data_Y4I
#
_chem_comp.id Y4I
_chem_comp.name
"1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H26 N5 O10 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-11-20
_chem_comp.pdbx_modified_date 2023-12-01
_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 547.476
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Y4I
_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 8R5V
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
Y4I O11 O1 O 0 1 N N N N N N 6.260 -0.080 18.981 -4.216 -0.184 -1.699 O11 Y4I 1
Y4I O13 O2 O 0 1 N N N N N N 3.276 -5.246 17.475 -8.984 1.484 1.612 O13 Y4I 2
Y4I C20 C1 C 0 1 N N N N N N 3.975 -4.330 17.923 -7.885 1.295 1.121 C20 Y4I 3
Y4I N19 N1 N 0 1 N N N N N N 3.987 -4.095 19.298 -7.123 2.339 0.737 N19 Y4I 4
Y4I C18 C2 C 0 1 N N N N N N 4.708 -3.121 19.960 -5.909 2.128 0.195 C18 Y4I 5
Y4I O12 O3 O 0 1 N N N N N N 4.655 -2.984 21.181 -5.232 3.079 -0.147 O12 Y4I 6
Y4I C21 C3 C 0 1 N N N N N N 4.811 -3.450 17.133 -7.395 -0.023 0.955 C21 Y4I 7
Y4I C22 C4 C 0 1 N N N N N N 5.521 -2.490 17.745 -6.174 -0.205 0.408 C22 Y4I 8
Y4I N17 N2 N 0 1 N N N N N N 5.474 -2.311 19.125 -5.433 0.881 0.026 N17 Y4I 9
Y4I C12 C5 C 0 1 N N R N N N 6.320 -1.266 19.753 -4.108 0.684 -0.567 C12 Y4I 10
Y4I C13 C6 C 0 1 N N N N N N 7.738 -1.848 19.834 -3.174 0.050 0.468 C13 Y4I 11
Y4I N14 N3 N 0 1 N N N N N N 8.775 -0.834 20.009 -1.870 -0.216 -0.156 N14 Y4I 12
Y4I C15 C7 C 0 1 N N N N N N 8.576 0.365 19.205 -2.019 -1.109 -1.314 C15 Y4I 13
Y4I C16 C8 C 0 1 N N S N N N 7.181 0.868 19.525 -2.964 -0.464 -2.331 C16 Y4I 14
Y4I C23 C9 C 0 1 N N N N N N 6.854 2.234 18.993 -3.186 -1.423 -3.502 C23 Y4I 15
Y4I O15 O4 O 0 1 N N N N N N 7.517 3.184 19.837 -3.978 -0.779 -4.502 O15 Y4I 16
Y4I P P1 P 0 1 N N S N N N 10.193 -1.720 20.642 -0.786 -0.854 0.963 P Y4I 17
Y4I SP S1 S 0 1 N N N N N N 11.544 -1.896 19.230 -1.463 -2.453 1.640 SP Y4I 18
Y4I OP1 O5 O 0 1 N N N N N N 9.963 -3.023 21.403 -0.579 0.193 2.167 OP1 Y4I 19
Y4I "O5'" O6 O 0 1 N N N N N N 10.673 -0.602 21.665 0.627 -1.132 0.243 "O5'" Y4I 20
Y4I "C5'" C10 C 0 1 N N N N N N 9.862 -0.183 22.809 1.723 -1.770 0.900 "C5'" Y4I 21
Y4I "C4'" C11 C 0 1 N N R N N N 10.791 0.406 23.848 2.906 -1.876 -0.065 "C4'" Y4I 22
Y4I "C3'" C12 C 0 1 N N S N N N 11.870 1.388 23.361 4.107 -2.577 0.618 "C3'" Y4I 23
Y4I "O3'" O7 O 0 1 N N N N N N 11.979 2.434 24.301 4.006 -3.997 0.495 "O3'" Y4I 24
Y4I "C2'" C13 C 0 1 N N N N N N 13.148 0.578 23.399 5.306 -2.035 -0.198 "C2'" Y4I 25
Y4I "C1'" C14 C 0 1 N N R N N N 12.908 -0.402 24.533 4.769 -0.743 -0.845 "C1'" Y4I 26
