Chemical Components in the PDB

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ILR : Summary

Code

ILR

One-letter code

X

Molecule name

Spiroimine (+)-4 R

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (6~{R})-7-methyl-1,4-dioxa-8-azadispiro[4.0.5^{6}.4^{5}]pentadec-7-ene

Formula

C13 H21 N O2

Formal charge

0

Molecular weight

223.311 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC1=NCCC[C]12CCCCC23OCCO3
SMILES OpenEye OEToolkits 2.0.7 CC1=NCCCC12CCCCC23OCCO3
Canonical SMILES CACTVS 3.385 CC1=NCCC[C@]12CCCCC23OCCO3
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1=NCCC[C@]12CCCCC23OCCO3

IUPAC InChI

InChI=1S/C13H21NO2/c1-11-12(6-4-8-14-11)5-2-3-7-13(12)15-9-10-16-13/h2-10H2,1H3/t12-/m1/s1

IUPAC InChI key

NFGZUBPFTHPCRY-GFCCVEGCSA-N
ILR

wwPDB Information

Atom count

37 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-08-01

Last modified at

2024-03-29

Status

Released

Obsoleted

Not Assigned



ILR : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C16 C C1 N N N 0 2.344 1.566 0.431
2 C15 C C2 N N N 0 2.289 1.553 -1.117
3 C10 C C3 N N N 0 -0.07 -2.674 0.683
4 O14 O O1 N N N 0 1.038 0.867 -1.362
5 C1 C C4 N N N 0 -0.121 1.829 1.542
6 C2 C C5 N N N 0 -1.02 1.032 0.632
7 C8 C C6 R N N 0 -0.504 -0.28 0.114
8 C7 C C7 N N N 0 -1.347 -0.73 -1.084
9 C6 C C8 N N N 0 -2.827 -0.596 -0.703
10 C5 C C9 N N N 0 -3.142 0.889 -0.51
11 N3 N N1 N N N 0 -2.153 1.512 0.359
12 C13 C C10 N N N 0 0.954 -0.124 -0.324
13 O17 O O2 N N N 0 1.748 0.303 0.789
14 C12 C C11 N N N 0 1.482 -1.459 -0.851
15 C11 C C12 N N N 0 1.389 -2.516 0.25
16 C9 C C13 N N N 0 -0.591 -1.338 1.217
17 H1 H H1 N N N 0 3.376 1.618 0.779
18 H2 H H2 N N N 0 1.761 2.395 0.832
19 H3 H H3 N N N 0 2.263 2.567 -1.516
20 H4 H H4 N N N 0 3.128 0.994 -1.533
21 H5 H H5 N N N 0 -0.671 -2.983 -0.172
22 H6 H H6 N N N 0 -0.137 -3.429 1.467
23 H7 H H7 N N N 0 0.767 1.244 1.779
24 H8 H H8 N N N 0 0.175 2.752 1.043
25 H12 H H12 N N N 0 -3.45 -1.003 -1.5
26 H9 H H9 N N N 0 -0.655 2.068 2.462
27 H10 H H10 N N N 0 -1.129 -0.099 -1.945
28 H11 H H11 N N N 0 -1.12 -1.77 -1.323
29 H13 H H13 N N N 0 -3.018 -1.136 0.224
30 H14 H H14 N N N 0 -3.135 1.387 -1.479
31 H15 H H15 N N N 0 -4.13 0.991 -0.061
32 H16 H H16 N N N 0 0.886 -1.773 -1.708
33 H21 H H21 N N N 0 0.013 -1.026 2.069
34 H17 H H17 N N N 0 2.522 -1.343 -1.156
35 H18 H H18 N N N 0 1.99 -2.204 1.105
36 H19 H H19 N N N 0 1.761 -3.468 -0.127
37 H20 H H20 N N N 0 -1.629 -1.452 1.53



ILR : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 N3 C N sing 1.46 N N
2 C5 C6 C C sing 1.53 N N
3 C15 C16 C C sing 1.55 N N
4 C15 O14 C O sing 1.45 N N
5 N3 C2 N C doub 1.26 N N
6 C16 O17 C O sing 1.44 N N
7 O14 C13 O C sing 1.44 N N
8 C6 C7 C C sing 1.53 N N
9 C2 C1 C C sing 1.51 N N
10 C2 C8 C C sing 1.5 N N
11 O17 C13 O C sing 1.43 N N
12 C13 C8 C C sing 1.53 N N
13 C13 C12 C C sing 1.53 N N
14 C8 C7 C C sing 1.53 N N
15 C8 C9 C C sing 1.53 N N
16 C12 C11 C C sing 1.53 N N
17 C9 C10 C C sing 1.53 N N
18 C11 C10 C C sing 1.53 N N
19 C16 H1 C H sing 1.09 N N
20 C16 H2 C H sing 1.09 N N
21 C15 H3 C H sing 1.09 N N
22 C15 H4 C H sing 1.09 N N
23 C10 H5 C H sing 1.09 N N
24 C10 H6 C H sing 1.09 N N
25 C1 H7 C H sing 1.09 N N
26 C1 H8 C H sing 1.09 N N
27 C1 H9 C H sing 1.09 N N
28 C7 H10 C H sing 1.09 N N
29 C7 H11 C H sing 1.09 N N
30 C6 H12 C H sing 1.09 N N
31 C6 H13 C H sing 1.09 N N
32 C5 H14 C H sing 1.09 N N
33 C5 H15 C H sing 1.09 N N
34 C12 H16 C H sing 1.09 N N
35 C12 H17 C H sing 1.09 N N
36 C11 H18 C H sing 1.09 N N
37 C11 H19 C H sing 1.09 N N
38 C9 H20 C H sing 1.09 N N
39 C9 H21 C H sing 1.09 N N



ILR : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
ILR 8q1m Open in New Window Bound ligand 5 1
ILR 8qx2 Open in New Window Bound ligand 5 1