data_V7E
#
_chem_comp.id V7E
_chem_comp.name "3',3'-c-di-araAMP"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H24 N10 O12 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-04-22
_chem_comp.pdbx_modified_date 2022-04-29
_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 658.412
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code V7E
_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 7OB3
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
V7E P P1 P 0 1 N N N N N N 73.101 58.549 31.802 0.716 2.275 0.685 P V7E 1
V7E O1P O1 O 0 1 N N N N N N 73.749 57.429 31.023 0.921 2.508 -0.762 O1P V7E 2
V7E O2P O2 O 0 1 N N N N N N 71.634 58.667 31.461 0.450 3.682 1.423 O2P V7E 3
V7E "O5'" O3 O 0 1 N N N N N N 73.259 58.248 33.373 -0.554 1.309 0.899 "O5'" V7E 4
V7E "C5'" C1 C 0 1 N N N N N N 72.585 59.076 34.313 -1.901 1.735 0.684 "C5'" V7E 5
V7E "C4'" C2 C 0 1 N N R N N N 73.187 58.903 35.696 -2.860 0.736 1.334 "C4'" V7E 6
V7E "O4'" O4 O 0 1 N N N N N N 73.274 57.524 36.085 -4.205 1.214 1.235 "O4'" V7E 7
V7E "C3'" C3 C 0 1 N N S N N N 74.612 59.436 35.802 -2.793 -0.609 0.592 "C3'" V7E 8
V7E "O3'" O5 O 0 1 N N N N N N 74.705 60.832 36.005 -2.033 -1.556 1.346 "O3'" V7E 9
V7E "C2'" C4 C 0 1 N N S N N N 75.175 58.648 36.977 -4.260 -1.067 0.472 "C2'" V7E 10
V7E "O2'" O6 O 0 1 N N N N N N 76.589 58.519 36.901 -4.581 -1.351 -0.891 "O2'" V7E 11
V7E "C1'" C5 C 0 1 N N R N N N 74.455 57.308 36.871 -5.090 0.121 0.980 "C1'" V7E 12
V7E N9 N1 N 0 1 Y N N N N N 75.367 56.339 36.216 -6.073 0.507 -0.035 N9 V7E 13
V7E C8 C6 C 0 1 Y N N N N N 75.440 56.089 34.895 -5.924 1.489 -0.969 C8 V7E 14
V7E N7 N2 N 0 1 Y N N N N N 76.389 55.152 34.638 -6.991 1.562 -1.710 N7 V7E 15
V7E C5 C7 C 0 1 Y N N N N N 76.944 54.797 35.810 -7.890 0.635 -1.300 C5 V7E 16
V7E C6 C8 C 0 1 Y N N N N N 78.002 53.860 36.257 -9.180 0.260 -1.711 C6 V7E 17
V7E N6 N3 N 0 1 N N N N N N 78.678 53.091 35.371 -9.801 0.901 -2.769 N6 V7E 18
V7E N1 N4 N 0 1 Y N N N N N 78.269 53.799 37.580 -9.791 -0.725 -1.060 N1 V7E 19
V7E C2 C9 C 0 1 Y N N N N N 77.611 54.555 38.480 -9.206 -1.342 -0.050 C2 V7E 20
V7E N3 N5 N 0 1 Y N N N N N 76.641 55.421 38.139 -7.999 -1.025 0.369 N3 V7E 21
V7E C4 C10 C 0 1 Y N N N N N 76.269 55.585 36.848 -7.309 -0.056 -0.223 C4 V7E 22
V7E P1 P2 P 0 1 N N N N N N 76.101 61.566 35.675 -0.700 -2.259 0.779 P1 V7E 23