Y4I "O4'" O8 O 0 1 N N N N N N 11.503 -0.669 24.552 3.419 -0.565 -0.386 "O4'" Y4I 27
Y4I N1 N4 N 0 1 N N N N N N 13.605 -1.741 24.356 5.592 0.398 -0.437 N1 Y4I 28
Y4I C6 C15 C 0 1 N N N N N N 13.097 -2.681 23.517 6.322 1.076 -1.375 C6 Y4I 29
Y4I C5 C16 C 0 1 N N N N N N 13.672 -3.886 23.346 7.081 2.128 -0.999 C5 Y4I 30
Y4I C5M C17 C 0 1 N N N N N N 13.138 -4.980 22.428 7.891 2.888 -2.017 C5M Y4I 31
Y4I C4 C18 C 0 1 N N N N N N 14.915 -4.125 24.037 7.103 2.509 0.365 C4 Y4I 32
Y4I O4 O9 O 0 1 N N N N N N 15.547 -5.176 23.990 7.779 3.454 0.728 O4 Y4I 33
Y4I N3 N5 N 0 1 N N N N N N 15.363 -3.156 24.891 6.370 1.814 1.258 N3 Y4I 34
Y4I C2 C19 C 0 1 N N N N N N 14.776 -1.939 25.076 5.619 0.773 0.855 C2 Y4I 35
Y4I O2 O10 O 0 1 N N N N N N 15.295 -1.128 25.783 4.958 0.159 1.670 O2 Y4I 36
Y4I H1 H1 H 0 1 N N N N N N 3.416 -4.692 19.861 -7.450 3.244 0.851 H1 Y4I 37
Y4I H2 H2 H 0 1 N N N N N N 4.862 -3.565 16.060 -7.989 -0.871 1.261 H2 Y4I 38
Y4I H22 H3 H 0 1 N N N N N N 6.146 -1.839 17.151 -5.783 -1.202 0.273 H22 Y4I 39
Y4I H12 H4 H 0 1 N N N N N N 5.961 -1.073 20.775 -3.704 1.645 -0.883 H12 Y4I 40
Y4I H131 H5 H 0 0 N N N N N N 7.782 -2.541 20.687 -3.044 0.734 1.307 H131 Y4I 41
Y4I H132 H6 H 0 0 N N N N N N 7.942 -2.398 18.904 -3.606 -0.885 0.823 H132 Y4I 42
Y4I H151 H7 H 0 0 N N N N N N 9.325 1.127 19.467 -1.045 -1.272 -1.775 H151 Y4I 43
Y4I H152 H8 H 0 0 N N N N N N 8.657 0.123 18.135 -2.431 -2.064 -0.987 H152 Y4I 44
Y4I H16 H9 H 0 1 N N N N N N 7.071 0.891 20.619 -2.526 0.464 -2.698 H16 Y4I 45
Y4I H231 H10 H 0 0 N N N N N N 5.767 2.399 19.020 -2.224 -1.706 -3.928 H231 Y4I 46
Y4I H232 H11 H 0 0 N N N N N N 7.214 2.332 17.958 -3.704 -2.315 -3.148 H232 Y4I 47
Y4I HO15 H12 H 0 0 N N N N N N 7.333 4.064 19.530 -4.159 -1.330 -5.276 HO15 Y4I 48
Y4I HOP1 H13 H 0 0 N N N N N N 10.527 -3.701 21.049 -0.228 1.050 1.887 HOP1 Y4I 49
Y4I "H5'2" H14 H 0 0 N N N N N N 9.130 0.574 22.491 2.016 -1.183 1.771 "H5'2" Y4I 50
Y4I "H5'1" H15 H 0 0 N N N N N N 9.333 -1.051 23.230 1.424 -2.768 1.219 "H5'1" Y4I 51
Y4I "H4'" H16 H 0 1 N N N N N N 10.170 0.941 24.582 2.613 -2.406 -0.971 "H4'" Y4I 52
Y4I "H3'" H17 H 0 1 N N N N N N 11.650 1.744 22.344 4.185 -2.283 1.665 "H3'" Y4I 53
Y4I "HO3'" H18 H 0 0 N N N N N N 12.643 3.050 24.014 4.735 -4.480 0.907 "HO3'" Y4I 54
Y4I "H2'2" H19 H 0 0 N N N N N N 13.307 0.049 22.448 6.145 -1.811 0.461 "H2'2" Y4I 55
Y4I "H2'1" H20 H 0 0 N N N N N N 14.015 1.221 23.611 5.603 -2.752 -0.962 "H2'1" Y4I 56
Y4I "H1'" H21 H 0 1 N N N N N N 13.228 0.053 25.482 4.781 -0.840 -1.931 "H1'" Y4I 57
Y4I H6 H22 H 0 1 N N N N N N 12.197 -2.453 22.966 6.293 0.771 -2.410 H6 Y4I 58
