Chemical Components in the PDB

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YWV : Summary

Code

YWV

One-letter code

X

Molecule name

[Ru2(DPhF)(Formate)]

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 6,8-diphenyl-2,4-dioxa-6,8-diaza-1$l^{3},5$l^{3}-diruthenabicyclo[3.3.0]octane

Formula

C14 H14 N2 O2 Ru2

Formal charge

0

Molecular weight

444.413 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C1O[Ru]N(CN([Ru]O1)c2ccccc2)c3ccccc3
SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)N2CN([Ru]3[Ru]2OCO3)c4ccccc4
Canonical SMILES CACTVS 3.385 C1O[Ru]N(CN([Ru]O1)c2ccccc2)c3ccccc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)N2CN([Ru]3[Ru]2OCO3)c4ccccc4

IUPAC InChI

InChI=1S/C13H12N2.CH2O2.2Ru/c1-3-7-12(8-4-1)14-11-15-13-9-5-2-6-10-13;2-1-3;;/h1-10H,11H2;1H2;;/q2*-2;2*+2

IUPAC InChI key

CVNAOZKWKIHKRL-UHFFFAOYSA-N
YWV

wwPDB Information

Atom count

34 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

D-beta-peptide, C-gamma linking

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-06-22

Last modified at

2023-09-08

Status

Released

Obsoleted

Not Assigned



YWV : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -34.581 -13.404 -20.392
2 RU1 RU RU1 N N N 0 -34.54 -11.379 -20.128
3 RU2 RU RU2 N N N 0 -35.827 -11.102 -21.997
4 O1 O O1 N N N 0 -36.235 -11.587 -18.99
5 O2 O O2 N N N 0 -37.498 -11.109 -20.81
6 N2 N N2 N N N 0 -35.985 -13.135 -22.164
7 C1 C C1 N N N 0 -37.401 -11.308 -19.539
8 C7 C C2 N N N 0 -35.228 -13.915 -21.405
9 C20 C C3 N Y N 0 -36.119 -15.089 -23.685
10 C9 C C4 N Y N 0 -32.449 -14.057 -19.435
11 C10 C C5 N Y N 0 -31.67 -14.939 -18.739
12 C15 C C6 N Y N 0 -36.574 -13.86 -23.229
13 C8 C C7 N Y N 0 -33.755 -14.318 -19.619
14 C13 C C8 N Y N 0 -34.323 -15.501 -19.048
15 C16 C C9 N Y N 0 -37.668 -13.501 -24.015
16 C17 C C10 N Y N 0 -38.345 -13.99 -25.096
17 C11 C C11 N Y N 0 -32.206 -16.079 -18.194
18 C12 C C12 N Y N 0 -33.558 -16.394 -18.357
19 C18 C C13 N Y N 0 -37.835 -15.2 -25.478
20 C19 C C14 N Y N 0 -36.778 -15.718 -24.761
21 H1 H H1 N N N 0 -37.769 -10.395 -19.049
22 H2 H H2 N N N 0 -38.07 -12.148 -19.3
23 H3 H H3 N N N 0 -35.884 -14.7 -21.001
24 H4 H H4 N N N 0 -34.476 -14.37 -22.066
25 H5 H H5 N N N 0 -35.266 -15.56 -23.219
26 H6 H H6 N N N 0 -32.016 -13.153 -19.836
27 H7 H H7 N N N 0 -30.617 -14.736 -18.616
28 H8 H H8 N N N 0 -35.38 -15.691 -19.167
29 H9 H H9 N N N 0 -38.104 -12.574 -23.672
30 H10 H H10 N N N 0 -39.17 -13.49 -25.582
31 H11 H H11 N N N 0 -31.571 -16.745 -17.629
32 H12 H H12 N N N 0 -33.978 -17.304 -17.954
33 H13 H H13 N N N 0 -38.25 -15.736 -26.319
34 H14 H H14 N N N 0 -36.422 -16.696 -25.05



YWV : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C18 C17 C C doub 1.37 N Y
2 C18 C19 C C sing 1.38 N Y
3 C17 C16 C C sing 1.37 N Y
4 C19 C20 C C doub 1.41 N Y
5 C16 C15 C C doub 1.39 N Y
6 C20 C15 C C sing 1.39 N Y
7 C15 N2 C N sing 1.42 N N
8 N2 RU2 N RU sing 2.05 N N
9 N2 C7 N C sing 1.33 N N
10 RU2 O2 RU O sing 2.05 N N
11 RU2 RU1 RU RU sing 2.29 N N
12 C7 N1 C N sing 1.31 N N
13 O2 C1 O C sing 1.29 N N
14 N1 RU1 N RU sing 2.04 N N
15 N1 C8 N C sing 1.45 N N
16 RU1 O1 RU O sing 2.05 N N
17 C8 C9 C C doub 1.34 N Y
18 C8 C13 C C sing 1.43 N Y
19 C1 O1 C O sing 1.32 N N
20 C9 C10 C C sing 1.37 N Y
21 C13 C12 C C doub 1.36 N Y
22 C10 C11 C C doub 1.37 N Y
23 C12 C11 C C sing 1.4 N Y
24 C1 H1 C H sing 1.1 N N
25 C1 H2 C H sing 1.1 N N
26 C7 H3 C H sing 1.1 N N
27 C7 H4 C H sing 1.1 N N
28 C20 H5 C H sing 1.08 N N
29 C9 H6 C H sing 1.08 N N
30 C10 H7 C H sing 1.08 N N
31 C13 H8 C H sing 1.08 N N
32 C16 H9 C H sing 1.08 N N
33 C17 H10 C H sing 1.08 N N
34 C11 H11 C H sing 1.08 N N
35 C12 H12 C H sing 1.08 N N
36 C18 H13 C H sing 1.08 N N
37 C19 H14 C H sing 1.08 N N



YWV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YWV 8ph6 Open in New Window Bound ligand 1 1