Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

YWR : Summary

Code

YWR

One-letter code

X

Molecule name

K2[Ru2(DAniF)(CO3)3]

Systematic names

Not Assigned

Formula

C18 H16 N2 O11 Ru2

Formal charge

0

Molecular weight

638.466 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1ccc(cc1)N2CN(c3ccc(OC)cc3)[Ru]45OC(=O)O[Ru]2(OC(=O)O4)OC(=O)O5
SMILES OpenEye OEToolkits 2.0.7 COc1ccc(cc1)N2CN([Ru]345[Ru]2(OC(=O)O3)(OC(=O)O4)OC(=O)O5)c6ccc(cc6)OC
Canonical SMILES CACTVS 3.385 COc1ccc(cc1)N2CN(c3ccc(OC)cc3)[Ru]45OC(=O)O[Ru]2(OC(=O)O4)OC(=O)O5
Canonical SMILES OpenEye OEToolkits 2.0.7 COc1ccc(cc1)N2CN([Ru]345[Ru]2(OC(=O)O3)(OC(=O)O4)OC(=O)O5)c6ccc(cc6)OC

IUPAC InChI

InChI=1S/C15H16N2O2.3CH2O3.2Ru/c1-18-14-7-3-12(4-8-14)16-11-17-13-5-9-15(19-2)10-6-13;3*2-1(3)4;;/h3-10H,11H2,1-2H3;3*(H2,2,3,4);;/q-2;;;;2*+4/p-6

IUPAC InChI key

ZRTJISXBTQGSGU-UHFFFAOYSA-H
YWR

wwPDB Information

Atom count

49 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-06-22

Last modified at

2023-07-14

Status

Released

Obsoleted

Not Assigned



YWR : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 RU1 RU RU1 N N N 0 -35.18 -3.279 -21.392
2 RU2 RU RU2 N N N 0 -37.092 -2.347 -22.197
3 O6 O O1 N N N 0 -36.716 -0.662 -21.085
4 O1 O O2 N N N 0 -35.48 -5.014 -22.448
5 O2 O O3 N N N 0 -37.419 -4.145 -23.189
6 O5 O O4 N N N 0 -34.849 -1.596 -20.303
7 O3 O O5 N N N 0 -36.286 -4.083 -19.824
8 O4 O O6 N N N 0 -38.112 -3.026 -20.56
9 N2 N N1 N N N 0 -36.066 -1.644 -23.785
10 N1 N N2 N N N 0 -34.11 -2.524 -22.958
11 C1 C C1 N N N 0 -36.54 -5.043 -23.129
12 C7 C C2 N N N 0 -34.783 -1.922 -23.912
13 C3 C C3 N N N 0 -37.488 -3.75 -19.712
14 C23 C C4 N N N 0 -27.962 -3.764 -23.194
15 C5 C C5 N N N 0 -35.732 -0.7 -20.266
16 O9 O O7 N N N 0 -36.753 -6.337 -23.813
17 C20 C C6 N Y N 0 -37.169 -1.767 -25.975
18 C9 C C7 N Y N 0 -32.459 -3.471 -24.51
19 C10 C C8 N Y N 0 -31.156 -3.823 -24.78
20 C15 C C9 N Y N 0 -36.849 -1.062 -24.822
21 C8 C C10 N Y N 0 -32.753 -2.887 -23.324
22 O11 O O8 N N N 0 -35.722 0.353 -19.19
23 C13 C C11 N Y N 0 -31.762 -2.582 -22.338
24 C16 C C12 N Y N 0 -37.349 0.233 -24.681
25 C17 C C13 N Y N 0 -38.12 0.774 -25.675
26 C11 C C14 N Y N 0 -30.225 -3.396 -23.873
27 O8 O O9 N N N 0 -28.905 -3.843 -24.191
28 C22 C C15 N N N 0 -39.675 -0.105 -28.858
29 C12 C C16 N Y N 0 -30.466 -2.891 -22.606
30 O10 O O10 N N N 0 -38.349 -4.073 -18.532
31 C18 C C17 N Y N 0 -38.467 0.075 -26.81
32 C19 C C18 N Y N 0 -37.951 -1.191 -27.008
33 O7 O O11 N N N 0 -39.274 0.68 -27.749
34 H1 H H1 N N N 0 -34.691 -2.558 -24.805
35 H2 H H2 N N N 0 -34.275 -0.963 -24.091
36 H3 H H3 N N N 0 -26.998 -4.137 -23.57
37 H4 H H4 N N N 0 -27.851 -2.717 -22.877
38 H5 H H5 N N N 0 -28.282 -4.375 -22.337
39 H6 H H6 N N N 0 -36.813 -2.78 -26.088
40 H7 H H7 N N N 0 -33.237 -3.658 -25.235
41 H8 H H8 N N N 0 -30.886 -4.4 -25.652
42 H9 H H9 N N N 0 -32.037 -2.117 -21.403
43 H10 H H10 N N N 0 -37.129 0.806 -23.792
44 H11 H H11 N N N 0 -38.47 1.79 -25.565
45 H12 H H12 N N N 0 -40.311 0.497 -29.524
46 H16 H H16 N N N 0 -38.138 -1.728 -27.926
47 H13 H H13 N N N 0 -38.785 -0.443 -29.409
48 H14 H H14 N N N 0 -40.241 -0.979 -28.503
49 H15 H H15 N N N 0 -29.678 -2.752 -21.881