V7E O1P1 O7 O 0 0 N N N N N N 75.987 63.032 36.017 -0.529 -3.581 1.420 O1P1 V7E 24
V7E O2P1 O8 O 0 0 N N N N N N 77.214 60.912 36.460 -0.829 -2.448 -0.815 O2P1 V7E 25
V7E "O5'1" O9 O 0 0 N N N N N N 76.408 61.409 34.106 0.575 -1.333 1.108 "O5'1" V7E 26
V7E "C5'1" C11 C 0 0 N N N N N N 75.571 62.070 33.164 1.920 -1.732 0.835 "C5'1" V7E 27
V7E "C4'1" C12 C 0 0 N N R N N N 75.753 61.468 31.783 2.883 -0.697 1.418 "C4'1" V7E 28
V7E "O4'1" O10 O 0 0 N N N N N N 77.136 61.389 31.406 4.230 -1.173 1.327 "O4'1" V7E 29
V7E "C3'1" C13 C 0 0 N N S N N N 75.232 60.040 31.670 2.800 0.607 0.607 "C3'1" V7E 30
V7E "O3'1" O11 O 0 0 N N N N N N 73.838 59.943 31.461 2.030 1.582 1.309 "O3'1" V7E 31
V7E "C2'1" C14 C 0 0 N N S N N N 76.023 59.497 30.488 4.263 1.074 0.463 "C2'1" V7E 32
V7E "O2'1" O12 O 0 0 N N N N N N 76.160 58.083 30.549 4.576 1.310 -0.912 "O2'1" V7E 33
V7E "C1'1" C15 C 0 0 N N R N N N 77.363 60.219 30.605 5.105 -0.088 1.011 "C1'1" V7E 34
V7E N91 N6 N 0 1 Y N N N N N 78.334 59.307 31.256 6.075 -0.515 -0.001 N91 V7E 35
V7E C81 C16 C 0 1 Y N N N N N 78.601 59.248 32.574 5.918 -1.538 -0.887 C81 V7E 36
V7E N71 N7 N 0 1 Y N N N N N 79.535 58.296 32.832 6.974 -1.640 -1.640 N71 V7E 37
V7E C51 C17 C 0 1 Y N N N N N 79.873 57.726 31.661 7.874 -0.691 -1.286 C51 V7E 38
V7E C61 C18 C 0 1 Y N N N N N 80.797 56.657 31.214 9.156 -0.329 -1.732 C61 V7E 39
V7E N61 N8 N 0 1 N N N N N N 81.573 55.985 32.097 9.764 -1.014 -2.769 N61 V7E 40
V7E N11 N9 N 0 1 Y N N N N N 80.841 56.375 29.893 9.771 0.688 -1.136 N11 V7E 41
V7E C21 C19 C 0 1 Y N N N N N 80.080 57.029 28.995 9.198 1.347 -0.146 C21 V7E 42
V7E N31 N10 N 0 1 Y N N N N N 79.222 58.007 29.336 7.999 1.043 0.305 N31 V7E 43
V7E C41 C20 C 0 1 Y N N N N N 79.076 58.394 30.625 7.305 0.045 -0.233 C41 V7E 44
V7E H1 H1 H 0 1 N N N N N N 71.404 58.007 30.817 -0.327 4.156 1.097 H1 V7E 45
V7E "H5'A" H2 H 0 0 N N N N N N 72.681 60.127 34.005 -2.046 2.719 1.129 "H5'A" V7E 46
V7E "H5'" H3 H 0 1 N N N N N N 71.521 58.799 34.343 -2.100 1.786 -0.386 "H5'" V7E 47
V7E "H4'" H4 H 0 1 N N N N N N 72.560 59.448 36.417 -2.597 0.595 2.382 "H4'" V7E 48
V7E "H3'" H5 H 0 1 N N N N N N 75.161 59.150 34.893 -2.359 -0.474 -0.398 "H3'" V7E 49
V7E "H2'" H6 H 0 1 N N N N N N 74.882 59.141 37.916 -4.435 -1.946 1.093 "H2'" V7E 50
V7E "HO2'" H7 H 0 0 N N N N N N 76.903 58.023 37.648 -5.493 -1.644 -1.027 "HO2'" V7E 51
