Chemical Components in the PDB

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DRB : Summary

Code

DRB

One-letter code

X

Molecule name

DELTA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C9-ADAMANTANE RUTHENIUM (II)

Systematic names

ProgramVersionName
ACDLabs 10.04 bis[1H,1'H-2,2'-bipyridinato(2-)-kappa~2~N~1~,N~1'~][9-(4'-methyl-1H,1'H-2,2'-bipyridin-4-yl-kappa~2~N~1~,N~1'~)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]nonanamidato(2-)]ruthenium(2+)

Formula

C50 H57 N7 O Ru

Formal charge

2

Molecular weight

873.104 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC3C1CC2CC(C1)CC3C2)CCCCCCCCc%12cc%11c4n(ccc(c4)C)[Ru+2]7%10(n5ccccc5c6ccccn67)(n8ccccc8c9ccccn9%10)n%11cc%12
SMILES CACTVS 3.341 CC1=CC2=C3C=C(CCCCCCCCC(=O)NC4C5CC6CC(C5)CC4C6)C=CN3[Ru++]78(N9C=CC=CC9=C%10C=CC=CN7%10)(N%11C=CC=CC%11=C%12C=CC=CN8%12)N2C=C1
SMILES OpenEye OEToolkits 1.5.0 CC1=CC2=C3C=C(C=CN3[Ru+2]45(N2C=C1)(N6C=CC=CC6=C7N4C=CC=C7)N8C=CC=CC8=C9N5C=CC=C9)CCCCCCCCC(=O)NC1C2CC3CC(C2)CC1C3
Canonical SMILES CACTVS 3.341 CC1=CC2=C3C=C(CCCCCCCCC(=O)NC4C5CC6CC(C5)CC4C6)C=CN3[Ru++]78(N9C=CC=CC9=C%10C=CC=CN7%10)(N%11C=CC=CC%11=C%12C=CC=CN8%12)N2C=C1
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=CC2=C3C=C(C=CN3[Ru+2]45(N2C=C1)(N6C=CC=CC6=C7N4C=CC=C7)N8C=CC=CC8=C9N5C=CC=C9)CCCCCCCCC(=O)NC1C2CC3CC(C2)CC1C3

IUPAC InChI

InChI=1S/C30H41N3O.2C10H8N2.Ru/c1-21-10-12-31-27(14-21)28-20-22(11-13-32-28)8-6-4-2-3-5-7-9-29(34)33-30-25-16-23-15-24(18-25)19-26(30)17-23;2*1-3-7-11-9(5-1)10-6-2-4-8-12-10;/h10-14,20,23-26,30H,2-9,15-19H2,1H3,(H,33,34);2*1-8H;/q3*-2;+8/b28-27-;2*10-9-;/t23-,24+,25-,26+,30-;;;

