data_56B
#
_chem_comp.id 56B
_chem_comp.name
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
_chem_comp.type "RNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C17 H24 N5 O10 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-08-03
_chem_comp.pdbx_modified_date 2020-06-27
_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 489.374
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 56B
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 5D0B
_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
56B N9 N1 N 0 1 Y N N N N N -24.162 -16.737 -35.563 0.257 1.569 0.022 N9 56B 1
56B "C2'" C1 C 0 1 N N R N N N -26.225 -17.695 -34.440 2.345 2.464 0.996 "C2'" 56B 2
56B "O2'" O1 O 0 1 N N N N N N -26.070 -19.093 -34.559 2.504 3.854 0.709 "O2'" 56B 3
56B P P1 P 0 1 N N N N N N -28.699 -12.960 -32.525 5.159 -2.961 -0.403 P 56B 4
56B "C1'" C2 C 0 1 N N R N N N -25.610 -16.953 -35.625 1.696 1.735 -0.201 "C1'" 56B 5
56B N10 N2 N 0 1 N N N N N N -19.577 -16.001 -34.489 -3.316 -1.045 0.010 N10 56B 6
56B O11 O2 O 0 1 N N N N N N -17.623 -14.033 -32.154 -3.763 -4.296 -0.240 O11 56B 7
56B C8 C3 C 0 1 Y N N N N N -23.449 -16.247 -34.488 -0.332 0.448 0.552 C8 56B 8
56B N3 N3 N 0 1 N N N N N N -23.629 -17.437 -37.818 -0.643 3.743 -0.780 N3 56B 9
56B O12 O3 O 0 1 N N N N N N -15.652 -13.561 -34.024 -6.277 -4.477 0.461 O12 56B 10
56B C7 C4 C 0 1 Y N N N N N -22.108 -16.143 -34.803 -1.661 0.627 0.620 C7 56B 11
56B N2 N4 N 0 1 N N N N N N -22.771 -17.991 -39.888 -1.633 5.707 -1.498 N2 56B 12
56B O6 O4 O 0 1 N N N N N N -19.729 -16.489 -36.859 -4.198 2.293 0.197 O6 56B 13
56B C9 C5 C 0 1 N N N N N N -20.928 -15.650 -33.976 -2.676 -0.359 1.140 C9 56B 14
56B N1 N5 N 0 1 N N N N N N -21.305 -17.223 -38.288 -2.970 3.969 -0.634 N1 56B 15
56B "O4'" O5 O 0 1 N N N N N N -26.252 -15.692 -35.666 2.349 0.448 -0.249 "O4'" 56B 16
56B C10 C6 C 0 1 N N S N N N -18.495 -15.842 -33.505 -4.313 -2.016 0.480 C10 56B 17
56B "O5'" O6 O 0 1 N N N N N N -28.522 -14.418 -33.140 4.489 -1.505 -0.556 "O5'" 56B 18
56B C11 C7 C 0 1 N N R N N N -17.961 -14.407 -33.489 -4.519 -3.130 -0.573 C11 56B 19
56B OP2 O7 O 0 1 N N N N N N -27.953 -11.995 -33.363 5.147 -3.710 -1.828 OP2 56B 20
56B C12 C8 C 0 1 N N S N N N -16.706 -14.449 -34.403 -6.036 -3.397 -0.444 C12 56B 21
56B C13 C9 C 0 1 N N N N N N -16.240 -15.884 -34.346 -6.607 -2.111 0.108 C13 56B 22
56B OP1 O8 O 0 1 N N N N N N -28.442 -13.023 -31.070 6.556 -2.815 0.065 OP1 56B 23
56B C14 C10 C 0 1 N N N N N N -17.242 -16.673 -33.851 -5.667 -1.358 0.612 C14 56B 24
