data_VDA
#
_chem_comp.id VDA
_chem_comp.name
(1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C28 H46 O5 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"(20S)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-04-09
_chem_comp.pdbx_modified_date 2021-03-13
_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 494.727
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VDA
_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 2ZL9
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
VDA O2 O2 O 0 1 N N N N N N 16.341 8.598 19.342 6.511 1.467 0.718 O2 VDA 1
VDA C1 C1 C 0 1 N N R N N N 14.808 6.038 19.069 5.293 -1.082 0.352 C1 VDA 2
VDA C2 C2 C 0 1 N N N N N N 14.284 7.441 18.444 6.490 -0.628 -0.485 C2 VDA 3
VDA C3 C3 C 0 1 N N R N N N 14.911 8.713 19.348 6.500 0.897 -0.592 C3 VDA 4
VDA C4 C4 C 0 1 N N N N N N 14.394 8.548 20.899 5.247 1.363 -1.342 C4 VDA 5
VDA C5 C5 C 0 1 N N N N N N 14.551 7.136 21.544 4.031 0.795 -0.645 C5 VDA 6
VDA C6 C6 C 0 1 N N N N N N 14.434 6.930 22.870 3.020 1.581 -0.291 C6 VDA 7
VDA C7 C7 C 0 1 N N N N N N 14.950 5.820 23.721 1.791 0.993 0.266 C7 VDA 8
VDA C8 C8 C 0 1 N N N N N N 14.727 5.701 24.946 0.743 1.768 0.525 C8 VDA 9
VDA C9 C9 C 0 1 N N N N N N 14.513 6.971 26.034 0.742 3.271 0.271 C9 VDA 10
VDA C10 C10 C 0 1 N N N N N N 14.254 5.919 20.542 3.995 -0.690 -0.362 C10 VDA 11
VDA C11 C11 C 0 1 N N N N N N 13.256 6.821 27.019 -0.475 3.687 -0.552 C11 VDA 12
VDA C12 C12 C 0 1 N N N N N N 13.092 5.250 27.577 -1.780 3.086 0.001 C12 VDA 13
VDA C13 C13 C 0 1 N N S N N N 13.302 4.041 26.408 -1.613 1.595 0.024 C13 VDA 14
VDA C14 C14 C 0 1 N N S N N N 14.728 4.352 25.728 -0.544 1.235 1.087 C14 VDA 15
VDA C15 C15 C 0 1 N N N N N N 15.217 2.898 25.026 -0.741 -0.283 1.082 C15 VDA 16
VDA C16 C16 C 0 1 N N N N N N 14.366 1.844 25.787 -2.246 -0.419 0.870 C16 VDA 17
VDA C17 C17 C 0 1 N N N N N N 13.624 2.598 26.944 -2.730 0.665 0.301 C17 VDA 18
VDA C18 C18 C 0 1 N N N N N N 11.938 4.196 25.417 -1.029 1.184 -1.329 C18 VDA 19
VDA C20 C20 C 0 1 N N S N N N 12.798 2.164 28.343 -4.181 0.911 -0.027 C20 VDA 20
VDA C21 C21 C 0 1 N N N N N N 13.549 0.791 28.732 -4.731 2.010 0.885 C21 VDA 21
VDA S22 S22 S 0 1 N N N N N N 11.124 2.228 28.324 -5.126 -0.616 0.228 S22 VDA 22
VDA C23 C23 C 0 1 N N N N N N 10.551 1.217 27.346 -6.785 -0.172 -0.355 C23 VDA 23
VDA C25 C25 C 0 1 N N N N N N 9.335 0.372 27.818 -7.718 -1.375 -0.204 C25 VDA 24
VDA O3 O3 O 0 1 N N N N N N 10.242 -0.752 28.394 -7.875 -1.685 1.182 O3 VDA 25