IUPAC InChI key

IGSCYCAKHRXAKK-KBBCMHLPSA-N
DRB

wwPDB Information

Atom count

116 (59 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-10-06

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DRB : Atoms of Molecule

Total Number of Atoms: 116
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 RU RU RU N N N 2 -5.096 -0.2 0.034
2 N2 N N2 N N N 0 -6.02 0.745 -1.512
3 C3 C C3 N N N 0 -5.47 1.327 -2.654
4 C4 C C4 N N N 0 -6.249 1.908 -3.575
5 C5 C C5 N N N 0 -7.696 1.934 -3.38
6 C6 C C6 N N N 0 -8.233 1.375 -2.275
7 C7 C C7 N N N 0 -7.396 0.753 -1.292
8 C8 C C8 N N N 0 -7.888 0.162 -0.142
9 C9 C C9 N N N 0 -9.284 0.115 0.182
10 C10 C C10 N N N 0 -9.705 -0.484 1.316
11 C11 C C11 N N N 0 -8.732 -1.088 2.222
12 C12 C C12 N N N 0 -7.43 -1.039 1.917
13 N13 N N13 N N N 0 -6.988 -0.422 0.747
14 N14 N N14 N N N 0 -4.797 1.552 1.022
15 C15 C C15 N N N 0 -5.635 2.231 1.906
16 C16 C C16 N N N 0 -5.256 3.383 2.47
17 C17 C C17 N N N 0 -3.943 3.94 2.155
18 C18 C C18 N N N 0 -3.128 3.29 1.298
19 C19 C C19 N N N 0 -3.539 2.055 0.694
20 C20 C C20 N N N 0 -2.749 1.347 -0.191
21 C21 C C21 N N N 0 -1.437 1.767 -0.59
22 C22 C C22 N N N 0 -0.718 1.036 -1.469
23 C23 C C23 N N N 0 -1.28 -0.194 -2.02
24 C24 C C24 N N N 0 -2.501 -0.587 -1.641
25 N25 N N25 N N N 0 -3.244 0.162 -0.729
26 N26 N N26 N N N 0 -4.316 -1.269 1.58
27 C27 C C27 N N N 0 -3.885 -0.831 2.831
28 C28 C C28 N N N 0 -3.396 -1.691 3.733
29 C29 C C29 N N N 0 -3.316 -3.11 3.398
30 C30 C C30 N N N 0 -3.73 -3.54 2.187
31 C31 C C31 N N N 0 -4.249 -2.614 1.222
32 C32 C C32 N N N 0 -4.679 -2.988 -0.036
33 C33 C C33 N N N 0 -4.643 -4.342 -0.51
34 C34 C C34 N N N 0 -5.078 -4.648 -1.75
35 C35 C C35 N N N 0 -5.593 -3.593 -2.62
36 C36 C C36 N N N 0 -5.624 -2.331 -2.175
37 N37 N N37 N N N 0 -5.173 -2.009 -0.896
38 C38 C C38 N N N 0 -3.499 5.235 2.783
39 C39 C C39 N N N 0 0.659 1.489 -1.879
40 C40 C C40 N N N 0 1.705 0.794 -1.005
41 C41 C C41 N N N 0 3.104 1.254 -1.421
42 C42 C C42 N N N 0 4.15 0.559 -0.547
43 C43 C C43 N N N 0 5.549 1.019 -0.963
44 C44 C C44 N N N 0 6.595 0.324 -0.089
45 C45 C C45 N N N 0 7.994 0.784 -0.505
46 C46 C C46 N N N 0 9.04 0.089 0.369
47 O47 O O47 N N N 0 10.55 1.342 -0.944
48 C48 C C48 N N N 0 10.418 0.542 -0.041
49 N49 N N49 N N N 0 11.503 0.059 0.595
50 C50 C C50 N N N 0 14.343 -1.98 0.628
51 C51 C C51 N N N 0 13.854 -1.128 1.8
52 C52 C C52 N N N 0 13.803 0.342 1.377
53 C53 C C53 N N N 0 12.842 0.499 0.196
54 C54 C C54 N N N 0 13.331 -0.354 -0.976
55 C55 C C55 N N N 0 14.73 0.106 -1.393