56B "O3'" O9 O 0 1 N N N N N N -28.263 -17.870 -35.657 4.778 2.727 0.963 "O3'" 56B 25
56B C5 C11 C 0 1 Y N N N N N -22.003 -16.608 -36.170 -1.934 1.962 0.092 C5 56B 26
56B C4 C12 C 0 1 Y N N N N N -23.297 -16.964 -36.598 -0.691 2.507 -0.262 C4 56B 27
56B C2 C13 C 0 1 N N N N N N -22.584 -17.548 -38.644 -1.736 4.448 -0.961 C2 56B 28
56B C6 C14 C 0 1 N N N N N N -20.917 -16.740 -37.054 -3.101 2.732 -0.104 C6 56B 29
56B "C4'" C15 C 0 1 N N R N N N -27.462 -15.742 -34.868 3.741 0.717 0.028 "C4'" 56B 30
56B "C5'" C16 C 0 1 N N N N N N -27.276 -14.841 -33.674 4.444 -0.554 0.509 "C5'" 56B 31
56B "C3'" C17 C 0 1 N N S N N N -27.664 -17.215 -34.535 3.723 1.782 1.152 "C3'" 56B 32
56B H1 H1 H 0 1 N N N N N N -25.776 -17.326 -33.506 1.747 2.326 1.897 H1 56B 33
56B H2 H2 H 0 1 N N N N N N -26.463 -19.521 -33.807 2.934 4.355 1.416 H2 56B 34
56B H3 H3 H 0 1 N N N N N N -25.846 -17.516 -36.540 1.875 2.287 -1.124 H3 56B 35
56B H4 H4 H 0 1 N N N N N N -19.593 -16.956 -34.785 -3.730 -0.382 -0.628 H4 56B 36
56B H6 H6 H 0 1 N N N N N N -18.409 -14.016 -31.621 -3.860 -5.021 -0.872 H6 56B 37
56B H7 H7 H 0 1 N N N N N N -23.879 -15.982 -33.534 0.194 -0.441 0.866 H7 56B 38
56B H8 H8 H 0 1 N N N N N N -15.963 -12.664 -34.066 -7.214 -4.656 0.618 H8 56B 39
56B H9 H9 H 0 1 N N N N N N -23.689 -18.238 -40.198 -2.431 6.241 -1.638 H9 56B 40
56B H10 H10 H 0 1 N N N N N N -21.993 -18.076 -40.511 -0.763 6.063 -1.736 H10 56B 41
56B H11 H11 H 0 1 N N N N N N -20.992 -14.553 -33.920 -3.432 0.170 1.720 H11 56B 42
56B H12 H12 H 0 1 N N N N N N -21.025 -16.075 -32.966 -2.178 -1.092 1.775 H12 56B 43
56B H13 H13 H 0 1 N N N N N N -20.592 -17.345 -38.978 -3.756 4.519 -0.779 H13 56B 44
56B H14 H14 H 0 1 N N N N N N -18.848 -16.115 -32.500 -4.004 -2.446 1.433 H14 56B 45
56B H15 H15 H 0 1 N N N N N N -18.709 -13.725 -33.920 -4.267 -2.775 -1.572 H15 56B 46
56B H16 H16 H 0 1 N N N N N N -27.355 -11.497 -32.818 5.536 -4.595 -1.811 H16 56B 47
56B H17 H17 H 0 1 N N N N N N -17.026 -14.225 -35.431 -6.469 -3.616 -1.420 H17 56B 48
56B H18 H18 H 0 1 N N N N N N -15.265 -16.234 -34.650 -7.654 -1.849 0.088 H18 56B 49
56B H21 H21 H 0 1 N N N N N N -17.166 -17.742 -33.719 -5.835 -0.392 1.064 H21 56B 50
56B H23 H23 H 0 1 N N N N N N -28.392 -18.789 -35.456 4.813 3.417 1.639 H23 56B 51
56B H24 H24 H 0 1 N N N N N N -28.319 -15.387 -35.460 4.235 1.112 -0.859 H24 56B 52
56B H25 H25 H 0 1 N N N N N N -26.722 -15.388 -32.897 3.895 -0.976 1.351 H25 56B 53
56B H26 H26 H 0 1 N N N N N N -26.700 -13.956 -33.981 5.459 -0.311 0.823 H26 56B 54