Y4I H5M3 H23 H 0 0 N N N N N N 12.190 -4.651 21.977 7.292 3.702 -2.425 H5M3 Y4I 59
Y4I H5M1 H24 H 0 0 N N N N N N 13.871 -5.182 21.633 8.782 3.296 -1.541 H5M1 Y4I 60
Y4I H5M2 H25 H 0 0 N N N N N N 12.968 -5.897 23.011 8.186 2.215 -2.822 H5M2 Y4I 61
Y4I H3 H26 H 0 1 N N N N N N 16.186 -3.355 25.422 6.380 2.069 2.194 H3 Y4I 62
#
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
Y4I OP1 P SING N N 1
Y4I SP P DOUB N N 2
Y4I "O5'" P SING N N 3
Y4I P N14 SING N N 4
Y4I "C5'" "O5'" SING N N 5
Y4I "C4'" "C5'" SING N N 6
Y4I "C4'" "O4'" SING N N 7
Y4I "C3'" "C4'" SING N N 8
Y4I "O4'" "C1'" SING N N 9
Y4I "O3'" "C3'" SING N N 10
Y4I "C2'" "C3'" SING N N 11
Y4I "C1'" "C2'" SING N N 12
Y4I N1 "C1'" SING N N 13
Y4I N1 C2 SING N N 14
Y4I C6 N1 SING N N 15
Y4I O2 C2 DOUB N N 16
Y4I C2 N3 SING N N 17
Y4I N3 C4 SING N N 18
Y4I O4 C4 DOUB N N 19
Y4I C4 C5 SING N N 20
Y4I C5M C5 SING N N 21
Y4I C5 C6 DOUB N N 22
Y4I O11 C12 SING N N 23
Y4I O11 C16 SING N N 24
Y4I C13 C12 SING N N 25
Y4I C12 N17 SING N N 26
Y4I O12 C18 DOUB N N 27
Y4I N14 C13 SING N N 28
Y4I C20 O13 DOUB N N 29
Y4I C15 N14 SING N N 30
Y4I C16 C15 SING N N 31
Y4I O15 C23 SING N N 32
Y4I C23 C16 SING N N 33
Y4I N17 C18 SING N N 34
Y4I N17 C22 SING N N 35
Y4I C18 N19 SING N N 36
Y4I N19 C20 SING N N 37
Y4I C21 C20 SING N N 38
Y4I C22 C21 DOUB N N 39
Y4I N19 H1 SING N N 40
Y4I C21 H2 SING N N 41
Y4I C22 H22 SING N N 42
Y4I C12 H12 SING N N 43
Y4I C13 H131 SING N N 44
Y4I C13 H132 SING N N 45
Y4I C15 H151 SING N N 46
Y4I C15 H152 SING N N 47
Y4I C16 H16 SING N N 48
Y4I C23 H231 SING N N 49
Y4I C23 H232 SING N N 50
Y4I O15 HO15 SING N N 51
Y4I OP1 HOP1 SING N N 52
Y4I "C5'" "H5'2" SING N N 53
Y4I "C5'" "H5'1" SING N N 54
Y4I "C4'" "H4'" SING N N 55
Y4I "C3'" "H3'" SING N N 56
Y4I "O3'" "HO3'" SING N N 57
Y4I "C2'" "H2'2" SING N N 58
Y4I "C2'" "H2'1" SING N N 59
Y4I "C1'" "H1'" SING N N 60
Y4I C6 H6 SING N N 61
Y4I C5M H5M3 SING N N 62
Y4I C5M H5M1 SING N N 63
Y4I C5M H5M2 SING N N 64
Y4I N3 H3 SING N N 65
#
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
Y4I InChI InChI 1.06 "InChI=1S/C19H26N5O10PS/c1-10-5-24(19(30)21-17(10)28)15-4-12(26)13(34-15)9-32-35(31,36)22-6-11(8-25)33-16(7-22)23-3-2-14(27)20-18(23)29/h2-3,5,11-13,15-16,25-26H,4,6-9H2,1H3,(H,31,36)(H,20,27,29)(H,21,28,30)/t11-,12-,13+,15+,16+,35-/m0/s1"
Y4I InChIKey InChI 1.06 JMOYBKKBBMXKAB-OTRGKRLXSA-N
Y4I SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(=S)N3C[C@@H](CO)O[C@H](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O"
Y4I SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=S)N3C[CH](CO)O[CH](C3)N4C=CC(=O)NC4=O)O2)C(=O)NC1=O"