VDA C26 C26 C 0 1 N N N N N N 8.236 0.757 28.508 -9.083 -1.041 -0.809 C26 VDA 26
VDA C27 C27 C 0 1 N N N N N N 9.195 -0.373 26.391 -7.118 -2.580 -0.931 C27 VDA 27
VDA O1 O1 O 0 1 N N N N N N 14.389 4.919 18.298 5.337 -2.500 0.518 O1 VDA 28
VDA O4 O4 O 0 1 N N N N N N 14.625 7.620 17.080 7.699 -1.069 0.137 O4 VDA 29
VDA C30 C30 C 0 1 N N N N N N 13.538 8.121 16.456 8.764 -1.326 -0.780 C30 VDA 30
VDA C31 C31 C 0 1 N N N N N N 14.128 8.244 14.878 10.001 -1.789 -0.007 C31 VDA 31
VDA O5 O5 O 0 1 N N N N N N 13.768 6.985 14.292 9.729 -3.045 0.619 O5 VDA 32
VDA C29 C29 C 0 1 N N N N N N 7.387 1.974 27.706 -9.650 0.208 -0.131 C29 VDA 33
VDA C28 C28 C 0 1 N N N N N N 8.167 -1.624 26.236 -8.052 -3.783 -0.782 C28 VDA 34
VDA HO2 HO2 H 0 1 N N N N N N 16.653 8.573 18.445 6.517 2.434 0.726 HO2 VDA 35
VDA H1 H1 H 0 1 N N N N N N 15.908 6.035 19.062 5.330 -0.600 1.329 H1 VDA 36
VDA H2 H2 H 0 1 N N N N N N 13.185 7.420 18.491 6.419 -1.061 -1.483 H2 VDA 37
VDA H3 H3 H 0 1 N N N N N N 14.592 9.680 18.933 7.389 1.218 -1.135 H3 VDA 38
VDA H4 H4 H 0 1 N N N N N N 14.978 9.251 21.512 5.199 2.452 -1.333 H4 VDA 39
VDA H4A H4A H 0 1 N N N N N N 13.311 8.738 20.869 5.281 1.003 -2.371 H4A VDA 40
VDA H6 H6 H 0 1 N N N N N N 13.878 7.689 23.401 3.100 2.651 -0.411 H6 VDA 41
VDA H7 H7 H 0 1 N N N N N N 15.559 5.065 23.246 1.741 -0.067 0.463 H7 VDA 42
VDA H9 H9 H 0 1 N N N N N N 15.418 7.032 26.656 0.724 3.795 1.227 H9 VDA 43
VDA H9A H9A H 0 1 N N N N N N 14.325 7.869 25.427 1.649 3.543 -0.268 H9A VDA 44
VDA H10 H10 H 0 1 N N N N N N 13.160 5.827 20.466 3.913 -1.240 -1.299 H10 VDA 45
VDA H10A H10A H 0 0 N N N N N N 14.780 5.056 20.976 3.142 -0.920 0.277 H10A VDA 46
VDA H11 H11 H 0 1 N N N N N N 13.400 7.489 27.881 -0.554 4.774 -0.542 H11 VDA 47
VDA H11A H11A H 0 0 N N N N N N 12.346 7.085 26.460 -0.338 3.353 -1.580 H11A VDA 48
VDA H12 H12 H 0 1 N N N N N N 13.852 5.093 28.357 -1.959 3.454 1.011 H12 VDA 49
VDA H12A H12A H 0 0 N N N N N N 12.056 5.157 27.933 -2.615 3.355 -0.646 H12A VDA 50
VDA H14 H14 H 0 1 N N N N N N 15.550 4.614 26.411 -0.770 1.679 2.056 H14 VDA 51
VDA H15 H15 H 0 1 N N N N N N 15.017 2.880 23.945 -0.191 -0.742 0.261 H15 VDA 52
VDA H15A H15A H 0 0 N N N N N N 16.300 2.721 25.108 -0.444 -0.714 2.038 H15A VDA 53
VDA H16 H16 H 0 1 N N N N N N 14.298 0.790 25.561 -2.833 -1.280 1.154 H16 VDA 54
VDA H18 H18 H 0 1 N N N N N N 11.033 4.230 26.041 -0.061 1.666 -1.469 H18 VDA 55
VDA H18A H18A H 0 0 N N N N N N 12.014 5.124 24.831 -0.903 0.102 -1.357 H18A VDA 56
VDA H18B H18B H 0 0 N N N N N N 11.881 3.335 24.735 -1.706 1.492 -2.126 H18B VDA 57