56B H27 H27 H 0 1 N N N N N N -28.214 -17.357 -33.593 3.808 1.307 2.129 H27 56B 55
56B OP3 O10 O 0 1 N Y N N N N ? ? ? 4.324 -3.828 0.666 O1 56B 56
56B HOP3 H5 H 0 0 N Y N N N N ? ? ? 3.398 -3.964 0.424 H5 56B 57
#
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
56B N2 C2 SING N N 1
56B C2 N1 SING N N 2
56B C2 N3 DOUB N N 3
56B N1 C6 SING N N 4
56B N3 C4 SING N N 5
56B C6 O6 DOUB N N 6
56B C6 C5 SING N N 7
56B C4 C5 DOUB Y N 8
56B C4 N9 SING Y N 9
56B C5 C7 SING Y N 10
56B "O4'" "C1'" SING N N 11
56B "O4'" "C4'" SING N N 12
56B "O3'" "C3'" SING N N 13
56B "C1'" N9 SING N N 14
56B "C1'" "C2'" SING N N 15
56B N9 C8 SING Y N 16
56B "C4'" "C3'" SING N N 17
56B "C4'" "C5'" SING N N 18
56B C7 C8 DOUB Y N 19
56B C7 C9 SING N N 20
56B "O2'" "C2'" SING N N 21
56B "C3'" "C2'" SING N N 22
56B N10 C9 SING N N 23
56B N10 C10 SING N N 24
56B C12 C13 SING N N 25
56B C12 O12 SING N N 26
56B C12 C11 SING N N 27
56B C13 C14 DOUB N N 28
56B C14 C10 SING N N 29
56B "C5'" "O5'" SING N N 30
56B C10 C11 SING N N 31
56B C11 O11 SING N N 32
56B OP2 P SING N N 33
56B "O5'" P SING N N 34
56B P OP1 DOUB N N 35
56B "C2'" H1 SING N N 36
56B "O2'" H2 SING N N 37
56B "C1'" H3 SING N N 38
56B N10 H4 SING N N 39
56B O11 H6 SING N N 40
56B C8 H7 SING N N 41
56B O12 H8 SING N N 42
56B N2 H9 SING N N 43
56B N2 H10 SING N N 44
56B C9 H11 SING N N 45
56B C9 H12 SING N N 46
56B N1 H13 SING N N 47
56B C10 H14 SING N N 48
56B C11 H15 SING N N 49
56B OP2 H16 SING N N 50
56B C12 H17 SING N N 51
56B C13 H18 SING N N 52
56B C14 H21 SING N N 53
56B "O3'" H23 SING N N 54
56B "C4'" H24 SING N N 55
56B "C5'" H25 SING N N 56
56B "C5'" H26 SING N N 57
56B "C3'" H27 SING N N 58
56B P OP3 SING N N 59
56B OP3 HOP3 SING N N 60
#
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
56B SMILES ACDLabs 12.01 n2(cc(CNC1C(O)C(O)C=C1)c3c2N=C(N)NC3=O)C4C(O)C(O)C(O4)COP(=O)(O)O
56B InChI InChI 1.03 InChI=1S/C17H24N5O10P/c18-17-20-14-10(15(27)21-17)6(3-19-7-1-2-8(23)11(7)24)4-22(14)16-13(26)12(25)9(32-16)5-31-33(28,29)30/h1-2,4,7-9,11-13,16,19,23-26H,3,5H2,(H2,28,29,30)(H3,18,20,21,27)/t7-,8-,9+,11+,12+,13+,16+/m0/s1
56B InChIKey InChI 1.03 BSABGNSIPKXNDL-AEZJAUAXSA-N
56B SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(cc(CN[C@H]3C=C[C@H](O)[C@@H]3O)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O
56B SMILES CACTVS 3.385 NC1=Nc2n(cc(CN[CH]3C=C[CH](O)[CH]3O)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O