56 C56 C C56 N N N 0 15.691 -0.051 -0.212
57 C57 C C57 N N N 0 15.742 -1.52 0.211
58 C58 C C58 N N N 0 13.383 -1.823 -0.553
59 C59 C C59 N N N 0 15.202 0.801 0.96
60 H3 H H3 N N N 0 -4.398 1.309 -2.797
61 H4 H H4 N N N 0 -5.81 2.352 -4.455
62 H5 H H5 N N N 0 -8.334 2.398 -4.117
63 H6 H H6 N N N 0 -9.305 1.396 -2.131
64 H9 H H9 N N N 0 -10.005 0.563 -0.487
65 H10 H H10 N N N 0 -10.758 -0.516 1.552
66 H11 H H11 N N N 0 -9.059 -1.571 3.13
67 H12 H H12 N N N 0 -6.708 -1.487 2.588
68 H15 H H15 N N N 0 -6.608 1.818 2.14
69 H16 H H16 N N N 0 -5.915 3.897 3.153
70 H18 H H18 N N N 0 -2.156 3.703 1.065
71 H21 H H21 N N N 0 -1.019 2.678 -0.183
72 H23 H H23 N N N 0 -0.716 -0.782 -2.728
73 H24 H H24 N N N 0 -2.92 -1.497 -2.048
74 H27 H H27 N N N 0 -3.945 0.222 3.077
75 H28 H H28 N N N 0 -3.065 -1.339 4.697
76 H29 H H29 N N N 0 -2.927 -3.815 4.117
77 H30 H H30 N N N 0 -3.669 -4.591 1.942
78 H33 H H33 N N N 0 -4.263 -5.124 0.132
79 H34 H H34 N N N 0 -5.046 -5.669 -2.098
80 H35 H H35 N N N 0 -5.943 -3.828 -3.612
81 H36 H H36 N N N 0 -6.005 -1.548 -2.818
82 H383 H 3H38 N N N 0 -2.414 5.234 2.89
83 H382 H 2H38 N N N 0 -3.96 5.339 3.766
84 H381 H 1H38 N N N 0 -3.801 6.069 2.15
85 H392 H 2H39 N N N 0 0.739 2.568 -1.752
86 H412 H 2H41 N N N 0 3.184 2.334 -1.295
87 H391 H 1H39 N N N 0 0.83 1.231 -2.924
88 H402 H 2H40 N N N 0 1.625 -0.286 -1.131
89 H401 H 1H40 N N N 0 1.534 1.052 0.041
90 H411 H 1H41 N N N 0 3.275 0.996 -2.466
91 H422 H 2H42 N N N 0 4.07 -0.52 -0.673
92 H421 H 1H42 N N N 0 3.979 0.817 0.498
93 H432 H 2H43 N N N 0 5.629 2.099 -0.837
94 H431 H 1H43 N N N 0 5.72 0.761 -2.008
95 H442 H 2H44 N N N 0 6.515 -0.755 -0.215
96 H441 H 1H44 N N N 0 6.424 0.582 0.956
97 H452 H 2H45 N N N 0 8.074 1.864 -0.379
98 H451 H 1H45 N N N 0 8.165 0.527 -1.551
99 H462 H 2H46 N N N 0 8.96 -0.99 0.243
100 H461 H 1H46 N N N 0 8.869 0.347 1.414
101 H49 H H49 N N N 0 11.398 -0.581 1.317
102 H50 H H50 N N N 0 14.38 -3.027 0.93
103 H512 H 2H51 N N N 0 12.858 -1.455 2.097
104 H511 H 1H51 N N N 0 14.539 -1.24 2.641
105 H52 H H52 N N N 0 13.455 0.949 2.212
106 H53 H H53 N N N 0 12.806 1.546 -0.106
107 H54 H H54 N N N 0 12.647 -0.242 -1.817
108 H552 H 2H55 N N N 0 15.078 -0.501 -2.228
109 H551 H 1H55 N N N 0 14.694 1.153 -1.695
110 H56 H H56 N N N 0 16.687 0.276 -0.509
111 H572 H 2H57 N N N 0 16.09 -2.128 -0.624
112 H571 H 1H57 N N N 0 16.426 -1.632 1.052
113 H582 H 2H58 N N N 0 12.386 -2.15 -0.256
114 H581 H 1H58 N N N 0 13.731 -2.43 -1.388
115 H592 H 2H59 N N N 0 15.886 0.689 1.801
116 H591 H 1H59 N N N 0 15.165 1.848 0.658



