data_VD3
#
_chem_comp.id VD3
_chem_comp.name
;(1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI
DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C27 H44 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "VITAMIN D3"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-06-15
_chem_comp.pdbx_modified_date 2020-06-17
_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 384.638
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VD3
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
VD3 O O O 0 1 N N N N N N -0.432 0.185 24.583 -5.539 -3.548 -0.709 O VD3 1
VD3 C1 C1 C 0 1 N N N N N N 0.634 1.412 21.416 -7.115 -0.429 0.671 C1 VD3 2
VD3 C2 C2 C 0 1 N N N N N N 0.289 1.765 22.818 -6.855 -1.930 0.507 C2 VD3 3
VD3 C3 C3 C 0 1 N N S N N N -0.929 0.981 23.494 -5.680 -2.151 -0.447 C3 VD3 4
VD3 C4 C4 C 0 1 N N N N N N -1.633 0.070 22.460 -4.391 -1.618 0.185 C4 VD3 5
VD3 C5 C5 C 0 1 N N N N N N -1.876 0.751 21.032 -4.587 -0.149 0.505 C5 VD3 6
VD3 C7 C7 C 0 1 N N N N N N -3.094 0.632 20.405 -3.656 0.774 0.185 C7 VD3 7
VD3 C8 C8 C 0 1 N N N N N N -4.496 1.237 20.391 -2.421 0.366 -0.488 C8 VD3 8
VD3 C9 C9 C 0 1 N N N N N N -4.760 2.544 19.971 -1.502 1.278 -0.804 C9 VD3 9
VD3 C10 C10 C 0 1 N N N N N N -4.835 2.045 18.426 -1.680 2.758 -0.492 C10 VD3 10
VD3 C6 C6 C 0 1 N N N N N N -0.619 1.528 20.525 -5.843 0.221 1.189 C6 VD3 11
VD3 C11 C11 C 0 1 N N N N N N -4.361 2.992 17.372 -0.448 3.313 0.219 C11 VD3 12
VD3 C12 C12 C 0 1 N N N N N N -4.501 4.544 17.630 0.852 2.920 -0.504 C12 VD3 13
VD3 C13 C13 C 0 1 N N R N N N -4.181 4.992 19.057 0.923 1.417 -0.558 C13 VD3 14
VD3 C14 C14 C 0 1 N N S N N N -3.760 3.797 19.985 -0.218 0.921 -1.492 C14 VD3 15
VD3 C15 C15 C 0 1 N N N N N N -3.510 4.548 21.388 0.110 -0.570 -1.603 C15 VD3 16
VD3 C16 C16 C 0 1 N N N N N N -2.940 6.012 20.970 1.656 -0.569 -1.769 C16 VD3 17
VD3 C17 C17 C 0 1 N N R N N N -2.873 5.914 19.400 2.162 0.757 -1.144 C17 VD3 18
VD3 C18 C18 C 0 1 N N N N N N -5.554 5.695 19.498 0.664 0.848 0.839 C18 VD3 19
VD3 C19 C19 C 0 1 N N N N N N -0.577 2.209 19.448 -5.863 1.087 2.202 C19 VD3 20
VD3 C20 C20 C 0 1 N N R N N N -2.899 7.364 18.620 3.183 0.469 -0.041 C20 VD3 21
VD3 C21 C21 C 0 1 N N N N N N -1.521 7.511 17.986 3.615 1.784 0.610 C21 VD3 22
VD3 C22 C22 C 0 1 N N N N N N -3.007 8.707 19.437 4.404 -0.226 -0.646 C22 VD3 23