56B SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1c(c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CN[C@H]4C=C[C@@H]([C@@H]4O)O
56B SMILES "OpenEye OEToolkits" 1.9.2 c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CNC4C=CC(C4O)O
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
56B "SYSTEMATIC NAME" ACDLabs 12.01 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
56B "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
56B 'Create component' 2015-08-03 RCSB
56B 'Initial release' 2016-09-28 RCSB
56B 'Other modification' 2020-06-27 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
56B N9 N 9.122 -1.685 1
56B "C2'" C 8.708 -4.326 2
56B "O2'" O 7.208 -4.329 3
56B P P 14.817 -6.219 4
56B "C1'" C 9.588 -3.111 5
56B N10 N 11.056 2.464 6
56B O11 O 14.161 3.467 7
56B C8 C 9.997 -0.478 8
56B N3 N 6.404 -1.978 9
56B O12 O 14.167 6.731 10
56B C7 C 9.122 0.729 11
56B N2 N 3.805 -1.978 12
56B O6 O 6.404 2.522 13
56B C9 C 9.588 2.155 14
56B N1 N 5.104 0.272 15
56B "O4'" O 11.015 -3.572 16
56B C10 C 11.522 3.890 17
56B "O5'" O 13.602 -5.339 18
56B C11 C 12.949 4.351 19
56B OP2 O 16.032 -7.098 20
56B C12 C 12.952 5.851 21
56B C13 C 11.526 6.317 22
56B OP1 O 15.697 -5.004 23
56B C14 C 10.642 5.105 24
56B "O3'" O 9.131 -6.965 25
56B C5 C 7.702 0.272 26
56B C4 C 7.702 -1.228 27
56B C2 C 5.104 -1.228 28
56B C6 C 6.404 1.022 29
56B "C4'" C 11.018 -5.072 30
56B "C5'" C 12.233 -5.952 31
56B "C3'" C 9.592 -5.538 32
56B OP3 O 13.938 -7.434 33
#
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
56B N2 C2 SINGLE NONE 1
56B C2 N1 SINGLE NONE 2
56B C2 N3 DOUBLE NONE 3
56B N1 C6 SINGLE NONE 4
56B N3 C4 SINGLE NONE 5
56B C6 O6 DOUBLE NONE 6
56B C6 C5 SINGLE NONE 7
56B C4 C5 DOUBLE NONE 8
56B C4 N9 SINGLE NONE 9
56B C5 C7 SINGLE NONE 10
56B "O4'" "C1'" SINGLE NONE 11
56B "O4'" "C4'" SINGLE NONE 12
56B "C3'" "O3'" SINGLE BEGINWEDGE 13
56B "C1'" N9 SINGLE BEGINDASH 14
56B "C1'" "C2'" SINGLE NONE 15
56B N9 C8 SINGLE NONE 16
56B "C4'" "C3'" SINGLE NONE 17
56B "C4'" "C5'" SINGLE BEGINDASH 18
56B C7 C8 DOUBLE NONE 19
56B C7 C9 SINGLE NONE 20
56B "C2'" "O2'" SINGLE BEGINWEDGE 21
56B "C3'" "C2'" SINGLE NONE 22
56B N10 C9 SINGLE NONE 23
56B C10 N10 SINGLE BEGINWEDGE 24
56B C12 C13 SINGLE NONE 25
56B C12 O12 SINGLE BEGINDASH 26
56B C12 C11 SINGLE NONE 27
56B C13 C14 DOUBLE NONE 28
56B C14 C10 SINGLE NONE 29
56B "C5'" "O5'" SINGLE NONE 30
56B C10 C11 SINGLE NONE 31
56B C11 O11 SINGLE BEGINDASH 32
56B OP2 P SINGLE NONE 33
56B "O5'" P SINGLE NONE 34
56B P OP1 DOUBLE NONE 35
56B P OP3 SINGLE NONE 36