V7E "H1'" H8 H 0 1 N N N N N N 74.192 56.954 37.879 -5.604 -0.157 1.900 "H1'" V7E 52
V7E H8 H9 H 0 1 N N N N N N 74.829 56.567 34.144 -5.050 2.114 -1.078 H8 V7E 53
V7E H3 H10 H 0 1 N N N N N N 79.346 52.529 35.859 -9.345 1.619 -3.236 H3 V7E 54
V7E HN6 H11 H 0 1 N N N N N N 78.035 52.499 34.885 -10.692 0.633 -3.043 HN6 V7E 55
V7E H2 H12 H 0 1 N N N N N N 77.875 54.461 39.523 -9.738 -2.138 0.451 H2 V7E 56
V7E H4 H13 H 0 1 N N N N N N 77.628 61.557 37.021 -0.060 -2.866 -1.225 H4 V7E 57
V7E "HC5'" H14 H 0 0 N N N N N N 74.521 61.960 33.472 2.111 -2.704 1.291 "HC5'" V7E 58
V7E HC5A H15 H 0 0 N N N N N N 75.834 63.138 33.132 2.068 -1.800 -0.243 HC5A V7E 59
V7E "HC4'" H16 H 0 0 N N N N N N 75.210 62.092 31.058 2.633 -0.500 2.460 "HC4'" V7E 60
V7E "HC3'" H17 H 0 0 N N N N N N 75.522 59.485 32.575 2.370 0.414 -0.376 "HC3'" V7E 61
V7E "HC2'" H18 H 0 0 N N N N N N 75.530 59.799 29.552 4.432 1.977 1.050 "HC2'" V7E 62
V7E HO2A H19 H 0 0 N N N N N N 75.313 57.690 30.725 5.484 1.607 -1.063 HO2A V7E 63
V7E "HC1'" H20 H 0 0 N N N N N N 77.719 60.496 29.602 5.632 0.232 1.910 "HC1'" V7E 64
V7E HC8 H21 H 0 1 N N N N N N 78.136 59.872 33.323 5.045 -2.171 -0.955 HC8 V7E 65
V7E H5 H22 H 0 1 N N N N N N 82.125 55.309 31.609 9.306 -1.754 -3.197 H5 V7E 66
V7E H1N6 H23 H 0 0 N N N N N N 82.175 56.629 32.569 10.650 -0.754 -3.069 H1N6 V7E 67
V7E HC2 H24 H 0 1 N N N N N N 80.162 56.756 27.953 9.733 2.167 0.311 HC2 V7E 68
#
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
V7E P O1P DOUB N N 1
V7E P O2P SING N N 2
V7E P "O5'" SING N N 3
V7E P "O3'1" SING N N 4
V7E "O5'" "C5'" SING N N 5
V7E "C5'" "C4'" SING N N 6
V7E "C4'" "O4'" SING N N 7
V7E "C4'" "C3'" SING N N 8
V7E "O4'" "C1'" SING N N 9
V7E "C3'" "O3'" SING N N 10
V7E "C3'" "C2'" SING N N 11
V7E "O3'" P1 SING N N 12
V7E "C2'" "O2'" SING N N 13
V7E "C2'" "C1'" SING N N 14
V7E "C1'" N9 SING N N 15
V7E N9 C8 SING Y N 16
V7E N9 C4 SING Y N 17
V7E C8 N7 DOUB Y N 18
V7E N7 C5 SING Y N 19
V7E C5 C6 DOUB Y N 20
V7E C5 C4 SING Y N 21
V7E C6 N6 SING N N 22
V7E C6 N1 SING Y N 23
V7E N1 C2 DOUB Y N 24
V7E C2 N3 SING Y N 25
V7E N3 C4 DOUB Y N 26
V7E P1 O1P1 DOUB N N 27
V7E P1 O2P1 SING N N 28
V7E P1 "O5'1" SING N N 29
V7E "O5'1" "C5'1" SING N N 30
V7E "C5'1" "C4'1" SING N N 31
V7E "C4'1" "O4'1" SING N N 32
V7E "C4'1" "C3'1" SING N N 33
V7E "O4'1" "C1'1" SING N N 34
V7E "C3'1" "O3'1" SING N N 35
V7E "C3'1" "C2'1" SING N N 36