VD3 C23 C23 C 0 1 N N N N N N -4.241 9.651 18.788 5.369 -0.626 0.472 C23 VD3 24
VD3 C24 C24 C 0 1 N N N N N N -3.387 10.910 18.467 6.590 -1.321 -0.133 C24 VD3 25
VD3 C25 C25 C 0 1 N N N N N N -3.686 12.301 19.059 7.556 -1.721 0.985 C25 VD3 26
VD3 C26 C26 C 0 1 N N N N N N -2.338 12.451 19.433 8.715 -2.525 0.394 C26 VD3 27
VD3 C27 C27 C 0 1 N N N N N N -3.671 13.599 18.440 8.101 -0.462 1.662 C27 VD3 28
VD3 HO HO H 0 1 N N N N N N -0.322 -0.714 24.295 -4.793 -3.645 -1.316 HO VD3 29
VD3 H11 1H1 H 0 1 N N N N N N 1.009 0.378 21.383 -7.388 0.004 -0.291 H11 VD3 30
VD3 H12 2H1 H 0 1 N N N N N N 1.409 2.100 21.047 -7.922 -0.273 1.387 H12 VD3 31
VD3 H21 1H2 H 0 1 N N N N N N -0.033 2.816 22.778 -7.746 -2.410 0.102 H21 VD3 32
VD3 H22 2H2 H 0 1 N N N N N N 1.181 1.560 23.429 -6.620 -2.366 1.478 H22 VD3 33
VD3 H3 H3 H 0 1 N N N N N N -1.661 1.712 23.868 -5.869 -1.624 -1.383 H3 VD3 34
VD3 H41 1H4 H 0 1 N N N N N N -2.626 -0.165 22.871 -3.563 -1.735 -0.514 H41 VD3 35
VD3 H42 2H4 H 0 1 N N N N N N -1.001 -0.817 22.307 -4.177 -2.168 1.102 H42 VD3 36
VD3 H7 H7 H 0 1 N N N N N N -3.041 -0.160 19.672 -3.823 1.814 0.424 H7 VD3 37
VD3 H8 H8 H 0 1 N N N N N N -5.323 0.626 20.721 -2.254 -0.674 -0.727 H8 VD3 38
VD3 H101 1H10 H 0 0 N N N N N N -5.907 1.905 18.223 -1.835 3.304 -1.422 H101 VD3 39
VD3 H102 2H10 H 0 0 N N N N N N -4.209 1.144 18.351 -2.553 2.887 0.149 H102 VD3 40
VD3 H111 1H11 H 0 0 N N N N N N -5.020 2.797 16.513 -0.519 4.400 0.256 H111 VD3 41
VD3 H112 2H11 H 0 0 N N N N N N -3.288 2.794 17.233 -0.419 2.924 1.237 H112 VD3 42
VD3 H121 1H12 H 0 0 N N N N N N -5.558 4.795 17.455 0.846 3.318 -1.518 H121 VD3 43
VD3 H122 2H12 H 0 0 N N N N N N -3.803 5.060 16.953 1.711 3.311 0.042 H122 VD3 44
VD3 H14 H14 H 0 1 N N N N N N -2.862 3.254 19.654 -0.157 1.403 -2.468 H14 VD3 45
VD3 H151 1H15 H 0 0 N N N N N N -2.811 3.998 22.035 -0.372 -1.008 -2.476 H151 VD3 46
VD3 H152 2H15 H 0 0 N N N N N N -4.443 4.635 21.964 -0.180 -1.098 -0.694 H152 VD3 47
VD3 H161 1H16 H 0 0 N N N N N N -1.972 6.252 21.434 1.918 -0.608 -2.827 H161 VD3 48
VD3 H162 2H16 H 0 0 N N N N N N -3.606 6.822 21.302 2.090 -1.420 -1.244 H162 VD3 49
VD3 H17 H17 H 0 1 N N N N N N -1.919 5.492 19.051 2.603 1.393 -1.911 H17 VD3 50
VD3 H181 1H18 H 0 0 N N N N N N -6.401 5.048 19.226 -0.321 1.165 1.183 H181 VD3 51
VD3 H182 2H18 H 0 0 N N N N N N -5.652 6.663 18.985 0.702 -0.240 0.801 H182 VD3 52