#
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
56B MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1c(CN[C@H]1C=CCC1)cn2[C@H]1CCCO1' InChI=1S/C16H20N4O2/c21-16-14-11(8-17-12-4-1-2-5-12)9-20(13-6-3-7-22-13)15(14)18-10-19-16/h1,4,9-10,12-13,17H,2-3,5-8H2,(H,18,19,21)/t12-,13+/m0/s1 FBGKYJFBLQTHNA-QWHCGFSZSA-N
56B phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
56B pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
56B pyrrole F3 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N
56B ribose F4 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
56B N9 S1 1
56B "C2'" S1 1
56B "C1'" S1 1
56B N10 S1 1
56B C8 S1 1
56B N3 S1 1
56B C7 S1 1
56B O6 S1 1
56B C9 S1 1
56B N1 S1 1
56B "O4'" S1 1
56B C10 S1 1
56B C11 S1 1
56B C12 S1 1
56B C13 S1 1
56B C14 S1 1
56B C5 S1 1
56B C4 S1 1
56B C2 S1 1
56B C6 S1 1
56B "C4'" S1 1
56B "C3'" S1 1
56B "O5'" F1 1
56B P F1 1
56B OP1 F1 1
56B OP2 F1 1
56B H1 F1 1
56B C5 F2 1
56B C6 F2 1
56B N1 F2 1
56B C2 F2 1
56B N3 F2 1
56B C4 F2 1
56B C8 F3 1
56B C7 F3 1
56B C5 F3 1
56B C4 F3 1
56B N9 F3 1
56B "C2'" F4 1
56B "C3'" F4 1
56B "C4'" F4 1
56B "O4'" F4 1
56B "C1'" F4 1
56B "C5'" F4 1
56B "O5'" F4 1
56B "O3'" F4 1
56B "O2'" F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 56B
_pdbe_chem_comp_rdkit_properties.exactmw 489.126
_pdbe_chem_comp_rdkit_properties.amw 489.378
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 15
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 14
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 14
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 33
_pdbe_chem_comp_rdkit_properties.NumAtoms 57
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.529
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 7
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 219.350
_pdbe_chem_comp_rdkit_properties.tpsa 245.640
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.179
_pdbe_chem_comp_rdkit_properties.CrippenMR 107.279
_pdbe_chem_comp_rdkit_properties.chi0v 16.160
_pdbe_chem_comp_rdkit_properties.chi1v 9.560
_pdbe_chem_comp_rdkit_properties.chi2v 4.099
_pdbe_chem_comp_rdkit_properties.chi3v 4.099
_pdbe_chem_comp_rdkit_properties.chi4v 2.671
_pdbe_chem_comp_rdkit_properties.chi0n 39.266
_pdbe_chem_comp_rdkit_properties.chi1n 19.338
_pdbe_chem_comp_rdkit_properties.chi2n 3.784
_pdbe_chem_comp_rdkit_properties.chi3n 3.784
_pdbe_chem_comp_rdkit_properties.chi4n 2.476
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.170
_pdbe_chem_comp_rdkit_properties.kappa1 8.203