V7E "C2'1" "O2'1" SING N N 37
V7E "C2'1" "C1'1" SING N N 38
V7E "C1'1" N91 SING N N 39
V7E N91 C81 SING Y N 40
V7E N91 C41 SING Y N 41
V7E C81 N71 DOUB Y N 42
V7E N71 C51 SING Y N 43
V7E C51 C61 DOUB Y N 44
V7E C51 C41 SING Y N 45
V7E C61 N61 SING N N 46
V7E C61 N11 SING Y N 47
V7E N11 C21 DOUB Y N 48
V7E C21 N31 SING Y N 49
V7E N31 C41 DOUB Y N 50
V7E O2P H1 SING N N 51
V7E "C5'" "H5'A" SING N N 52
V7E "C5'" "H5'" SING N N 53
V7E "C4'" "H4'" SING N N 54
V7E "C3'" "H3'" SING N N 55
V7E "C2'" "H2'" SING N N 56
V7E "O2'" "HO2'" SING N N 57
V7E "C1'" "H1'" SING N N 58
V7E C8 H8 SING N N 59
V7E N6 H3 SING N N 60
V7E N6 HN6 SING N N 61
V7E C2 H2 SING N N 62
V7E O2P1 H4 SING N N 63
V7E "C5'1" "HC5'" SING N N 64
V7E "C5'1" HC5A SING N N 65
V7E "C4'1" "HC4'" SING N N 66
V7E "C3'1" "HC3'" SING N N 67
V7E "C2'1" "HC2'" SING N N 68
V7E "O2'1" HO2A SING N N 69
V7E "C1'1" "HC1'" SING N N 70
V7E C81 HC8 SING N N 71
V7E N61 H5 SING N N 72
V7E N61 H1N6 SING N N 73
V7E C21 HC2 SING N N 74
#
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
V7E InChI InChI 1.03 InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11+,12+,13-,14-,19-,20-/m1/s1
V7E InChIKey InChI 1.03 PDXMFTWFFKBFIN-SVHUXIIHSA-N
V7E SMILES_CANONICAL CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P](O)(=O)O[C@H]5[C@H](O)[C@@H](O[C@@H]5CO[P](O)(=O)O[C@H]4[C@@H]3O)n6cnc7c(N)ncnc67
V7E SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67
V7E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@H]4[C@H](O3)COP(=O)(O[C@@H]5[C@@H](COP(=O)(O4)O)O[C@H]([C@H]5O)n6cnc7c6ncnc7N)O)O)N
V7E SMILES "OpenEye OEToolkits" 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N
#
_pdbx_chem_comp_identifier.comp_id V7E
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
(1~{S},6~{R},8~{R},9~{S},10~{S},15~{R},17~{R},18~{S})-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id V7E
_pdbx_chem_comp_synonyms.name
(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
V7E 'Create component' 2021-04-22 PDBE
V7E 'Initial release' 2022-05-04 RCSB
#
_pdbe_chem_comp_synonyms.comp_id V7E
_pdbe_chem_comp_synonyms.name
'(1S,6R,8R,9S,10S,15R,17R,18S)-8,17-bis(6-aminopurin-9-yl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-9,18-diol'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
V7E P P 14.387 -1.639 1
V7E O1P O 15.615 -2.501 2
V7E O2P O 14.516 -3.133 3