VD3 H183 3H18 H 0 0 N N N N N N -5.551 5.856 20.586 1.425 1.215 1.528 H183 VD3 53
VD3 H191 1H19 H 0 0 N N N N N N -1.374 2.365 18.736 -6.799 1.341 2.677 H191 VD3 54
VD3 H192 2H19 H 0 0 N N N N N N 0.430 2.596 19.404 -4.943 1.534 2.549 H192 VD3 55
VD3 H20 H20 H 0 1 N N N N N N -3.808 7.291 18.005 2.732 -0.178 0.712 H20 VD3 56
VD3 H211 1H21 H 0 0 N N N N N N -0.894 6.652 18.268 4.066 2.431 -0.143 H211 VD3 57
VD3 H212 2H21 H 0 0 N N N N N N -1.052 8.440 18.341 2.745 2.280 1.041 H212 VD3 58
VD3 H213 3H21 H 0 0 N N N N N N -1.622 7.546 16.891 4.342 1.579 1.395 H213 VD3 59
VD3 H221 1H22 H 0 0 N N N N N N -2.054 9.253 19.378 4.906 0.454 -1.333 H221 VD3 60
VD3 H222 2H22 H 0 0 N N N N N N -3.231 8.481 20.490 4.084 -1.118 -1.186 H222 VD3 61
VD3 H231 1H23 H 0 0 N N N N N N -5.117 9.813 19.434 4.867 -1.307 1.159 H231 VD3 62
VD3 H232 2H23 H 0 0 N N N N N N -4.720 9.205 17.904 5.689 0.265 1.012 H232 VD3 63
VD3 H241 1H24 H 0 0 N N N N N N -3.601 11.065 17.399 7.093 -0.640 -0.820 H241 VD3 64
VD3 H242 2H24 H 0 0 N N N N N N -2.371 10.664 18.809 6.271 -2.212 -0.673 H242 VD3 65
VD3 H25 H25 H 0 1 N N N N N N -4.677 12.210 19.527 7.029 -2.329 1.720 H25 VD3 66
VD3 H261 1H26 H 0 0 N N N N N N -2.033 11.597 20.056 9.403 -2.809 1.191 H261 VD3 67
VD3 H262 2H26 H 0 0 N N N N N N -2.218 13.383 20.005 8.327 -3.422 -0.088 H262 VD3 68
VD3 H263 3H26 H 0 0 N N N N N N -1.709 12.490 18.531 9.243 -1.916 -0.340 H263 VD3 69
VD3 H271 1H27 H 0 0 N N N N N N -4.565 13.715 17.810 7.274 0.111 2.083 H271 VD3 70
VD3 H272 2H27 H 0 0 N N N N N N -2.769 13.698 17.818 8.788 -0.746 2.459 H272 VD3 71
VD3 H273 3H27 H 0 0 N N N N N N -3.667 14.377 19.218 8.628 0.147 0.928 H273 VD3 72
#
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
VD3 O C3 SING N N 1
VD3 O HO SING N N 2
VD3 C1 C2 SING N N 3
VD3 C1 C6 SING N N 4
VD3 C1 H11 SING N N 5
VD3 C1 H12 SING N N 6
VD3 C2 C3 SING N N 7
VD3 C2 H21 SING N N 8
VD3 C2 H22 SING N N 9
VD3 C3 C4 SING N N 10
VD3 C3 H3 SING N N 11
VD3 C4 C5 SING N N 12
VD3 C4 H41 SING N N 13
VD3 C4 H42 SING N N 14
VD3 C5 C7 DOUB N E 15
VD3 C5 C6 SING N N 16
VD3 C7 C8 SING N N 17
VD3 C7 H7 SING N N 18
VD3 C8 C9 DOUB N Z 19
VD3 C8 H8 SING N N 20
VD3 C9 C10 SING N N 21
VD3 C9 C14 SING N N 22
VD3 C10 C11 SING N N 23
VD3 C10 H101 SING N N 24
VD3 C10 H102 SING N N 25