_pdbe_chem_comp_rdkit_properties.kappa2 8.883
_pdbe_chem_comp_rdkit_properties.kappa3 4.738
_pdbe_chem_comp_rdkit_properties.Phi 2.208
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
56B UniChem PDBe 56B
56B UniChem ZINC ZINC000584905107
56B UniChem PubChem 137348315
#
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
56B N9 0.864 0.386 -0.797 ETKDGv3 1
56B "C2'" 2.249 2.139 -1.834 ETKDGv3 2
56B "O2'" 1.531 3.116 -2.542 ETKDGv3 3
56B P 5.241 -1.645 0.827 ETKDGv3 4
56B "C1'" 1.612 0.757 -2.002 ETKDGv3 5
56B N10 -3.298 0.242 0.598 ETKDGv3 6
56B O11 -6.191 -1.081 1.552 ETKDGv3 7
56B C8 -0.253 1.096 -0.254 ETKDGv3 8
56B N3 1.671 -2.000 -0.386 ETKDGv3 9
56B O12 -7.880 0.943 1.299 ETKDGv3 10
56B C7 -0.877 0.361 0.668 ETKDGv3 11
56B N2 2.395 -4.214 0.017 ETKDGv3 12
56B O6 -1.377 -2.243 2.304 ETKDGv3 13
56B C9 -2.147 0.735 1.367 ETKDGv3 14
56B N1 0.449 -3.257 1.235 ETKDGv3 15
56B "O4'" 2.621 -0.198 -2.271 ETKDGv3 16
56B C10 -4.569 0.687 1.195 ETKDGv3 17
56B "O5'" 4.707 -1.275 -0.750 ETKDGv3 18
56B C11 -5.763 -0.111 0.630 ETKDGv3 19
56B OP2 6.601 -0.716 1.225 ETKDGv3 20
56B C12 -6.855 0.939 0.335 ETKDGv3 21
56B C13 -6.116 2.233 0.347 ETKDGv3 22
56B OP1 5.611 -3.110 0.886 ETKDGv3 23
56B C14 -4.882 2.097 0.805 ETKDGv3 24
56B "O3'" 3.744 2.313 -3.735 ETKDGv3 25
56B C5 -0.185 -0.926 0.718 ETKDGv3 26
56B C4 0.803 -0.881 -0.148 ETKDGv3 27
56B C2 1.512 -3.121 0.265 ETKDGv3 28
56B C6 -0.433 -2.152 1.475 ETKDGv3 29
56B "C4'" 3.873 0.447 -2.195 ETKDGv3 30
56B "C5'" 4.534 0.119 -0.848 ETKDGv3 31
56B "C3'" 3.648 1.948 -2.377 ETKDGv3 32
56B H1 2.308 2.411 -0.753 ETKDGv3 33
56B H2 1.900 3.994 -2.263 ETKDGv3 34
56B H3 0.911 0.762 -2.866 ETKDGv3 35
56B H4 -3.269 -0.804 0.646 ETKDGv3 36
56B H6 -6.831 -1.665 1.068 ETKDGv3 37
56B H7 -0.568 2.079 -0.584 ETKDGv3 38
56B H8 -7.469 1.131 2.184 ETKDGv3 39
56B H9 3.168 -4.123 -0.680 ETKDGv3 40
56B H10 2.282 -5.114 0.534 ETKDGv3 41
56B H11 -2.187 1.841 1.467 ETKDGv3 42
56B H12 -2.146 0.299 2.391 ETKDGv3 43
56B H13 0.320 -4.154 1.755 ETKDGv3 44
56B H14 -4.547 0.611 2.308 ETKDGv3 45
56B H15 -5.470 -0.601 -0.329 ETKDGv3 46
56B H16 7.266 -0.928 0.523 ETKDGv3 47
56B H17 -7.299 0.768 -0.670 ETKDGv3 48
56B H18 -6.549 3.187 0.067 ETKDGv3 49
56B H21 -4.212 2.938 0.945 ETKDGv3 50
56B H23 3.107 1.754 -4.253 ETKDGv3 51
56B H24 4.529 0.063 -3.007 ETKDGv3 52
56B H25 3.880 0.505 -0.033 ETKDGv3 53
56B H26 5.523 0.628 -0.804 ETKDGv3 54
56B H27 4.380 2.553 -1.798 ETKDGv3 55
56B OP3 4.000 -1.350 1.940 ETKDGv3 56
56B HOP3 4.134 -0.414 2.232 ETKDGv3 57
#