V7E "O5'" O 13.088 -2.389 4
V7E "C5'" C 12.338 -3.688 5
V7E "C4'" C 10.838 -3.688 6
V7E "O4'" O 9.838 -4.793 7
V7E "C3'" C 10.088 -2.389 8
V7E "O3'" O 10.838 -1.090 9
V7E "C2'" C 8.631 -2.702 10
V7E "O2'" O 7.514 -1.701 11
V7E "C1'" C 8.476 -4.185 12
V7E N9 N 7.177 -4.935 13
V7E C8 C 5.816 -4.328 14
V7E N7 N 4.815 -5.433 15
V7E C5 C 5.555 -6.728 16
V7E C6 C 5.089 -8.154 17
V7E N6 N 3.621 -8.463 18
V7E N1 N 6.091 -9.270 19
V7E C2 C 7.558 -8.961 20
V7E N3 N 8.024 -7.535 21
V7E C4 C 7.023 -6.419 22
V7E P1 P 10.088 0.209 23
V7E O1P1 O 9.028 1.270 24
V7E O2P1 O 8.640 -0.179 25
V7E "O5'1" O 10.838 1.509 26
V7E "C5'1" C 12.338 1.509 27
V7E "C4'1" C 13.637 2.259 28
V7E "O4'1" O 13.951 3.716 29
V7E "C3'1" C 14.937 1.509 30
V7E "O3'1" O 14.937 0.009 31
V7E "C2'1" C 16.042 2.509 32
V7E "O2'1" O 17.510 2.200 33
V7E "C1'1" C 15.434 3.871 34
V7E N91 N 16.184 5.170 35
V7E C81 C 15.577 6.532 36
V7E N71 N 16.682 7.532 37
V7E C51 C 17.977 6.792 38
V7E C61 C 19.403 7.258 39
V7E N61 N 19.712 8.726 40
V7E N11 N 20.519 6.256 41
V7E C21 C 20.210 4.789 42
V7E N31 N 18.784 4.323 43
V7E C41 C 17.668 5.324 44
#
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
V7E P O1P DOUBLE NONE 1
V7E P O2P SINGLE BEGINDASH 2
V7E P "O5'" SINGLE NONE 3
V7E P "O3'1" SINGLE NONE 4
V7E "O5'" "C5'" SINGLE NONE 5
V7E "C5'" "C4'" SINGLE NONE 6
V7E "C4'" "O4'" SINGLE NONE 7
V7E "C4'" "C3'" SINGLE NONE 8
V7E "O4'" "C1'" SINGLE NONE 9
V7E "C3'" "O3'" SINGLE NONE 10
V7E "C3'" "C2'" SINGLE NONE 11
V7E "O3'" P1 SINGLE NONE 12
V7E "C2'" "O2'" SINGLE BEGINWEDGE 13
V7E "C2'" "C1'" SINGLE NONE 14
V7E "C1'" N9 SINGLE BEGINWEDGE 15
V7E N9 C8 SINGLE NONE 16
V7E N9 C4 SINGLE NONE 17
V7E C8 N7 DOUBLE NONE 18
V7E N7 C5 SINGLE NONE 19
V7E C5 C6 SINGLE NONE 20
V7E C5 C4 DOUBLE NONE 21
V7E C6 N6 SINGLE NONE 22
V7E C6 N1 DOUBLE NONE 23
V7E N1 C2 SINGLE NONE 24
V7E C2 N3 DOUBLE NONE 25
V7E N3 C4 SINGLE NONE 26
V7E P1 O1P1 DOUBLE NONE 27
V7E P1 O2P1 SINGLE BEGINWEDGE 28
V7E P1 "O5'1" SINGLE NONE 29
V7E "O5'1" "C5'1" SINGLE NONE 30
V7E "C5'1" "C4'1" SINGLE NONE 31
V7E "C4'1" "O4'1" SINGLE NONE 32
V7E "C4'1" "C3'1" SINGLE NONE 33
V7E "O4'1" "C1'1" SINGLE NONE 34
V7E "C3'1" "O3'1" SINGLE NONE 35
V7E "C3'1" "C2'1" SINGLE NONE 36
V7E "C2'1" "O2'1" SINGLE BEGINWEDGE 37
V7E "C2'1" "C1'1" SINGLE NONE 38
V7E "C1'1" N91 SINGLE BEGINWEDGE 39
V7E N91 C81 SINGLE NONE 40
V7E N91 C41 SINGLE NONE 41