VDA H20 H20 H 0 1 N N N N N N 12.855 2.909 29.151 -4.270 1.224 -1.067 H20 VDA 58
VDA H21 H21 H 0 1 N N N N N N 13.720 0.196 27.823 -4.642 1.696 1.926 H21 VDA 59
VDA H21A H21A H 0 0 N N N N N N 14.515 1.023 29.205 -4.163 2.927 0.732 H21A VDA 60
VDA H21B H21B H 0 0 N N N N N N 12.925 0.218 29.433 -5.780 2.187 0.648 H21B VDA 61
VDA H23 H23 H 0 1 N N N N N N 10.224 1.780 26.459 -7.167 0.661 0.236 H23 VDA 62
VDA H23A H23A H 0 0 N N N N N N 11.359 0.488 27.183 -6.735 0.120 -1.404 H23A VDA 63
VDA HO3 HO3 H 0 1 N N N N N N 10.427 -1.390 27.715 -8.251 -0.964 1.706 HO3 VDA 64
VDA H26 H26 H 0 1 N N N N N N 7.574 -0.113 28.631 -8.970 -0.855 -1.878 H26 VDA 65
VDA H26A H26A H 0 0 N N N N N N 8.563 1.151 29.482 -9.763 -1.879 -0.656 H26A VDA 66
VDA H27 H27 H 0 1 N N N N N N 8.858 0.392 25.676 -6.997 -2.343 -1.988 H27 VDA 67
VDA H27A H27A H 0 0 N N N N N N 10.185 -0.824 26.230 -6.146 -2.818 -0.499 H27A VDA 68
VDA HO1 HO1 H 0 1 N N N N N N 14.296 5.178 17.389 4.606 -2.858 1.040 HO1 VDA 69
VDA H30 H30 H 0 1 N N N N N N 12.663 7.459 16.531 8.461 -2.105 -1.480 H30 VDA 70
VDA H30A H30A H 0 0 N N N N N N 13.162 9.064 16.879 8.999 -0.415 -1.329 H30A VDA 71
VDA H31 H31 H 0 1 N N N N N N 13.670 9.087 14.339 10.839 -1.900 -0.696 H31 VDA 72
VDA H31A H31A H 0 0 N N N N N N 15.210 8.440 14.840 10.252 -1.050 0.754 H31A VDA 73
VDA HO5 HO5 H 0 1 N N N N N N 13.688 7.085 13.351 10.472 -3.399 1.128 HO5 VDA 74
VDA H29 H29 H 0 1 N N N N N N 7.202 2.809 28.397 -9.677 0.054 0.948 H29 VDA 75
VDA H29A H29A H 0 0 N N N N N N 7.979 2.331 26.850 -9.017 1.065 -0.360 H29A VDA 76
VDA H29B H29B H 0 0 N N N N N N 6.426 1.576 27.348 -10.660 0.393 -0.498 H29B VDA 77
VDA H28 H28 H 0 1 N N N N N N 7.935 -1.779 25.172 -8.246 -3.962 0.276 H28 VDA 78
VDA H28A H28A H 0 0 N N N N N N 8.631 -2.533 26.646 -8.992 -3.578 -1.294 H28A VDA 79
VDA H28B H28B H 0 0 N N N N N N 7.239 -1.406 26.785 -7.583 -4.663 -1.220 H28B VDA 80
#
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
VDA O2 C3 SING N N 1
VDA C1 C2 SING N N 2
VDA C1 C10 SING N N 3
VDA C1 O1 SING N N 4
VDA C2 C3 SING N N 5
VDA C2 O4 SING N N 6
VDA C3 C4 SING N N 7
VDA C4 C5 SING N N 8
VDA C5 C6 DOUB N N 9
VDA C5 C10 SING N N 10
VDA C6 C7 SING N N 11
VDA C7 C8 DOUB N N 12
VDA C8 C9 SING N N 13
VDA C8 C14 SING N N 14
VDA C9 C11 SING N N 15
VDA C11 C12 SING N N 16
VDA C12 C13 SING N N 17
VDA C13 C14 SING N N 18
VDA C13 C17 SING N E 19
VDA C13 C18 SING N N 20
VDA C14 C15 SING N N 21
VDA C15 C16 SING N N 22
VDA C16 C17 DOUB N N 23
