Chemical Components in the PDB

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R2R : Summary

Code

R2R

One-letter code

X

Molecule name

ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)

Systematic names

ProgramVersionName
ACDLabs 12.01 ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)

Formula

H28 N14 O2 Ru3

Formal charge

0

Molecular weight

559.525 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N[Ru](N)(N)(N)(O[Ru](N)(N)(N)(N)N)O[Ru](N)(N)(N)(N)N
SMILES CACTVS 3.385 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
SMILES OpenEye OEToolkits 2.0.7 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
Canonical SMILES CACTVS 3.385 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
Canonical SMILES OpenEye OEToolkits 2.0.7 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N

IUPAC InChI

InChI=1S/14H2N.2O.3Ru/h14*1H2;;;;;/q14*-1;;;+4;2*+5

IUPAC InChI key

FOOPNNMQSUSGAT-UHFFFAOYSA-N
R2R

wwPDB Information

Atom count

47 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-10-02

Last modified at

2019-11-22

Status

Released

Obsoleted

Not Assigned



R2R : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N01 N N1 N N N 0 -0.204 3.082 -0.65
2 N03 N N2 N N N 0 0.211 -0.922 0.68
3 N04 N N3 N N N 0 -0.569 0.383 -1.904
4 N05 N N4 N N N 0 0.576 1.776 1.933
5 O06 O O1 N N N 0 1.766 1.087 -0.514
6 N08 N N5 N N N 0 3.763 -2.181 0.494
7 N09 N N6 N N N 0 3.993 0.733 1.158
8 N10 N N7 N N N 0 1.395 -1.597 -1.25
9 N11 N N8 N N N 0 1.404 -0.708 1.614
10 N12 N N9 N N N 0 3.984 -0.155 -1.705
11 O13 O O2 N N N 0 -1.759 1.073 0.543
12 N15 N N10 N N N 0 -3.758 -2.163 -0.558
13 N16 N N11 N N N 0 -4.307 0.148 1.271
14 N17 N N12 N N N 0 -1.068 -1.01 -1.208
15 N18 N N13 N N N 0 -3.539 0.646 -1.584
16 N19 N N14 N N N 0 -1.836 -1.507 1.647
17 RU2 RU RU1 N N N 0 0.004 1.08 0.015
18 RU3 RU RU2 N N N 0 2.694 -0.432 -0.046
19 RU1 RU RU3 N N N 0 -2.688 -0.431 0.031
20 H1 H H1 N N N 0 0.219 3.207 -1.558
21 H2 H H2 N N N 0 -1.173 3.361 -0.662
22 H3 H H3 N N N 0 -0.643 -1.44 0.539
23 H4 H H4 N N N 0 0.988 -1.376 0.224
24 H5 H H5 N N N 0 -0.021 -0.419 -2.176
25 H6 H H6 N N N 0 -1.556 0.173 -1.933
26 H7 H H7 N N N 0 0.692 1.008 2.577
27 H8 H H8 N N N 0 1.416 2.333 1.88
28 H9 H H9 N N N 0 3.132 -2.932 0.729
29 H10 H H10 N N N 0 4.397 -2.458 -0.24
30 H11 H H11 N N N 0 4.284 1.569 0.673
31 H12 H H12 N N N 0 3.561 0.96 2.042
32 H13 H H13 N N N 0 0.584 -1.892 -0.726
33 H14 H H14 N N N 0 1.125 -1.094 -2.082
34 H15 H H15 N N N 0 0.803 -1.507 1.476
35 H16 H H16 N N N 0 1.93 -0.795 2.47
36 H17 H H17 N N N 0 3.849 0.754 -2.121
37 H18 H H18 N N N 0 4.948 -0.292 -1.44
38 H19 H H19 N N N 0 -3.707 -2.878 0.151
39 H20 H H20 N N N 0 -4.717 -1.938 -0.777
40 H21 H H21 N N N 0 -4.189 1.094 1.602
41 H22 H H22 N N N 0 -5.188 0.041 0.789
42 H23 H H23 N N N 0 -0.184 -0.772 -0.783
43 H24 H H24 N N N 0 -1.112 -1.994 -1.424
44 H25 H H25 N N N 0 -4.53 0.467 -1.656
45 H26 H H26 N N N 0 -3.356 1.634 -1.497
46 H27 H H27 N N N 0 -0.884 -1.217 1.813
47 H28 H H28 N N N 0 -2.394 -1.408 2.482



R2R : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N08 RU3 N RU sing 2.12 N N
2 N11 RU3 N RU sing 2.12 N N
3 N10 RU3 N RU sing 2.12 N N
4 RU3 N09 RU N sing 2.12 N N
5 RU3 N12 RU N sing 2.12 N N
6 RU3 O06 RU O sing 1.84 N N
7 O06 RU2 O RU sing 1.84 N N
8 N01 RU2 N RU sing 2.12 N N
9 N05 RU2 N RU sing 2.12 N N
10 RU2 N04 RU N sing 2.12 N N
11 RU2 N03 RU N sing 2.12 N N
12 RU2 O13 RU O sing 1.84 N N
13 O13 RU1 O RU sing 1.84 N N
14 N18 RU1 N RU sing 2.12 N N
15 N16 RU1 N RU sing 2.12 N N
16 RU1 N17 RU N sing 2.12 N N
17 RU1 N19 RU N sing 2.12 N N
18 RU1 N15 RU N sing 2.12 N N
19 N01 H1 N H sing 1.01 N N
20 N01 H2 N H sing 1.01 N N
21 N03 H3 N H sing 1.01 N N
22 N03 H4 N H sing 1.01 N N
23 N04 H5 N H sing 1.01 N N
24 N04 H6 N H sing 1.01 N N
25 N05 H7 N H sing 1.01 N N
26 N05 H8 N H sing 1.01 N N
27 N08 H9 N H sing 1.01 N N
28 N08 H10 N H sing 1.01 N N
29 N09 H11 N H sing 1.01 N N
30 N09 H12 N H sing 1.01 N N
31 N10 H13 N H sing 1.01 N N
32 N10 H14 N H sing 1.01 N N
33 N11 H15 N H sing 1.01 N N
34 N11 H16 N H sing 1.01 N N
35 N12 H17 N H sing 1.01 N N
36 N12 H18 N H sing 1.01 N N
37 N15 H19 N H sing 1.01 N N
38 N15 H20 N H sing 1.01 N N
39 N16 H21 N H sing 1.01 N N
40 N16 H22 N H sing 1.01 N N
41 N17 H23 N H sing 1.01 N N
42 N17 H24 N H sing 1.01 N N
43 N18 H25 N H sing 1.01 N N
44 N18 H26 N H sing 1.01 N N
45 N19 H27 N H sing 1.01 N N
46 N19 H28 N H sing 1.01 N N



R2R : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
R2R 6uiw Open in New Window Bound ligand 11 1
R2R 6v37 Open in New Window Bound ligand 1 1
R2R 6v3i Open in New Window Bound ligand 1 1
R2R 7s8b Open in New Window Bound ligand 1 1
R2R 8ffm Open in New Window Bound ligand 1 1
R2R 8ffn Open in New Window Bound ligand 1 1
R2R 8ffq Open in New Window Bound ligand 1 1
R2R 8j1b Open in New Window Bound ligand 1 1
R2R 8s8z Open in New Window Bound ligand 1 1
R2R 8s90 Open in New Window Bound ligand 1 1