Y4I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(N3C[C@H](O[C@H](C3)N4C=CC(=O)NC4=O)CO)O)O"
Y4I SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(N3CC(OC(C3)N4C=CC(=O)NC4=O)CO)O)O"
#
_pdbx_chem_comp_identifier.comp_id Y4I
_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-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Y4I 'Create component' 2023-11-20 PDBE
Y4I 'Initial release' 2023-12-06 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
Y4I O11 O -3.865 -4.434 1
Y4I O13 O -9.063 0.061 2
Y4I C20 C -7.764 -0.687 3
Y4I N19 N -7.762 -2.187 4
Y4I C18 C -6.463 -2.937 5
Y4I O12 O -6.462 -4.435 6
Y4I C21 C -6.465 0.063 7
Y4I C22 C -5.166 -0.685 8
Y4I N17 N -5.166 -2.185 9
Y4I C12 C -3.865 -2.934 10
Y4I C13 C -2.568 -2.183 11
Y4I N14 N -1.267 -2.931 12
Y4I C15 C -1.267 -4.432 13
Y4I C16 C -2.564 -5.182 14
Y4I C23 C -2.564 -6.683 15
Y4I O15 O -3.863 -7.434 16
Y4I P P 0.031 -2.181 17
Y4I SP S -0.720 -0.882 18
Y4I OP1 O 0.782 -3.479 19
Y4I "O5'" O 1.329 -1.430 20
Y4I "C5'" C 1.329 0.070 21
Y4I "C4'" C 2.626 0.822 22
Y4I "C3'" C 3.998 0.212 23
Y4I "O3'" O 4.309 -1.254 24
Y4I "C2'" C 4.999 1.328 25
Y4I "C1'" C 4.249 2.627 26
Y4I "O4'" O 2.783 2.313 27
Y4I N1 N 4.858 3.995 28
Y4I C6 C 6.349 4.157 29
Y4I C5 C 6.960 5.525 30
Y4I C5M C 8.451 5.684 31
Y4I C4 C 6.075 6.741 32
Y4I O4 O 6.684 8.111 33
Y4I N3 N 4.585 6.580 34
Y4I C2 C 3.974 5.211 35
Y4I O2 O 2.483 5.052 36
#
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
Y4I P OP1 SINGLE BEGINDASH 1
Y4I SP P DOUBLE NONE 2
Y4I "O5'" P SINGLE NONE 3
Y4I P N14 SINGLE NONE 4
Y4I "C5'" "O5'" SINGLE NONE 5
Y4I "C4'" "C5'" SINGLE BEGINWEDGE 6
Y4I "C4'" "O4'" SINGLE NONE 7
Y4I "C3'" "C4'" SINGLE NONE 8
Y4I "O4'" "C1'" SINGLE NONE 9
Y4I "C3'" "O3'" SINGLE BEGINDASH 10
Y4I "C2'" "C3'" SINGLE NONE 11
Y4I "C1'" "C2'" SINGLE NONE 12
Y4I "C1'" N1 SINGLE BEGINWEDGE 13
Y4I N1 C2 SINGLE NONE 14
Y4I C6 N1 SINGLE NONE 15
Y4I O2 C2 DOUBLE NONE 16
Y4I C2 N3 SINGLE NONE 17
Y4I N3 C4 SINGLE NONE 18
Y4I O4 C4 DOUBLE NONE 19
Y4I C4 C5 SINGLE NONE 20
Y4I C5M C5 SINGLE NONE 21
Y4I C5 C6 DOUBLE NONE 22
Y4I O11 C12 SINGLE NONE 23
Y4I O11 C16 SINGLE NONE 24
Y4I C13 C12 SINGLE NONE 25
Y4I C12 N17 SINGLE BEGINWEDGE 26
Y4I O12 C18 DOUBLE NONE 27
Y4I N14 C13 SINGLE NONE 28
Y4I C20 O13 DOUBLE NONE 29
Y4I C15 N14 SINGLE NONE 30
Y4I C16 C15 SINGLE NONE 31
Y4I O15 C23 SINGLE NONE 32
Y4I C16 C23 SINGLE BEGINWEDGE 33
Y4I N17 C18 SINGLE NONE 34
Y4I N17 C22 SINGLE NONE 35
Y4I C18 N19 SINGLE NONE 36
Y4I N19 C20 SINGLE NONE 37
Y4I C21 C20 SINGLE NONE 38