VDA C17 C20 SING N N 24
VDA C20 C21 SING N N 25
VDA C20 S22 SING N N 26
VDA S22 C23 SING N N 27
VDA C23 C25 SING N N 28
VDA C25 O3 SING N N 29
VDA C25 C26 SING N N 30
VDA C25 C27 SING N N 31
VDA C26 C29 SING N N 32
VDA C27 C28 SING N N 33
VDA O4 C30 SING N N 34
VDA C30 C31 SING N N 35
VDA C31 O5 SING N N 36
VDA O2 HO2 SING N N 37
VDA C1 H1 SING N N 38
VDA C2 H2 SING N N 39
VDA C3 H3 SING N N 40
VDA C4 H4 SING N N 41
VDA C4 H4A SING N N 42
VDA C6 H6 SING N N 43
VDA C7 H7 SING N N 44
VDA C9 H9 SING N N 45
VDA C9 H9A SING N N 46
VDA C10 H10 SING N N 47
VDA C10 H10A SING N N 48
VDA C11 H11 SING N N 49
VDA C11 H11A SING N N 50
VDA C12 H12 SING N N 51
VDA C12 H12A SING N N 52
VDA C14 H14 SING N N 53
VDA C15 H15 SING N N 54
VDA C15 H15A SING N N 55
VDA C16 H16 SING N N 56
VDA C18 H18 SING N N 57
VDA C18 H18A SING N N 58
VDA C18 H18B SING N N 59
VDA C20 H20 SING N N 60
VDA C21 H21 SING N N 61
VDA C21 H21A SING N N 62
VDA C21 H21B SING N N 63
VDA C23 H23 SING N N 64
VDA C23 H23A SING N N 65
VDA O3 HO3 SING N N 66
VDA C26 H26 SING N N 67
VDA C26 H26A SING N N 68
VDA C27 H27 SING N N 69
VDA C27 H27A SING N N 70
VDA O1 HO1 SING N N 71
VDA C30 H30 SING N N 72
VDA C30 H30A SING N N 73
VDA C31 H31 SING N N 74
VDA C31 H31A SING N N 75
VDA O5 HO5 SING N N 76
VDA C29 H29 SING N N 77
VDA C29 H29A SING N N 78
VDA C29 H29B SING N N 79
VDA C28 H28 SING N N 80
VDA C28 H28A SING N N 81
VDA C28 H28B SING N N 82
#
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
VDA SMILES ACDLabs 10.04 O(CCO)C3C(O)C/C(=C/C=C1\CCCC2(C(=CCC12)C(SCC(O)(CC)CC)C)C)CC3O
VDA SMILES_CANONICAL CACTVS 3.341 CCC(O)(CC)CS[C@@H](C)C1=CC[C@H]2C(/CCC[C@]12C)=C/C=C3/C[C@@H](O)[C@@H](OCCO)[C@H](O)C3
VDA SMILES CACTVS 3.341 CCC(O)(CC)CS[CH](C)C1=CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)[CH](OCCO)[CH](O)C3
VDA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CCC(CC)(CS[C@@H](C)C1=CC[C@@H]2[C@@]1(CCCC2=CC=C3C[C@H](C([C@@H](C3)O)OCCO)O)C)O
VDA SMILES "OpenEye OEToolkits" 1.5.0 CCC(CC)(CSC(C)C1=CCC2C1(CCCC2=CC=C3CC(C(C(C3)O)OCCO)O)C)O
VDA InChI InChI 1.03 InChI=1S/C28H46O5S/c1-5-28(32,6-2)18-34-19(3)22-11-12-23-21(8-7-13-27(22,23)4)10-9-20-16-24(30)26(25(31)17-20)33-15-14-29/h9-11,19,23-26,29-32H,5-8,12-18H2,1-4H3/b20-9-,21-10+/t19-,23-,24+,25+,26+,27+/m0/s1
VDA InChIKey InChI 1.03 DUIYWCMQVXJTIP-YYDWSLPPSA-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
VDA "SYSTEMATIC NAME" ACDLabs 10.04 (1R,2S,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol
VDA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (1R,3R)-5-[2-[(3aS,7aS)-1-[(1S)-1-(2-ethyl-2-hydroxy-butyl)sulfanylethyl]-7a-methyl-3a,5,6,7-tetrahydro-3H-inden-4-ylidene]ethylidene]-2-(2-hydroxyethoxy)cyclohexane-1,3-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VDA 'Create component' 2008-04-09 PDBJ
VDA 'Modify descriptor' 2011-06-04 RCSB
VDA 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VDA
_pdbx_chem_comp_synonyms.name
"(20S)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id VDA
_pdbe_chem_comp_synonyms.name
'(20S)-1alpha,25-dihydroxy-2beta-(2-hydroxyethoxy)-16-ene-22-thia-26,27-dimethyl-19,24-dinorvitamin D3'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
VDA O2 O -8.265 1.188 1
VDA C1 C -4.862 3.231 2
VDA C2 C -6.330 2.922 3
VDA C3 C -6.797 1.497 4
VDA C4 C -5.795 0.380 5
VDA C5 C -4.328 0.688 6
VDA C6 C -3.326 -0.429 7
VDA C7 C -1.858 -0.120 8
VDA C8 C -0.857 -1.237 9
VDA C9 C -1.324 -2.663 10
VDA C10 C -3.861 2.114 11
VDA C11 C -0.323 -3.780 12
VDA C12 C 1.145 -3.471 13
VDA C13 C 1.612 -2.045 14
VDA C14 C 0.611 -0.929 15
VDA C15 C 1.364 0.369 16
VDA C16 C 2.830 0.053 17
VDA C17 C 2.984 -1.439 18
VDA C18 C 2.724 -3.051 19
VDA C20 C 4.281 -2.191 20
VDA C21 C 4.277 -3.692 21
VDA S22 S 5.582 -1.444 22
VDA C23 C 6.879 -2.197 23
VDA C25 C 8.180 -1.450 24
VDA O3 O 7.433 -0.149 25
VDA C26 C 8.933 -0.153 26
VDA C27 C 9.477 -2.203 27
VDA O1 O -4.395 4.656 28
VDA O4 O -7.331 4.039 29
VDA C30 C -8.799 3.731 30
VDA C31 C -9.800 4.848 31
VDA O5 O -11.268 4.539 32
VDA C29 C 10.433 -0.156 33
VDA C28 C 10.778 -1.456 34
#
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
VDA C3 O2 SINGLE BEGINWEDGE 1
VDA C1 C2 SINGLE NONE 2
VDA C1 C10 SINGLE NONE 3
VDA C1 O1 SINGLE BEGINDASH 4
VDA C2 C3 SINGLE NONE 5
VDA C2 O4 SINGLE NONE 6
VDA C3 C4 SINGLE NONE 7
VDA C4 C5 SINGLE NONE 8
VDA C5 C6 DOUBLE NONE 9
VDA C5 C10 SINGLE NONE 10
VDA C6 C7 SINGLE ENDUPRIGHT 11
VDA C7 C8 DOUBLE NONE 12
VDA C8 C9 SINGLE ENDDOWNRIGHT 13
VDA C8 C14 SINGLE ENDUPRIGHT 14
VDA C9 C11 SINGLE NONE 15
VDA C11 C12 SINGLE NONE 16
VDA C12 C13 SINGLE NONE 17
VDA C13 C14 SINGLE NONE 18
VDA C13 C17 SINGLE NONE 19
VDA C13 C18 SINGLE BEGINDASH 20
VDA C14 C15 SINGLE NONE 21
VDA C15 C16 SINGLE NONE 22
VDA C16 C17 DOUBLE NONE 23
VDA C17 C20 SINGLE NONE 24
VDA C20 C21 SINGLE BEGINWEDGE 25
VDA C20 S22 SINGLE NONE 26
VDA S22 C23 SINGLE NONE 27
VDA C23 C25 SINGLE NONE 28
VDA C25 O3 SINGLE NONE 29
VDA C25 C26 SINGLE NONE 30
VDA C25 C27 SINGLE NONE 31
VDA C26 C29 SINGLE NONE 32
VDA C27 C28 SINGLE NONE 33
VDA O4 C30 SINGLE NONE 34