VD3 C6 C19 DOUB N N 26
VD3 C11 C12 SING N N 27
VD3 C11 H111 SING N N 28
VD3 C11 H112 SING N N 29
VD3 C12 C13 SING N N 30
VD3 C12 H121 SING N N 31
VD3 C12 H122 SING N N 32
VD3 C13 C14 SING N N 33
VD3 C13 C17 SING N N 34
VD3 C13 C18 SING N N 35
VD3 C14 C15 SING N N 36
VD3 C14 H14 SING N N 37
VD3 C15 C16 SING N N 38
VD3 C15 H151 SING N N 39
VD3 C15 H152 SING N N 40
VD3 C16 C17 SING N N 41
VD3 C16 H161 SING N N 42
VD3 C16 H162 SING N N 43
VD3 C17 C20 SING N N 44
VD3 C17 H17 SING N N 45
VD3 C18 H181 SING N N 46
VD3 C18 H182 SING N N 47
VD3 C18 H183 SING N N 48
VD3 C19 H191 SING N N 49
VD3 C19 H192 SING N N 50
VD3 C20 C21 SING N N 51
VD3 C20 C22 SING N N 52
VD3 C20 H20 SING N N 53
VD3 C21 H211 SING N N 54
VD3 C21 H212 SING N N 55
VD3 C21 H213 SING N N 56
VD3 C22 C23 SING N N 57
VD3 C22 H221 SING N N 58
VD3 C22 H222 SING N N 59
VD3 C23 C24 SING N N 60
VD3 C23 H231 SING N N 61
VD3 C23 H232 SING N N 62
VD3 C24 C25 SING N N 63
VD3 C24 H241 SING N N 64
VD3 C24 H242 SING N N 65
VD3 C25 C26 SING N N 66
VD3 C25 C27 SING N N 67
VD3 C25 H25 SING N N 68
VD3 C26 H261 SING N N 69
VD3 C26 H262 SING N N 70
VD3 C26 H263 SING N N 71
VD3 C27 H271 SING N N 72
VD3 C27 H272 SING N N 73
VD3 C27 H273 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
VD3 SMILES ACDLabs 10.04 OC3CC(=C/C=C1\CCCC2(C)C(C(C)CCCC(C)C)CCC12)\C(=C)CC3
VD3 SMILES_CANONICAL CACTVS 3.341 CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C\C=C3/C[C@@H](O)CCC3=C
VD3 SMILES CACTVS 3.341 CC(C)CCC[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)CCC3=C
VD3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](CCC3=C)O)C
VD3 SMILES "OpenEye OEToolkits" 1.5.0 CC(C)CCCC(C)C1CCC2C1(CCCC2=CC=C3CC(CCC3=C)O)C
VD3 InChI InChI 1.03 InChI=1S/C27H44O/c1-19(2)8-6-9-21(4)25-15-16-26-22(10-7-17-27(25,26)5)12-13-23-18-24(28)14-11-20(23)3/h12-13,19,21,24-26,28H,3,6-11,14-18H2,1-2,4-5H3/t21-,24+,25-,26+,27-/m1/s1
VD3 InChIKey InChI 1.03 QYSXJUFSXHHAJI-RWDMXNMGSA-N
#
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
VD3 "SYSTEMATIC NAME" ACDLabs 10.04 (3S,5E,7Z,14beta,17alpha)-9,10-secocholesta-5,7,10-trien-3-ol
VD3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (1S)-3-[2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methylheptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VD3 'Create component' 2006-06-15 EBI
VD3 'Modify descriptor' 2011-06-04 RCSB