V7E C81 N71 DOUBLE NONE 42
V7E N71 C51 SINGLE NONE 43
V7E C51 C61 SINGLE NONE 44
V7E C51 C41 DOUBLE NONE 45
V7E C61 N61 SINGLE NONE 46
V7E C61 N11 DOUBLE NONE 47
V7E N11 C21 SINGLE NONE 48
V7E C21 N31 DOUBLE NONE 49
V7E N31 C41 SINGLE NONE 50
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
V7E MurckoScaffold S1 scaffold 'O=[PH]1OC[C@H]2O[C@@H](n3cnc4cncnc43)C[C@@H]2O[PH](=O)OC[C@H]2O[C@@H](n3cnc4cncnc43)C[C@@H]2O1' InChI=1S/C20H22N8O8P2/c29-37-32-6-16-14(2-18(34-16)28-10-26-12-4-22-8-24-20(12)28)36-38(30)31-5-15-13(35-37)1-17(33-15)27-9-25-11-3-21-7-23-19(11)27/h3-4,7-10,13-18,37-38H,1-2,5-6H2/t13-,14-,15+,16+,17+,18+/m0/s1 DKYGFCPFAYPPMQ-DWMDIXPDSA-N
V7E adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
V7E imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
V7E phosphate F3 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
V7E purine F4 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
V7E pyrimidine F5 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
V7E ribose F6 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
V7E P S1 1
V7E O1P S1 1
V7E "O5'" S1 1
V7E "C5'" S1 1
V7E "C4'" S1 1
V7E "O4'" S1 1
V7E "C3'" S1 1
V7E "O3'" S1 1
V7E "C2'" S1 1
V7E "C1'" S1 1
V7E N9 S1 1
V7E C8 S1 1
V7E N7 S1 1
V7E C5 S1 1
V7E C6 S1 1
V7E N1 S1 1
V7E C2 S1 1
V7E N3 S1 1
V7E C4 S1 1
V7E P1 S1 1
V7E O1P1 S1 1
V7E "O5'1" S1 1
V7E "C5'1" S1 1
V7E "C4'1" S1 1
V7E "O4'1" S1 1
V7E "C3'1" S1 1
V7E "O3'1" S1 1
V7E "C2'1" S1 1
V7E "C1'1" S1 1
V7E N91 S1 1
V7E C81 S1 1
V7E N71 S1 1
V7E C51 S1 1
V7E C61 S1 1
V7E N11 S1 1
V7E C21 S1 1
V7E N31 S1 1
V7E C41 S1 1
V7E N1 F1 1
V7E C6 F1 1
V7E C5 F1 1
V7E C4 F1 1
V7E N3 F1 1
V7E C2 F1 1
V7E N9 F1 1
V7E C8 F1 1
V7E N7 F1 1
V7E N6 F1 1
V7E N11 F1 2
V7E C61 F1 2
V7E C51 F1 2
V7E C41 F1 2
V7E N31 F1 2
V7E C21 F1 2
V7E N91 F1 2
V7E C81 F1 2
V7E N71 F1 2
V7E N61 F1 2
V7E C5 F2 1
V7E C4 F2 1
V7E N9 F2 1
V7E C8 F2 1
V7E N7 F2 1
V7E C51 F2 2
V7E C41 F2 2
V7E N91 F2 2
V7E C81 F2 2
V7E N71 F2 2
V7E O2P F3 1
V7E P F3 1
V7E O1P F3 1
V7E "O5'" F3 1
V7E "O3'1" F3 1
V7E "O3'" F3 2
V7E P1 F3 2
V7E O1P1 F3 2
V7E O2P1 F3 2
V7E "O5'1" F3 2
V7E N7 F4 1
V7E C8 F4 1
V7E N9 F4 1
V7E C4 F4 1
V7E C5 F4 1
V7E C6 F4 1
V7E N1 F4 1
V7E C2 F4 1
V7E N3 F4 1
V7E N71 F4 2
V7E C81 F4 2
V7E N91 F4 2
V7E C41 F4 2
V7E C51 F4 2
V7E C61 F4 2
V7E N11 F4 2
V7E C21 F4 2
V7E N31 F4 2
V7E C5 F5 1