Y4I C22 C21 DOUBLE NONE 39
#
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
Y4I MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CN([PH](=S)OC[C@@H]3CC[C@H](n4ccc(=O)[nH]c4=O)O3)CCO2)c(=O)[nH]1' InChI=1S/C17H22N5O7PS/c23-12-3-5-21(16(25)18-12)14-2-1-11(29-14)10-28-30(31)20-7-8-27-15(9-20)22-6-4-13(24)19-17(22)26/h3-6,11,14-15,30H,1-2,7-10H2,(H,18,23,25)(H,19,24,26)/t11-,14+,15+/m0/s1 CYTSUYIBZZOLAB-NILFDRSVSA-N
Y4I deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
Y4I pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
Y4I O11 S1 1
Y4I O13 S1 1
Y4I C20 S1 1
Y4I N19 S1 1
Y4I C18 S1 1
Y4I O12 S1 1
Y4I C21 S1 1
Y4I C22 S1 1
Y4I N17 S1 1
Y4I C12 S1 1
Y4I C13 S1 1
Y4I N14 S1 1
Y4I C15 S1 1
Y4I C16 S1 1
Y4I P S1 1
Y4I SP S1 1
Y4I "O5'" S1 1
Y4I "C5'" S1 1
Y4I "C4'" S1 1
Y4I "C3'" S1 1
Y4I "C2'" S1 1
Y4I "C1'" S1 1
Y4I "O4'" S1 1
Y4I N1 S1 1
Y4I C6 S1 1
Y4I C5 S1 1
Y4I C4 S1 1
Y4I O4 S1 1
Y4I N3 S1 1
Y4I C2 S1 1
Y4I O2 S1 1
Y4I "C1'" F1 1
Y4I "C2'" F1 1
Y4I "C3'" F1 1
Y4I "O3'" F1 1
Y4I "C4'" F1 1
Y4I "O4'" F1 1
Y4I "C5'" F1 1
Y4I "O5'" F1 1
Y4I C21 F2 1
Y4I C20 F2 1
Y4I N19 F2 1
Y4I C18 F2 1
Y4I N17 F2 1
Y4I C22 F2 1
Y4I C5 F2 2
Y4I C4 F2 2
Y4I N3 F2 2
Y4I C2 F2 2
Y4I N1 F2 2
Y4I C6 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id Y4I
_pdbe_chem_comp_rdkit_properties.exactmw 547.114
_pdbe_chem_comp_rdkit_properties.amw 547.483
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 15
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 62
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 17
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.579
_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 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 244.174
_pdbe_chem_comp_rdkit_properties.tpsa 201.340
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.014
_pdbe_chem_comp_rdkit_properties.CrippenMR 127.107
_pdbe_chem_comp_rdkit_properties.chi0v 18.385
_pdbe_chem_comp_rdkit_properties.chi1v 11.267
_pdbe_chem_comp_rdkit_properties.chi2v 5.445
_pdbe_chem_comp_rdkit_properties.chi3v 5.445
_pdbe_chem_comp_rdkit_properties.chi4v 3.300
_pdbe_chem_comp_rdkit_properties.chi0n 42.674
_pdbe_chem_comp_rdkit_properties.chi1n 21.296
_pdbe_chem_comp_rdkit_properties.chi2n 3.720
_pdbe_chem_comp_rdkit_properties.chi3n 3.720
_pdbe_chem_comp_rdkit_properties.chi4n 2.242
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.270
_pdbe_chem_comp_rdkit_properties.kappa1 9.182
_pdbe_chem_comp_rdkit_properties.kappa2 10.610
_pdbe_chem_comp_rdkit_properties.kappa3 5.665
_pdbe_chem_comp_rdkit_properties.Phi 2.706