VD3 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VD3
_pdbx_chem_comp_synonyms.name "VITAMIN D3"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id VD3
_pdbe_chem_comp_synonyms.name 'VITAMIN D3'
_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
VD3 O O 8.196 -7.270 1
VD3 C1 C 4.299 -6.520 2
VD3 C2 C 5.598 -7.270 3
VD3 C3 C 6.897 -6.520 4
VD3 C4 C 6.897 -5.020 5
VD3 C5 C 5.598 -4.270 6
VD3 C7 C 5.598 -2.770 7
VD3 C8 C 6.897 -2.020 8
VD3 C9 C 6.897 -0.520 9
VD3 C10 C 5.598 0.230 10
VD3 C6 C 4.299 -5.020 11
VD3 C11 C 5.598 1.730 12
VD3 C12 C 6.897 2.480 13
VD3 C13 C 8.196 1.730 14
VD3 C14 C 8.196 0.230 15
VD3 C15 C 9.616 -0.227 16
VD3 C16 C 10.491 0.980 17
VD3 C17 C 9.616 2.187 18
VD3 C18 C 8.196 3.230 19
VD3 C19 C 3.000 -4.270 20
VD3 C20 C 10.082 3.613 21
VD3 C21 C 9.080 4.729 22
VD3 C22 C 11.549 3.922 23
VD3 C23 C 12.015 5.348 24
VD3 C24 C 13.483 5.658 25
VD3 C25 C 13.949 7.083 26
VD3 C26 C 15.417 7.393 27
VD3 C27 C 12.947 8.200 28
#
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
VD3 C3 O SINGLE BEGINWEDGE 1
VD3 C1 C2 SINGLE NONE 2
VD3 C1 C6 SINGLE NONE 3
VD3 C2 C3 SINGLE NONE 4
VD3 C3 C4 SINGLE NONE 5
VD3 C4 C5 SINGLE ENDUPRIGHT 6
VD3 C5 C7 DOUBLE NONE 7
VD3 C5 C6 SINGLE ENDUPRIGHT 8
VD3 C7 C8 SINGLE ENDDOWNRIGHT 9
VD3 C8 C9 DOUBLE NONE 10
VD3 C9 C10 SINGLE ENDUPRIGHT 11
VD3 C9 C14 SINGLE ENDDOWNRIGHT 12
VD3 C10 C11 SINGLE NONE 13
VD3 C6 C19 DOUBLE NONE 14
VD3 C11 C12 SINGLE NONE 15
VD3 C12 C13 SINGLE NONE 16
VD3 C13 C14 SINGLE NONE 17
VD3 C13 C17 SINGLE NONE 18
VD3 C13 C18 SINGLE BEGINWEDGE 19
VD3 C14 C15 SINGLE NONE 20
VD3 C15 C16 SINGLE NONE 21
VD3 C17 C16 SINGLE BEGINWEDGE 22
VD3 C17 C20 SINGLE NONE 23
VD3 C20 C21 SINGLE BEGINDASH 24
VD3 C20 C22 SINGLE NONE 25
VD3 C22 C23 SINGLE NONE 26
VD3 C23 C24 SINGLE NONE 27
VD3 C24 C25 SINGLE NONE 28
VD3 C25 C26 SINGLE NONE 29
VD3 C25 C27 SINGLE NONE 30
#
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
VD3 MurckoScaffold S1 scaffold 'C=C1CCCC/C1=C\C=C1/CCCC2CCC[C@@H]12' InChI=1S/C18H26/c1-14-6-2-3-7-15(14)12-13-17-9-4-8-16-10-5-11-18(16)17/h12-13,16,18H,1-11H2/b15-12+,17-13+/t16?,18-/m1/s1 GBDZMYYBUXFGPL-GCDIQCJMSA-N
VD3 cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
VD3 cyclopentane F2 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-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