V7E C6 F5 1
V7E N1 F5 1
V7E C2 F5 1
V7E N3 F5 1
V7E C4 F5 1
V7E C51 F5 2
V7E C61 F5 2
V7E N11 F5 2
V7E C21 F5 2
V7E N31 F5 2
V7E C41 F5 2
V7E "C2'" F6 1
V7E "C3'" F6 1
V7E "C4'" F6 1
V7E "O4'" F6 1
V7E "C1'" F6 1
V7E "C5'" F6 1
V7E "O5'" F6 1
V7E "O3'" F6 1
V7E "O2'" F6 1
V7E "C2'1" F6 2
V7E "C3'1" F6 2
V7E "C4'1" F6 2
V7E "O4'1" F6 2
V7E "C1'1" F6 2
V7E "C5'1" F6 2
V7E "O5'1" F6 2
V7E "O3'1" F6 2
V7E "O2'1" F6 2
#
_pdbe_chem_comp_rdkit_properties.comp_id V7E
_pdbe_chem_comp_rdkit_properties.exactmw 658.105
_pdbe_chem_comp_rdkit_properties.amw 658.418
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 22
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 22
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 44
_pdbe_chem_comp_rdkit_properties.NumAtoms 68
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 24
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 7
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 7
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 278.575
_pdbe_chem_comp_rdkit_properties.tpsa 309.680
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.253
_pdbe_chem_comp_rdkit_properties.CrippenMR 134.545
_pdbe_chem_comp_rdkit_properties.chi0v 22.054
_pdbe_chem_comp_rdkit_properties.chi1v 13.895
_pdbe_chem_comp_rdkit_properties.chi2v 6.784
_pdbe_chem_comp_rdkit_properties.chi3v 6.784
_pdbe_chem_comp_rdkit_properties.chi4v 4.813
_pdbe_chem_comp_rdkit_properties.chi0n 44.266
_pdbe_chem_comp_rdkit_properties.chi1n 22.396
_pdbe_chem_comp_rdkit_properties.chi2n 5.342
_pdbe_chem_comp_rdkit_properties.chi3n 5.342
_pdbe_chem_comp_rdkit_properties.chi4n 3.570
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.240
_pdbe_chem_comp_rdkit_properties.kappa1 12.869
_pdbe_chem_comp_rdkit_properties.kappa2 10.687
_pdbe_chem_comp_rdkit_properties.kappa3 5.036
_pdbe_chem_comp_rdkit_properties.Phi 3.126
#
_pdbe_chem_comp_external_mappings.comp_id V7E
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id V7E
#
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
V7E P 0.894 -3.002 -0.161 ETKDGv3 1
V7E O1P 0.434 -4.339 0.374 ETKDGv3 2
V7E O2P 1.816 -3.282 -1.552 ETKDGv3 3
V7E "O5'" -0.485 -2.098 -0.610 ETKDGv3 4
V7E "C5'" -1.175 -1.655 0.538 ETKDGv3 5
V7E "C4'" -1.869 -0.327 0.198 ETKDGv3 6
V7E "O4'" -3.000 -0.584 -0.606 ETKDGv3 7
V7E "C3'" -2.297 0.460 1.453 ETKDGv3 8