DRB : Chemical Bonds

Total Number of Bonds: 127
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 RU N2 RU N sing 2.03 N N
2 RU N13 RU N sing 2.03 N N
3 RU N14 RU N sing 2.03 N N
4 RU N25 RU N sing 2.04 N N
5 RU N26 RU N sing 2.04 N N
6 RU N37 RU N sing 2.04 N N
7 N2 C3 N C sing 1.39 N N
8 N2 C7 N C sing 1.39 N N
9 C3 C4 C C doub 1.34 N N
10 C3 H3 C H sing 1.08 N N
11 C4 C5 C C sing 1.46 N N
12 C4 H4 C H sing 1.08 N N
13 C5 C6 C C doub 1.35 N N
14 C5 H5 C H sing 1.08 N N
15 C6 C7 C C sing 1.43 N N
16 C6 H6 C H sing 1.08 N N
17 C7 C8 C C doub 1.38 N N
18 C8 C9 C C sing 1.43 N N
19 C8 N13 C N sing 1.39 N N
20 C9 C10 C C doub 1.35 N N
21 C9 H9 C H sing 1.08 N N
22 C10 C11 C C sing 1.46 N N
23 C10 H10 C H sing 1.08 N N
24 C11 C12 C C doub 1.34 N N
25 C11 H11 C H sing 1.08 N N
26 C12 N13 C N sing 1.39 N N
27 C12 H12 C H sing 1.08 N N
28 N14 C15 N C sing 1.39 N N
29 N14 C19 N C sing 1.39 N N
30 C15 C16 C C doub 1.34 N N
31 C15 H15 C H sing 1.08 N N
32 C16 C17 C C sing 1.46 N N
33 C16 H16 C H sing 1.08 N N
34 C17 C18 C C doub 1.35 N N
35 C17 C38 C C sing 1.51 N N
36 C18 C19 C C sing 1.43 N N
37 C18 H18 C H sing 1.08 N N
38 C19 C20 C C doub 1.38 N N
39 C20 C21 C C sing 1.43 N N
40 C20 N25 C N sing 1.39 N N
41 C21 C22 C C doub 1.35 N N
42 C21 H21 C H sing 1.08 N N
43 C22 C23 C C sing 1.46 N N
44 C22 C39 C C sing 1.51 N N
45 C23 C24 C C doub 1.34 N N
46 C23 H23 C H sing 1.08 N N
47 C24 N25 C N sing 1.39 N N
48 C24 H24 C H sing 1.08 N N
49 N26 C27 N C sing 1.39 N N
50 N26 C31 N C sing 1.39 N N
51 C27 C28 C C doub 1.34 N N
52 C27 H27 C H sing 1.08 N N
53 C28 C29 C C sing 1.46 N N
54 C28 H28 C H sing 1.08 N N
55 C29 C30 C C doub 1.35 N N
56 C29 H29 C H sing 1.08 N N
57 C30 C31 C C sing 1.43 N N
58 C30 H30 C H sing 1.08 N N
59 C31 C32 C C doub 1.38 N N
60 C32 C33 C C sing 1.44 N N
61 C32 N37 C N sing 1.39 N N
62 C33 C34 C C doub 1.35 N N
63 C33 H33 C H sing 1.08 N N
64 C34 C35 C C sing 1.46 N N
65 C34 H34 C H sing 1.08 N N
66 C35 C36 C C doub 1.34 N N
67 C35 H35 C H sing 1.08 N N
68 C36 N37 C N sing 1.39 N N
69 C36 H36 C H sing 1.08 N N
70 C38 H383 C H sing 1.09 N N
71 C38 H382 C H sing 1.09 N N
72 C38 H381 C H sing 1.09 N N
73 C39 C40 C C sing 1.53 N N
74 C39 H392 C H sing 1.09 N N
75 C39 H391 C H sing 1.09 N N
76 C40 C41 C C sing 1.53 N N
77 C40 H402 C H sing 1.09 N N
78 C40 H401 C H sing 1.09 N N
79 C41 C42 C C sing 1.53 N N
80 C41 H412 C H sing 1.09 N N
81 C41 H411 C H sing 1.09 N N
82 C42 C43 C C sing 1.53 N N
83 C42 H422 C H sing 1.09 N N
84 C42 H421 C H sing 1.09 N N
85 C43 C44 C C sing 1.53 N N
86 C43 H432 C H sing 1.09 N N
87 C43 H431 C H sing 1.09 N N
88 C44 C45 C C sing 1.53 N N
89 C44 H442 C H sing 1.09 N N
90 C44 H441 C H sing 1.09 N N
91 C45 C46 C C sing 1.53 N N
92 C45 H452 C H sing 1.09 N N
93 C45 H451 C H sing 1.09 N N
94 C46 C48 C C sing 1.51 N N
95 C46 H462 C H sing 1.09 N N
96 C46 H461 C H sing 1.09 N N
97 O47 C48 O C doub 1.21 N N
98 C48 N49 C N sing 1.35 N N
99 N49 C53 N C sing 1.46 N N
100 N49 H49 N H sing 0.97 N N
101 C50 C51 C C sing 1.53 N N
102 C50 C57 C C sing 1.53 N N
103 C50 C58 C C sing 1.53 N N
104 C50 H50 C H sing 1.09 N N
105 C51 C52 C C sing 1.53 N N
106 C51 H512 C H sing 1.09 N N
107 C51 H511 C H sing 1.09 N N
108 C52 C53 C C sing 1.53 N N
109 C52 C59 C C sing 1.53 N N
110 C52 H52 C H sing 1.09 N N
111 C53 C54 C C sing 1.53 N N
112 C53 H53 C H sing 1.09 N N
113 C54 C55 C C sing 1.53 N N
114 C54 C58 C C sing 1.53 N N
115 C54 H54 C H sing 1.09 N N
116 C55 C56 C C sing 1.53 N N
117 C55 H552 C H sing 1.09 N N
118 C55 H551 C H sing 1.09 N N
119 C56 C57 C C sing 1.53 N N
120 C56 C59 C C sing 1.53 N N
121 C56 H56 C H sing 1.09 N N
122 C57 H572 C H sing 1.09 N N
123 C57 H571 C H sing 1.09 N N
124 C58 H582 C H sing 1.09 N N
125 C58 H581 C H sing 1.09 N N
126 C59 H592 C H sing 1.09 N N
127 C59 H591 C H sing 1.09 N N



DRB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DRB 1qmq Open in New Window Bound ligand 2 1