VD3 C1 S1 1
VD3 C2 S1 1
VD3 C3 S1 1
VD3 C4 S1 1
VD3 C5 S1 1
VD3 C7 S1 1
VD3 C8 S1 1
VD3 C9 S1 1
VD3 C10 S1 1
VD3 C6 S1 1
VD3 C11 S1 1
VD3 C12 S1 1
VD3 C13 S1 1
VD3 C14 S1 1
VD3 C15 S1 1
VD3 C16 S1 1
VD3 C17 S1 1
VD3 C19 S1 1
VD3 C1 F1 1
VD3 C2 F1 1
VD3 C3 F1 1
VD3 C4 F1 1
VD3 C5 F1 1
VD3 C6 F1 1
VD3 C9 F1 2
VD3 C10 F1 2
VD3 C11 F1 2
VD3 C12 F1 2
VD3 C13 F1 2
VD3 C14 F1 2
VD3 C13 F2 1
VD3 C14 F2 1
VD3 C15 F2 1
VD3 C16 F2 1
VD3 C17 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VD3
_pdbe_chem_comp_rdkit_properties.exactmw 384.339
_pdbe_chem_comp_rdkit_properties.amw 384.648
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 28
_pdbe_chem_comp_rdkit_properties.NumAtoms 72
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 235.841
_pdbe_chem_comp_rdkit_properties.tpsa 20.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP 7.619
_pdbe_chem_comp_rdkit_properties.CrippenMR 121.189
_pdbe_chem_comp_rdkit_properties.chi0v 13.908
_pdbe_chem_comp_rdkit_properties.chi1v 7.454
_pdbe_chem_comp_rdkit_properties.chi2v 3.477
_pdbe_chem_comp_rdkit_properties.chi3v 3.477
_pdbe_chem_comp_rdkit_properties.chi4v 2.233
_pdbe_chem_comp_rdkit_properties.chi0n 57.908
_pdbe_chem_comp_rdkit_properties.chi1n 29.362
_pdbe_chem_comp_rdkit_properties.chi2n 3.477
_pdbe_chem_comp_rdkit_properties.chi3n 3.477
_pdbe_chem_comp_rdkit_properties.chi4n 2.233
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.820
_pdbe_chem_comp_rdkit_properties.kappa1 3.479
_pdbe_chem_comp_rdkit_properties.kappa2 9.330
_pdbe_chem_comp_rdkit_properties.kappa3 4.835
_pdbe_chem_comp_rdkit_properties.Phi 1.159
#
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
VD3 UniChem PDBe VD3
VD3 UniChem eMolecules 30513009
VD3 UniChem SureChEMBL SCHEMBL15695
VD3 UniChem PharmGKB PA164748138
VD3 UniChem PubChem 6221
#
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
VD3 O 6.186 -2.197 -2.941 ETKDGv3 1
VD3 C1 7.938 -0.773 -1.152 ETKDGv3 2
VD3 C2 7.546 -2.242 -0.956 ETKDGv3 3
VD3 C3 6.180 -2.544 -1.579 ETKDGv3 4
VD3 C4 5.083 -1.774 -0.827 ETKDGv3 5
VD3 C5 5.425 -0.315 -0.574 ETKDGv3 6
VD3 C7 4.540 0.492 0.057 ETKDGv3 7
VD3 C8 3.189 0.055 0.493 ETKDGv3 8
VD3 C9 2.181 0.903 0.790 ETKDGv3 9
VD3 C10 2.332 2.420 0.742 ETKDGv3 10
VD3 C6 6.785 0.191 -0.960 ETKDGv3 11
VD3 C11 1.018 3.179 0.421 ETKDGv3 12
VD3 C12 -0.254 2.573 1.058 ETKDGv3 13
