data_R2R
#
_chem_comp.id R2R
_chem_comp.name "ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "H28 N14 O2 Ru3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-10-02
_chem_comp.pdbx_modified_date 2019-11-22
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 559.525
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code R2R
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6UIW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
R2R N01 N1 N 0 1 N N N N N N 141.338 162.688 165.339 -0.204 3.082 -0.650 N01 R2R 1
R2R N03 N2 N 0 1 N N N N N N 144.926 162.797 167.272 0.211 -0.922 0.680 N03 R2R 2
R2R N04 N3 N 0 1 N N N N N N 143.006 160.737 166.651 -0.569 0.383 -1.904 N04 R2R 3
R2R N05 N4 N 0 1 N N N N N N 143.257 164.748 165.961 0.576 1.776 1.933 N05 R2R 4
R2R O06 O1 O 0 1 N N N N N N 143.998 162.415 164.716 1.766 1.087 -0.514 O06 R2R 5
R2R N08 N5 N 0 1 N N N N N N 145.825 161.724 161.365 3.763 -2.181 0.494 N08 R2R 6
R2R N09 N6 N 0 1 N N N N N N 144.740 160.083 163.471 3.993 0.733 1.158 N09 R2R 7
R2R N10 N7 N 0 1 N N N N N N 144.990 164.093 162.781 1.395 -1.597 -1.250 N10 R2R 8
R2R N11 N8 N 0 1 N N N N N N 143.071 162.034 162.160 1.404 -0.708 1.614 N11 R2R 9
R2R N12 N9 N 0 1 N N N N N N 146.659 162.142 164.094 3.984 -0.155 -1.705 N12 R2R 10
R2R O13 O2 O 0 1 N N N N N N 142.264 163.070 167.896 -1.759 1.073 0.543 O13 R2R 11
R2R N15 N10 N 0 1 N N N N N N 140.437 163.761 171.247 -3.758 -2.163 -0.558 N15 R2R 12
R2R N16 N11 N 0 1 N N N N N N 141.523 165.403 169.140 -4.307 0.148 1.271 N16 R2R 13
R2R N17 N12 N 0 1 N N N N N N 141.273 161.392 169.830 -1.068 -1.010 -1.208 N17 R2R 14
R2R N18 N13 N 0 1 N N N N N N 139.604 163.343 168.519 -3.539 0.646 -1.584 N18 R2R 15
R2R N19 N14 N 0 1 N N N N N N 143.192 163.452 170.452 -1.836 -1.507 1.647 N19 R2R 16
R2R RU2 RU1 RU 0 0 N N N N N N 143.131 162.743 166.306 0.004 1.080 0.015 RU2 R2R 17
R2R RU3 RU2 RU 0 0 N N N N N N 144.865 162.088 163.127 2.694 -0.432 -0.046 RU3 R2R 18
R2R RU1 RU3 RU 0 0 N N N N N N 141.398 163.397 169.485 -2.688 -0.431 0.031 RU1 R2R 19
R2R H1 H1 H 0 1 N N N N N N 140.600 162.847 165.995 0.219 3.207 -1.558 H1 R2R 20
R2R H2 H2 H 0 1 N N N N N N 141.317 163.398 164.635 -1.173 3.361 -0.662 H2 R2R 21
R2R H3 H3 H 0 1 N N N N N N 144.776 162.974 168.245 -0.643 -1.440 0.539 H3 R2R 22
R2R H4 H4 H 0 1 N N N N N N 145.391 161.919 167.161 0.988 -1.376 0.224 H4 R2R 23
R2R H5 H5 H 0 1 N N N N N N 142.541 160.576 167.522 -0.021 -0.419 -2.176 H5 R2R 24
R2R H6 H6 H 0 1 N N N N N N 142.489 160.303 165.913 -1.556 0.173 -1.933 H6 R2R 25
R2R H7 H7 H 0 1 N N N N N N 142.834 165.244 166.719 0.692 1.008 2.577 H7 R2R 26
R2R H8 H8 H 0 1 N N N N N N 144.218 165.013 165.885 1.416 2.333 1.880 H8 R2R 27
