Chemical Components in the PDB

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QME : Summary

Code

QME

One-letter code

X

Molecule name

2-[(2~{R})-piperidin-2-yl]-1~{H}-indole

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-[(2~{R})-piperidin-2-yl]-1~{H}-indole

Formula

C13 H16 N2

Formal charge

0

Molecular weight

200.28 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C1CC[CH](NC1)c2[nH]c3ccccc3c2
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)cc([nH]2)C3CCCCN3
Canonical SMILES CACTVS 3.385 C1CC[C@@H](NC1)c2[nH]c3ccccc3c2
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)cc([nH]2)[C@H]3CCCCN3

IUPAC InChI

InChI=1S/C13H16N2/c1-2-6-11-10(5-1)9-13(15-11)12-7-3-4-8-14-12/h1-2,5-6,9,12,14-15H,3-4,7-8H2/t12-/m1/s1

IUPAC InChI key

BNKHEDZUOBHGMW-GFCCVEGCSA-N
QME

wwPDB Information

Atom count

31 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-06-30

Last modified at

2020-08-14

Status

Released

Obsoleted

Not Assigned



QME : Atoms of Molecule

Total Number of Atoms: 31
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C5 C C1 N N N 0 -2.27 -0.147 1.255
2 C7 C C2 N Y N 0 2.04 -0.756 -0.09
3 C8 C C3 N Y N 0 1.827 0.626 0.066
4 C10 C C4 N N N 0 -3.704 0.143 -1.245
5 C13 C C5 N N N 0 -4.354 0.558 0.077
6 C15 C C6 N Y N 0 4.198 0.958 0.128
7 C1 C C7 N Y N 0 -0.184 -0.368 -0.067
8 C11 C C8 N Y N 0 3.341 -1.259 -0.14
9 C12 C C9 N Y N 0 2.922 1.476 0.175
10 C14 C C10 N Y N 0 4.403 -0.406 -0.03
11 C2 C C11 R N N 0 -1.68 -0.542 -0.101
12 C3 C C12 N Y N 0 0.71 -1.364 -0.172
13 C9 C C13 N N N 0 -3.793 -0.306 1.21
14 N4 N N1 N Y N 0 0.465 0.828 0.076
15 N6 N N2 N N N 0 -2.249 0.314 -1.151
16 H1 H H1 N N N 0 -1.86 -0.792 2.032
17 H2 H H2 N N N 0 -2.019 0.891 1.474
18 H3 H H3 N N N 0 -3.934 -0.902 -1.451
19 H4 H H4 N N N 0 -4.091 0.766 -2.051
20 H5 H H5 N N N 0 -4.136 1.607 0.276
21 H6 H H6 N N N 0 -5.433 0.417 0.012
22 H7 H H7 N N N 0 5.048 1.62 0.213
23 H8 H H8 N N N 0 3.509 -2.319 -0.265
24 H9 H H9 N N N 0 2.773 2.538 0.298
25 H10 H H10 N N N 0 5.41 -0.796 -0.065
26 H11 H H11 N N N 0 -1.921 -1.584 -0.312
27 H12 H H12 N N N 0 0.49 -2.414 -0.295
28 H13 H H13 N N N 0 -4.045 -1.351 1.03
29 H14 H H14 N N N 0 -4.221 0.015 2.159
30 H15 H H15 N N N 0 0.031 1.69 0.171
31 H16 H H16 N N N 0 -2.007 1.281 -0.999



QME : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 C14 C C doub 1.39 N Y
2 C15 C12 C C sing 1.38 N Y
3 C14 C11 C C sing 1.37 N Y
4 C12 C8 C C doub 1.39 N Y
5 C11 C7 C C doub 1.4 N Y
6 C8 C7 C C sing 1.41 N Y
7 C8 N4 C N sing 1.38 N Y
8 C7 C3 C C sing 1.46 N Y
9 N4 C1 N C sing 1.37 N Y
10 C3 C1 C C doub 1.34 N Y
11 C1 C2 C C sing 1.51 N N
12 C2 C5 C C sing 1.53 N N
13 C2 N6 C N sing 1.47 N N
14 C5 C9 C C sing 1.53 N N
15 N6 C10 N C sing 1.47 N N
16 C9 C13 C C sing 1.53 N N
17 C10 C13 C C sing 1.53 N N
18 C5 H1 C H sing 1.09 N N
19 C5 H2 C H sing 1.09 N N
20 C10 H3 C H sing 1.09 N N
21 C10 H4 C H sing 1.09 N N
22 C13 H5 C H sing 1.09 N N
23 C13 H6 C H sing 1.09 N N
24 C15 H7 C H sing 1.08 N N
25 C11 H8 C H sing 1.08 N N
26 C12 H9 C H sing 1.08 N N
27 C14 H10 C H sing 1.08 N N
28 C2 H11 C H sing 1.09 N N
29 C3 H12 C H sing 1.08 N N
30 C9 H13 C H sing 1.09 N N
31 C9 H14 C H sing 1.09 N N
32 N4 H15 N H sing 0.97 N N
33 N6 H16 N H sing 1.01 N N



QME : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
QME 6zli Open in New Window Bound ligand 1 1