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 medium
Native mixed
SASA done
Strain ΔE
21.0 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.200 kcal/mol/HA)
✓ Good fit quality (FQ -10.24)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (21.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-25.209
kcal/mol
LE
-1.200
kcal/mol/HA
Fit Quality
-10.24
FQ (Leeson)
HAC
21
heavy atoms
MW
302
Da
LogP
2.65
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 0
Interaction summary
HB 5
HY 24
PI 2
CLASH 0
| Final rank | 2.124 | Score | -25.209 |
|---|---|---|---|
| Inter norm | -1.226 | Intra norm | 0.026 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 5 clashes; 2 protein clashes; moderate strain Δ 21.0 | ||
| Residues |
ALA10
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR137
TRP25
TYR122
TYR34
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 | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 528 | 2.124232310020372 | -1.22616 | -25.2086 | 5 | 15 | 11 | 0.52 | 0.00 | - | no | Current |
| 519 | 2.131253891363639 | -1.27863 | -25.4778 | 5 | 15 | 11 | 0.52 | 0.00 | - | no | Open |
| 481 | 2.213161850603409 | -1.23828 | -25.4847 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 170 | 2.246887908533105 | -1.23637 | -25.1405 | 5 | 15 | 11 | 0.52 | 0.00 | - | no | Open |
| 163 | 2.275852750180273 | -1.26991 | -25.4586 | 5 | 16 | 11 | 0.52 | 0.00 | - | no | Open |
| 126 | 2.3797589319540444 | -1.23414 | -25.3363 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 2.461393635290505 | -1.22589 | -21.5221 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 2.4720918578520474 | -1.18798 | -20.4201 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 4.648705661952587 | -1.41519 | -27.3298 | 10 | 14 | 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
-25.209kcal/mol
Ligand efficiency (LE)
-1.2004kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.239
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
302.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.65
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.82kcal/mol
Minimised FF energy
1.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
594.4Ų
Total solvent-accessible surface area of free ligand
BSA total
495.0Ų
Buried surface area upon binding
BSA apolar
349.1Ų
Hydrophobic contacts buried
BSA polar
145.9Ų
Polar contacts buried
Fraction buried
83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1493.5Ų
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
611.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)