R2R H9 H9 H 0 1 N N N N N N 146.812 161.689 161.523 3.132 -2.932 0.729 H9 R2R 28
R2R H10 H10 H 0 1 N N N N N N 145.516 160.849 160.992 4.397 -2.458 -0.240 H10 R2R 29
R2R H11 H11 H 0 1 N N N N N N 144.276 159.922 164.342 4.284 1.569 0.673 H11 R2R 30
R2R H12 H12 H 0 1 N N N N N N 144.223 159.650 162.733 3.561 0.960 2.042 H12 R2R 31
R2R H13 H13 H 0 1 N N N N N N 144.567 164.590 163.539 0.584 -1.892 -0.726 H13 R2R 32
R2R H14 H14 H 0 1 N N N N N N 145.951 164.359 162.704 1.125 -1.094 -2.082 H14 R2R 33
R2R H15 H15 H 0 1 N N N N N N 142.333 162.193 162.816 0.803 -1.507 1.476 H15 R2R 34
R2R H16 H16 H 0 1 N N N N N N 143.050 162.744 161.456 1.930 -0.795 2.470 H16 R2R 35
R2R H17 H17 H 0 1 N N N N N N 146.509 162.319 165.067 3.849 0.754 -2.121 H17 R2R 36
R2R H18 H18 H 0 1 N N N N N N 147.124 161.264 163.983 4.948 -0.292 -1.440 H18 R2R 37
R2R H19 H19 H 0 1 N N N N N N 140.559 162.981 171.861 -3.707 -2.878 0.151 H19 R2R 38
R2R H20 H20 H 0 1 N N N N N N 140.819 164.582 171.672 -4.717 -1.938 -0.777 H20 R2R 39
R2R H21 H21 H 0 1 N N N N N N 141.100 165.899 169.898 -4.189 1.094 1.602 H21 R2R 40
R2R H22 H22 H 0 1 N N N N N N 142.484 165.669 169.063 -5.188 0.041 0.789 H22 R2R 41
R2R H23 H23 H 0 1 N N N N N N 140.809 161.231 170.701 -0.184 -0.772 -0.783 H23 R2R 42
R2R H24 H24 H 0 1 N N N N N N 140.756 160.958 169.092 -1.112 -1.994 -1.424 H24 R2R 43
R2R H25 H25 H 0 1 N N N N N N 138.867 163.502 169.175 -4.530 0.467 -1.656 H25 R2R 44
R2R H26 H26 H 0 1 N N N N N N 139.583 164.054 167.816 -3.356 1.634 -1.497 H26 R2R 45
R2R H27 H27 H 0 1 N N N N N N 143.042 163.629 171.425 -0.884 -1.217 1.813 H27 R2R 46
R2R H28 H28 H 0 1 N N N N N N 143.658 162.574 170.341 -2.394 -1.408 2.482 H28 R2R 47
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
R2R N08 RU3 SING N N 1
R2R N11 RU3 SING N N 2
R2R N10 RU3 SING N N 3
R2R RU3 N09 SING N N 4
R2R RU3 N12 SING N N 5
R2R RU3 O06 SING N N 6
R2R O06 RU2 SING N N 7
R2R N01 RU2 SING N N 8
R2R N05 RU2 SING N N 9
R2R RU2 N04 SING N N 10
R2R RU2 N03 SING N N 11
R2R RU2 O13 SING N N 12
R2R O13 RU1 SING N N 13
R2R N18 RU1 SING N N 14
R2R N16 RU1 SING N N 15
R2R RU1 N17 SING N N 16
R2R RU1 N19 SING N N 17
R2R RU1 N15 SING N N 18
R2R N01 H1 SING N N 19
R2R N01 H2 SING N N 20
R2R N03 H3 SING N N 21
R2R N03 H4 SING N N 22
R2R N04 H5 SING N N 23
R2R N04 H6 SING N N 24
R2R N05 H7 SING N N 25
R2R N05 H8 SING N N 26
R2R N08 H9 SING N N 27
R2R N08 H10 SING N N 28
R2R N09 H11 SING N N 29
R2R N09 H12 SING N N 30
R2R N10 H13 SING N N 31
R2R N10 H14 SING N N 32
R2R N11 H15 SING N N 33
R2R N11 H16 SING N N 34
R2R N12 H17 SING N N 35
R2R N12 H18 SING N N 36
R2R N15 H19 SING N N 37
R2R N15 H20 SING N N 38
R2R N16 H21 SING N N 39
R2R N16 H22 SING N N 40