VDA C30 C31 SINGLE NONE 35
VDA C31 O5 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
VDA MurckoScaffold S1 scaffold 'C1=CC2CCC/C(=C\C=C3CCCCC3)[C@@H]2C1' InChI=1S/C17H24/c1-2-6-14(7-3-1)12-13-16-9-4-8-15-10-5-11-17(15)16/h5,10,12-13,15,17H,1-4,6-9,11H2/b16-13+/t15-,17-/m1/s1 NRACBJUKLYUIPN-DGOVAZGXSA-N
VDA cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-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
VDA C1 S1 1
VDA C2 S1 1
VDA C3 S1 1
VDA C4 S1 1
VDA C5 S1 1
VDA C6 S1 1
VDA C7 S1 1
VDA C8 S1 1
VDA C9 S1 1
VDA C10 S1 1
VDA C11 S1 1
VDA C12 S1 1
VDA C13 S1 1
VDA C14 S1 1
VDA C15 S1 1
VDA C16 S1 1
VDA C17 S1 1
VDA C1 F1 1
VDA C2 F1 1
VDA C3 F1 1
VDA C4 F1 1
VDA C5 F1 1
VDA C10 F1 1
VDA C8 F1 2
VDA C9 F1 2
VDA C11 F1 2
VDA C12 F1 2
VDA C13 F1 2
VDA C14 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id VDA
_pdbe_chem_comp_rdkit_properties.exactmw 494.307
_pdbe_chem_comp_rdkit_properties.amw 494.738
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 18
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 34
_pdbe_chem_comp_rdkit_properties.NumAtoms 80
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.786
_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 2
_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 274.895
_pdbe_chem_comp_rdkit_properties.tpsa 90.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.542
_pdbe_chem_comp_rdkit_properties.CrippenMR 139.839
_pdbe_chem_comp_rdkit_properties.chi0v 17.266
_pdbe_chem_comp_rdkit_properties.chi1v 9.449
_pdbe_chem_comp_rdkit_properties.chi2v 4.820
_pdbe_chem_comp_rdkit_properties.chi3v 4.820
_pdbe_chem_comp_rdkit_properties.chi4v 3.121
_pdbe_chem_comp_rdkit_properties.chi0n 62.449
_pdbe_chem_comp_rdkit_properties.chi1n 31.266
_pdbe_chem_comp_rdkit_properties.chi2n 4.023
_pdbe_chem_comp_rdkit_properties.chi3n 4.023
_pdbe_chem_comp_rdkit_properties.chi4n 2.467
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.630
_pdbe_chem_comp_rdkit_properties.kappa1 5.281
_pdbe_chem_comp_rdkit_properties.kappa2 12.071
_pdbe_chem_comp_rdkit_properties.kappa3 6.190
_pdbe_chem_comp_rdkit_properties.Phi 1.875
#
#
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
VDA O2 5.725 0.522 3.316 ETKDGv3 1
VDA C1 6.864 -1.053 1.088 ETKDGv3 2
VDA C2 6.921 0.495 1.216 ETKDGv3 3
VDA C3 5.729 1.056 2.015 ETKDGv3 4
VDA C4 4.412 0.731 1.287 ETKDGv3 5
VDA C5 4.349 -0.708 0.819 ETKDGv3 6
VDA C6 3.312 -1.179 0.097 ETKDGv3 7
VDA C7 2.160 -0.346 -0.329 ETKDGv3 8
VDA C8 1.175 -0.799 -1.127 ETKDGv3 9