VD3 C13 -0.333 1.046 0.821 ETKDGv3 14
VD3 C14 0.911 0.414 1.453 ETKDGv3 15
VD3 C15 0.580 -1.077 1.552 ETKDGv3 16
VD3 C16 -0.941 -1.122 1.794 ETKDGv3 17
VD3 C17 -1.450 0.333 1.627 ETKDGv3 18
VD3 C18 -0.434 0.735 -0.704 ETKDGv3 19
VD3 C19 7.010 1.484 -1.238 ETKDGv3 20
VD3 C20 -2.930 0.533 1.132 ETKDGv3 21
VD3 C21 -3.882 0.627 2.339 ETKDGv3 22
VD3 C22 -3.447 -0.542 0.135 ETKDGv3 23
VD3 C23 -4.735 -0.119 -0.611 ETKDGv3 24
VD3 C24 -5.961 -0.935 -0.160 ETKDGv3 25
VD3 C25 -7.290 -0.382 -0.722 ETKDGv3 26
VD3 C26 -7.376 -0.537 -2.248 ETKDGv3 27
VD3 C27 -8.477 -1.092 -0.059 ETKDGv3 28
VD3 HO 5.409 -2.655 -3.356 ETKDGv3 29
VD3 H11 8.338 -0.651 -2.183 ETKDGv3 30
VD3 H12 8.754 -0.519 -0.441 ETKDGv3 31
VD3 H21 8.319 -2.893 -1.419 ETKDGv3 32
VD3 H22 7.518 -2.476 0.132 ETKDGv3 33
VD3 H3 5.987 -3.638 -1.474 ETKDGv3 34
VD3 H41 4.133 -1.844 -1.402 ETKDGv3 35
VD3 H42 4.929 -2.276 0.154 ETKDGv3 36
VD3 H7 4.843 1.494 0.318 ETKDGv3 37
VD3 H8 3.023 -1.004 0.609 ETKDGv3 38
VD3 H101 2.712 2.759 1.729 ETKDGv3 39
VD3 H102 3.065 2.727 -0.031 ETKDGv3 40
VD3 H111 0.886 3.230 -0.681 ETKDGv3 41
VD3 H112 1.121 4.230 0.765 ETKDGv3 42
VD3 H121 -0.245 2.796 2.148 ETKDGv3 43
VD3 H122 -1.147 3.075 0.628 ETKDGv3 44
VD3 H14 0.994 0.764 2.510 ETKDGv3 45
VD3 H151 1.135 -1.556 2.388 ETKDGv3 46
VD3 H152 0.822 -1.604 0.603 ETKDGv3 47
VD3 H161 -1.165 -1.491 2.819 ETKDGv3 48
VD3 H162 -1.388 -1.827 1.067 ETKDGv3 49
VD3 H17 -1.396 0.775 2.650 ETKDGv3 50
VD3 H181 0.458 1.085 -1.261 ETKDGv3 51
VD3 H182 -1.321 1.233 -1.146 ETKDGv3 52
VD3 H183 -0.500 -0.354 -0.898 ETKDGv3 53
VD3 H191 7.996 1.820 -1.538 ETKDGv3 54
VD3 H192 6.225 2.226 -1.221 ETKDGv3 55
VD3 H20 -2.973 1.521 0.625 ETKDGv3 56
VD3 H211 -3.555 1.432 3.031 ETKDGv3 57
VD3 H212 -3.905 -0.336 2.892 ETKDGv3 58
VD3 H213 -4.910 0.886 2.012 ETKDGv3 59
VD3 H221 -2.678 -0.746 -0.632 ETKDGv3 60
VD3 H222 -3.609 -1.504 0.670 ETKDGv3 61
VD3 H231 -4.580 -0.287 -1.699 ETKDGv3 62
VD3 H232 -4.935 0.966 -0.479 ETKDGv3 63
VD3 H241 -6.012 -0.918 0.950 ETKDGv3 64
VD3 H242 -5.832 -1.995 -0.470 ETKDGv3 65
VD3 H25 -7.365 0.700 -0.474 ETKDGv3 66
VD3 H261 -6.613 0.094 -2.749 ETKDGv3 67
VD3 H262 -8.371 -0.203 -2.613 ETKDGv3 68
VD3 H263 -7.225 -1.597 -2.545 ETKDGv3 69
VD3 H271 -8.449 -0.944 1.041 ETKDGv3 70
VD3 H272 -8.451 -2.182 -0.275 ETKDGv3 71
VD3 H273 -9.435 -0.674 -0.435 ETKDGv3 72
#