V7E "O3'" -1.810 1.790 1.386 ETKDGv3 9
V7E "C2'" -3.805 0.485 1.339 ETKDGv3 10
V7E "O2'" -4.366 -0.572 2.079 ETKDGv3 11
V7E "C1'" -4.026 0.261 -0.149 ETKDGv3 12
V7E N9 -5.334 -0.337 -0.423 ETKDGv3 13
V7E C8 -5.665 -1.148 -1.563 ETKDGv3 14
V7E N7 -6.925 -1.116 -1.889 ETKDGv3 15
V7E C5 -7.504 -0.224 -0.945 ETKDGv3 16
V7E C6 -8.858 0.344 -0.923 ETKDGv3 17
V7E N6 -9.874 -0.122 -1.809 ETKDGv3 18
V7E N1 -9.109 1.300 -0.069 ETKDGv3 19
V7E C2 -8.082 1.799 0.825 ETKDGv3 20
V7E N3 -6.874 1.300 0.792 ETKDGv3 21
V7E C4 -6.597 0.236 -0.127 ETKDGv3 22
V7E P1 -0.298 1.887 2.176 ETKDGv3 23
V7E O1P1 0.304 3.255 1.938 ETKDGv3 24
V7E O2P1 -0.531 1.684 3.840 ETKDGv3 25
V7E "O5'1" 0.740 0.651 1.619 ETKDGv3 26
V7E "C5'1" 1.528 1.121 0.547 ETKDGv3 27
V7E "C4'1" 2.067 -0.072 -0.259 ETKDGv3 28
V7E "O4'1" 3.087 0.366 -1.126 ETKDGv3 29
V7E "C3'1" 2.672 -1.174 0.635 ETKDGv3 30
V7E "O3'1" 1.805 -2.219 1.072 ETKDGv3 31
V7E "C2'1" 3.913 -1.643 -0.116 ETKDGv3 32
V7E "O2'1" 5.082 -1.481 0.657 ETKDGv3 33
V7E "C1'1" 3.902 -0.758 -1.375 ETKDGv3 34
V7E N91 5.242 -0.335 -1.783 ETKDGv3 35
V7E C81 6.277 -1.171 -2.317 ETKDGv3 36
V7E N71 7.467 -0.646 -2.239 ETKDGv3 37
V7E C51 7.251 0.614 -1.614 ETKDGv3 38
V7E C61 8.237 1.581 -1.116 ETKDGv3 39
V7E N61 9.631 1.424 -1.380 ETKDGv3 40
V7E N11 7.803 2.595 -0.414 ETKDGv3 41
V7E C21 6.393 2.761 -0.122 ETKDGv3 42
V7E N31 5.519 1.891 -0.556 ETKDGv3 43
V7E C41 5.986 0.788 -1.343 ETKDGv3 44
V7E H1 1.168 -3.619 -2.222 ETKDGv3 45
V7E "H5'A" -1.937 -2.412 0.824 ETKDGv3 46
V7E "H5'" -0.514 -1.498 1.416 ETKDGv3 47
V7E "H4'" -1.162 0.291 -0.398 ETKDGv3 48
V7E "H3'" -2.020 -0.050 2.408 ETKDGv3 49
V7E "H2'" -4.237 1.462 1.661 ETKDGv3 50
V7E "HO2'" -4.412 -0.263 3.021 ETKDGv3 51
V7E "H1'" -3.956 1.232 -0.691 ETKDGv3 52
V7E H8 -4.936 -1.720 -2.121 ETKDGv3 53
V7E H3 -9.676 -0.886 -2.492 ETKDGv3 54
V7E HN6 -10.831 0.296 -1.782 ETKDGv3 55
V7E H2 -8.314 2.599 1.515 ETKDGv3 56
V7E H4 -1.252 2.321 4.074 ETKDGv3 57
V7E "HC5'" 0.947 1.763 -0.156 ETKDGv3 58
V7E HC5A 2.382 1.709 0.952 ETKDGv3 59
V7E "HC4'" 1.245 -0.444 -0.895 ETKDGv3 60
V7E "HC3'" 3.019 -0.680 1.570 ETKDGv3 61
V7E "HC2'" 3.851 -2.713 -0.396 ETKDGv3 62
V7E HO2A 5.155 -0.526 0.918 ETKDGv3 63
V7E "HC1'" 3.454 -1.330 -2.219 ETKDGv3 64
V7E HC8 6.098 -2.158 -2.723 ETKDGv3 65
V7E H5 10.319 2.120 -1.015 ETKDGv3 66
V7E H1N6 9.979 0.615 -1.940 ETKDGv3 67
V7E HC2 6.063 3.604 0.470 ETKDGv3 68
#