | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 3 | Strict recall | 0.60 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 275 | 1.2800102035544119 | -1.07992 | -23.2762 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 398 | 1.7423448159409054 | -1.17816 | -26.2298 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 334 | 2.168932137414599 | -1.4266 | -30.2851 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 2.238615620155472 | -1.18153 | -25.1714 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 371 | 2.6107657595377027 | -1.11929 | -23.9803 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 2.6839312495860876 | -1.36596 | -29.3412 | 8 | 15 | 11 | 0.52 | 0.80 | - | no | Current |
| 335 | 2.984846058218942 | -1.34842 | -28.8321 | 8 | 15 | 11 | 0.52 | 0.80 | - | no | Open |
| 255 | 3.4499319879559054 | -1.26631 | -30.5607 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 4.285080726682143 | -1.2932 | -28.7348 | 10 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 4.729656743975371 | -1.23678 | -27.4648 | 11 | 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
-29.341kcal/mol
Ligand efficiency (LE)
-1.3972kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.918
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
327.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.46
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-63.70kcal/mol
Minimised FF energy
-89.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
531.9Ų
Total solvent-accessible surface area of free ligand
BSA total
449.1Ų
Buried surface area upon binding
BSA apolar
305.9Ų
Hydrophobic contacts buried
BSA polar
143.3Ų
Polar contacts buried
Fraction buried
84.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1430.8Ų
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
595.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)