R2R N17 H23 SING N N 41
R2R N17 H24 SING N N 42
R2R N18 H25 SING N N 43
R2R N18 H26 SING N N 44
R2R N19 H27 SING N N 45
R2R N19 H28 SING N N 46
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
R2R SMILES ACDLabs 12.01 N[Ru](N)(N)(N)(O[Ru](N)(N)(N)(N)N)O[Ru](N)(N)(N)(N)N
R2R InChI InChI 1.03 InChI=1S/14H2N.2O.3Ru/h14*1H2;;;;;/q14*-1;;;+4;2*+5
R2R InChIKey InChI 1.03 FOOPNNMQSUSGAT-UHFFFAOYSA-N
R2R SMILES_CANONICAL CACTVS 3.385 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
R2R SMILES CACTVS 3.385 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
R2R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 N[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)O[Ru](N)(N)(N)(N)N
R2R 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
#
_pdbx_chem_comp_identifier.comp_id R2R
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 12.01
_pdbx_chem_comp_identifier.identifier "ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
R2R 'Create component' 2019-10-02 RCSB
R2R 'Initial release' 2019-11-27 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
R2R N01 N -1.620 1.629 1
R2R N03 N -1.491 -1.747 2
R2R N04 N -2.667 -0.805 3
R2R N05 N -2.720 0.601 4
R2R O06 O 0.397 -0.834 5
R2R N08 N 1.987 -1.499 6
R2R N09 N -0.431 -3.270 7
R2R N10 N 0.927 -3.942 8
R2R N11 N 2.188 -3.068 9
R2R N12 N -0.303 -1.852 10
R2R O13 O 0.333 0.861 11
R2R N15 N -0.443 1.826 12
R2R N16 N 1.949 3.225 13
R2R N17 N 0.626 4.001 14
R2R N18 N 1.868 1.645 15
R2R N19 N -0.677 3.228 16
R2R RU2 Ru -1.350 -0.051 17
R2R RU3 Ru 0.807 -2.413 18
R2R RU1 Ru 0.623 2.466 19
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
R2R N08 RU3 SINGLE NONE 1
R2R N11 RU3 SINGLE NONE 2
R2R N10 RU3 SINGLE NONE 3
R2R RU3 N09 SINGLE NONE 4
R2R RU3 N12 SINGLE NONE 5
R2R RU3 O06 SINGLE NONE 6
R2R O06 RU2 SINGLE NONE 7
R2R N01 RU2 SINGLE NONE 8
R2R N05 RU2 SINGLE NONE 9
R2R RU2 N04 SINGLE NONE 10
R2R RU2 N03 SINGLE NONE 11
R2R RU2 O13 SINGLE NONE 12
R2R O13 RU1 SINGLE NONE 13
R2R N18 RU1 SINGLE NONE 14
R2R N16 RU1 SINGLE NONE 15
R2R RU1 N17 SINGLE NONE 16
R2R RU1 N19 SINGLE NONE 17
R2R RU1 N15 SINGLE NONE 18
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id R2R
_pdbe_chem_comp_rdkit_properties.exactmw 561.965
_pdbe_chem_comp_rdkit_properties.amw 559.530
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 28
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 14
_pdbe_chem_comp_rdkit_properties.NumHBA 16
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 47
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 19
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 149.851
_pdbe_chem_comp_rdkit_properties.tpsa 382.740
_pdbe_chem_comp_rdkit_properties.CrippenClogP -8.413