#
_pdbe_chem_comp_external_mappings.comp_id Y4I
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id Y4I
#
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
Y4I O11 -3.149 1.073 -0.579 ETKDGv3 1
Y4I O13 -9.163 0.503 -1.944 ETKDGv3 2
Y4I C20 -7.944 0.325 -1.682 ETKDGv3 3
Y4I N19 -7.531 -0.817 -0.931 ETKDGv3 4
Y4I C18 -6.144 -0.999 -0.640 ETKDGv3 5
Y4I O12 -5.769 -2.027 -0.015 ETKDGv3 6
Y4I C21 -6.940 1.286 -2.153 ETKDGv3 7
Y4I C22 -5.647 1.112 -1.865 ETKDGv3 8
Y4I N17 -5.190 -0.005 -1.072 ETKDGv3 9
Y4I C12 -3.750 -0.187 -0.824 ETKDGv3 10
Y4I C13 -3.108 -0.889 -2.047 ETKDGv3 11
Y4I N14 -1.634 -0.921 -1.985 ETKDGv3 12
Y4I C15 -1.067 0.372 -1.568 ETKDGv3 13
Y4I C16 -1.770 0.914 -0.311 ETKDGv3 14
Y4I C23 -1.190 2.275 0.094 ETKDGv3 15
Y4I O15 0.164 2.161 0.443 ETKDGv3 16
Y4I P -1.010 -2.292 -1.042 ETKDGv3 17
Y4I SP -0.715 -3.592 -2.145 ETKDGv3 18
Y4I OP1 -2.149 -2.806 0.103 ETKDGv3 19
Y4I "O5'" 0.449 -1.845 -0.264 ETKDGv3 20
Y4I "C5'" 0.891 -2.901 0.561 ETKDGv3 21
Y4I "C4'" 2.017 -2.408 1.476 ETKDGv3 22
Y4I "C3'" 1.554 -1.304 2.432 ETKDGv3 23
Y4I "O3'" 1.237 -1.830 3.695 ETKDGv3 24
Y4I "C2'" 2.753 -0.388 2.523 ETKDGv3 25
Y4I "C1'" 3.757 -0.991 1.545 ETKDGv3 26
Y4I "O4'" 3.082 -1.901 0.709 ETKDGv3 27
Y4I N1 4.417 0.056 0.748 ETKDGv3 28
Y4I C6 5.737 0.496 1.130 ETKDGv3 29
Y4I C5 6.373 1.485 0.479 ETKDGv3 30
Y4I C5M 7.766 1.884 0.886 ETKDGv3 31
Y4I C4 5.729 2.131 -0.683 ETKDGv3 32
Y4I O4 6.333 3.022 -1.338 ETKDGv3 33
Y4I N3 4.409 1.744 -1.067 ETKDGv3 34
Y4I C2 3.739 0.716 -0.340 ETKDGv3 35
Y4I O2 2.561 0.399 -0.655 ETKDGv3 36
Y4I H1 -8.235 -1.518 -0.606 ETKDGv3 37
Y4I H2 -7.249 2.139 -2.746 ETKDGv3 38
Y4I H22 -4.933 1.834 -2.243 ETKDGv3 39
Y4I H12 -3.630 -0.815 0.082 ETKDGv3 40
Y4I H131 -3.519 -1.917 -2.151 ETKDGv3 41
Y4I H132 -3.400 -0.340 -2.969 ETKDGv3 42
Y4I H151 0.027 0.289 -1.412 ETKDGv3 43
Y4I H152 -1.205 1.097 -2.400 ETKDGv3 44
Y4I H16 -1.612 0.218 0.545 ETKDGv3 45
Y4I H231 -1.770 2.691 0.950 ETKDGv3 46
Y4I H232 -1.283 2.992 -0.750 ETKDGv3 47
Y4I HO15 0.192 1.744 1.344 ETKDGv3 48
Y4I HOP1 -1.992 -2.237 0.898 ETKDGv3 49
Y4I "H5'2" 0.081 -3.301 1.210 ETKDGv3 50
Y4I "H5'1" 1.290 -3.729 -0.065 ETKDGv3 51
Y4I "H4'" 2.393 -3.280 2.061 ETKDGv3 52
Y4I "H3'" 0.688 -0.732 2.023 ETKDGv3 53
Y4I "HO3'" 0.352 -2.270 3.601 ETKDGv3 54
Y4I "H2'2" 2.465 0.646 2.230 ETKDGv3 55
Y4I "H2'1" 3.182 -0.359 3.549 ETKDGv3 56
Y4I "H1'" 4.520 -1.567 2.120 ETKDGv3 57
Y4I H6 6.230 0.014 1.966 ETKDGv3 58
Y4I H5M3 8.502 1.357 0.244 ETKDGv3 59
Y4I H5M1 7.902 2.979 0.770 ETKDGv3 60
Y4I H5M2 7.966 1.629 1.949 ETKDGv3 61
Y4I H3 3.936 2.213 -1.872 ETKDGv3 62
#