YWR : Chemical Bonds

Total Number of Bonds: 54
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C22 O7 C O sing 1.42 N N
2 O7 C18 O C sing 1.38 N N
3 C19 C18 C C doub 1.38 N Y
4 C19 C20 C C sing 1.42 N Y
5 C18 C17 C C sing 1.38 N Y
6 C20 C15 C C doub 1.39 N Y
7 C17 C16 C C doub 1.37 N Y
8 C15 C16 C C sing 1.4 N Y
9 C15 N2 C N sing 1.42 N N
10 C10 C9 C C doub 1.38 N Y
11 C10 C11 C C sing 1.37 N Y
12 C9 C8 C C sing 1.35 N Y
13 O8 C11 O C sing 1.43 N N
14 O8 C23 O C sing 1.37 N N
15 C7 N2 C N sing 1.32 N N
16 C7 N1 C N sing 1.31 N N
17 C11 C12 C C doub 1.39 N Y
18 O9 C1 O C doub 1.48 N N
19 N2 RU2 N RU sing 2.02 N N
20 C8 N1 C N sing 1.45 N N
21 C8 C13 C C doub 1.43 N Y
22 O2 C1 O C sing 1.26 N N
23 O2 RU2 O RU sing 2.08 N N
24 C1 O1 C O sing 1.26 N N
25 N1 RU1 N RU sing 2.04 N N
26 C12 C13 C C sing 1.36 N Y
27 O1 RU1 O RU sing 2.05 N N
28 RU2 RU1 RU RU sing 2.27 N N
29 RU2 O6 RU O sing 2.05 N N
30 RU2 O4 RU O sing 2.04 N N
31 RU1 O5 RU O sing 2.03 N N
32 RU1 O3 RU O sing 2.08 N N
33 O6 C5 O C sing 1.28 N N
34 O4 C3 O C sing 1.28 N N
35 O5 C5 O C sing 1.26 N N
36 C5 O11 C O doub 1.51 N N
37 O3 C3 O C sing 1.25 N N
38 C3 O10 C O doub 1.5 N N
39 C7 H1 C H sing 1.1 N N
40 C7 H2 C H sing 1.1 N N
41 C23 H3 C H sing 1.1 N N
42 C23 H4 C H sing 1.1 N N
43 C23 H5 C H sing 1.1 N N
44 C20 H6 C H sing 1.08 N N
45 C9 H7 C H sing 1.08 N N
46 C10 H8 C H sing 1.08 N N
47 C13 H9 C H sing 1.08 N N
48 C16 H10 C H sing 1.08 N N
49 C17 H11 C H sing 1.08 N N
50 C22 H12 C H sing 1.1 N N
51 C22 H13 C H sing 1.1 N N
52 C22 H14 C H sing 1.1 N N
53 C12 H15 C H sing 1.08 N N
54 C19 H16 C H sing 1.08 N N



YWR : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YWR 8pfw Open in New Window Bound ligand 3 1