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.794
_pdbe_chem_comp_rdkit_properties.chi0v 13.352
_pdbe_chem_comp_rdkit_properties.chi1v 16.511
_pdbe_chem_comp_rdkit_properties.chi2v 15.836
_pdbe_chem_comp_rdkit_properties.chi3v 15.836
_pdbe_chem_comp_rdkit_properties.chi4v 19.075
_pdbe_chem_comp_rdkit_properties.chi0n 36.138
_pdbe_chem_comp_rdkit_properties.chi1n 15.313
_pdbe_chem_comp_rdkit_properties.chi2n 0.452
_pdbe_chem_comp_rdkit_properties.chi3n 0.452
_pdbe_chem_comp_rdkit_properties.chi4n 0.509
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 1.230
_pdbe_chem_comp_rdkit_properties.kappa1 3.354
_pdbe_chem_comp_rdkit_properties.kappa2 2.747
_pdbe_chem_comp_rdkit_properties.kappa3 12.666
_pdbe_chem_comp_rdkit_properties.Phi 0.485
#
_pdbe_chem_comp_external_mappings.comp_id R2R
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id R2R
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
R2R N01 0.072 1.934 -1.101 ETKDGv3 1
R2R N03 -0.270 -2.046 1.118 ETKDGv3 2
R2R N04 -0.180 -1.043 -2.040 ETKDGv3 3
R2R N05 0.119 1.012 2.008 ETKDGv3 4
R2R O06 0.291 -0.086 -0.002 ETKDGv3 5
R2R N08 5.033 0.130 -0.447 ETKDGv3 6
R2R N09 2.880 -2.508 -0.234 ETKDGv3 7
R2R N10 3.249 1.501 0.688 ETKDGv3 8
R2R N11 3.076 0.079 -2.006 ETKDGv3 9
R2R N12 3.040 -1.477 1.972 ETKDGv3 10
R2R O13 0.304 -0.102 0.011 ETKDGv3 11
R2R N15 -5.425 1.517 -0.412 ETKDGv3 12
R2R N16 -3.316 -1.942 -0.573 ETKDGv3 13
R2R N17 -2.798 2.358 0.859 ETKDGv3 14
R2R N18 -2.902 1.588 -2.871 ETKDGv3 15
R2R N19 -3.453 -0.938 2.529 ETKDGv3 16
R2R RU2 0.059 -0.654 0.223 ETKDGv3 17
R2R RU3 2.807 0.270 -0.490 ETKDGv3 18
R2R RU1 -2.787 -0.056 0.374 ETKDGv3 19
R2R H1 0.110 2.115 -2.128 ETKDGv3 20
R2R H2 -0.099 2.856 -0.640 ETKDGv3 21
R2R H3 -0.338 -2.987 0.670 ETKDGv3 22
R2R H4 -0.269 -2.206 2.150 ETKDGv3 23
R2R H5 -0.091 -0.604 -2.983 ETKDGv3 24
R2R H6 -0.323 -2.066 -2.198 ETKDGv3 25
R2R H7 0.206 2.045 2.131 ETKDGv3 26
R2R H8 -0.040 0.609 2.959 ETKDGv3 27
R2R H9 5.834 0.693 -0.811 ETKDGv3 28
R2R H10 5.445 -0.688 0.055 ETKDGv3 29
R2R H11 3.721 -2.772 -0.795 ETKDGv3 30
R2R H12 2.046 -2.728 -0.823 ETKDGv3 31
R2R H13 3.141 1.588 1.723 ETKDGv3 32
R2R H14 2.681 2.267 0.263 ETKDGv3 33
R2R H15 2.808 -0.674 -2.678 ETKDGv3 34
R2R H16 2.627 0.958 -2.347 ETKDGv3 35
R2R H17 3.940 -1.113 2.358 ETKDGv3 36
R2R H18 2.275 -1.018 2.516 ETKDGv3 37
R2R H19 -4.950 0.632 -0.700 ETKDGv3 38
R2R H20 -5.714 1.391 0.584 ETKDGv3 39
R2R H21 -2.652 -2.711 -0.814 ETKDGv3 40
R2R H22 -2.740 -1.083 -0.429 ETKDGv3 41
R2R H23 -2.479 1.461 0.429 ETKDGv3 42
R2R H24 -2.856 2.192 1.888 ETKDGv3 43
R2R H25 -2.585 0.761 -2.318 ETKDGv3 44
R2R H26 -2.847 2.413 -2.234 ETKDGv3 45
R2R H27 -4.134 -0.360 1.987 ETKDGv3 46
R2R H28 -2.513 -0.506 2.386 ETKDGv3 47
#