VDA C9 1.187 -2.191 -1.749 ETKDGv3 10
VDA C10 5.445 -1.656 1.250 ETKDGv3 11
VDA C11 0.090 -2.394 -2.835 ETKDGv3 12
VDA C12 -1.324 -1.821 -2.502 ETKDGv3 13
VDA C13 -1.300 -0.745 -1.387 ETKDGv3 14
VDA C14 0.001 0.062 -1.512 ETKDGv3 15
VDA C15 -0.310 1.391 -0.821 ETKDGv3 16
VDA C16 -1.770 1.530 -1.128 ETKDGv3 17
VDA C17 -2.313 0.362 -1.499 ETKDGv3 18
VDA C18 -1.493 -1.409 0.006 ETKDGv3 19
VDA C20 -3.781 0.156 -1.791 ETKDGv3 20
VDA C21 -4.203 0.954 -3.025 ETKDGv3 21
VDA S22 -4.775 0.661 -0.336 ETKDGv3 22
VDA C23 -6.121 -0.566 -0.573 ETKDGv3 23
VDA C25 -7.334 -0.395 0.392 ETKDGv3 24
VDA O3 -8.103 -1.576 0.312 ETKDGv3 25
VDA C26 -6.856 -0.207 1.868 ETKDGv3 26
VDA C27 -8.274 0.753 -0.086 ETKDGv3 27
VDA O1 7.400 -1.424 -0.158 ETKDGv3 28
VDA O4 8.137 0.855 1.855 ETKDGv3 29
VDA C30 8.696 2.033 1.302 ETKDGv3 30
VDA C31 9.645 1.684 0.154 ETKDGv3 31
VDA O5 10.279 2.841 -0.321 ETKDGv3 32
VDA C29 -7.995 -0.185 2.890 ETKDGv3 33
VDA C28 -7.704 2.173 -0.047 ETKDGv3 34
VDA HO2 5.126 1.097 3.860 ETKDGv3 35
VDA H1 7.497 -1.490 1.898 ETKDGv3 36
VDA H2 6.847 0.910 0.179 ETKDGv3 37
VDA H3 5.832 2.165 2.074 ETKDGv3 38
VDA H4 3.552 0.948 1.958 ETKDGv3 39
VDA H4A 4.338 1.399 0.400 ETKDGv3 40
VDA H6 3.315 -2.226 -0.175 ETKDGv3 41
VDA H7 2.104 0.673 0.027 ETKDGv3 42
VDA H9 1.066 -2.956 -0.954 ETKDGv3 43
VDA H9A 2.172 -2.366 -2.236 ETKDGv3 44
VDA H10 5.276 -1.897 2.322 ETKDGv3 45
VDA H10A 5.391 -2.624 0.704 ETKDGv3 46
VDA H11 0.002 -3.478 -3.063 ETKDGv3 47
VDA H11A 0.447 -1.905 -3.768 ETKDGv3 48
VDA H12 -2.002 -2.655 -2.216 ETKDGv3 49
VDA H12A -1.747 -1.382 -3.433 ETKDGv3 50
VDA H14 0.162 0.325 -2.586 ETKDGv3 51
VDA H15 0.274 2.228 -1.259 ETKDGv3 52
VDA H15A -0.162 1.337 0.279 ETKDGv3 53
VDA H16 -2.327 2.456 -1.025 ETKDGv3 54
VDA H18 -0.785 -2.242 0.175 ETKDGv3 55
VDA H18A -2.519 -1.828 0.089 ETKDGv3 56
VDA H18B -1.360 -0.674 0.828 ETKDGv3 57
VDA H20 -3.948 -0.922 -1.999 ETKDGv3 58
VDA H21 -5.265 0.746 -3.272 ETKDGv3 59
VDA H21A -4.089 2.044 -2.847 ETKDGv3 60
VDA H21B -3.580 0.663 -3.898 ETKDGv3 61
VDA H23 -6.477 -0.532 -1.624 ETKDGv3 62
VDA H23A -5.668 -1.568 -0.415 ETKDGv3 63
VDA HO3 -7.562 -2.332 0.664 ETKDGv3 64
VDA H26 -6.175 -1.045 2.135 ETKDGv3 65
VDA H26A -6.267 0.724 1.989 ETKDGv3 66
VDA H27 -8.596 0.544 -1.130 ETKDGv3 67
VDA H27A -9.205 0.739 0.520 ETKDGv3 68
VDA HO1 7.692 -2.370 -0.080 ETKDGv3 69
VDA H30 7.926 2.767 0.967 ETKDGv3 70
VDA H30A 9.283 2.537 2.099 ETKDGv3 71
VDA H31 10.421 0.981 0.523 ETKDGv3 72
VDA H31A 9.093 1.181 -0.671 ETKDGv3 73
VDA HO5 9.610 3.326 -0.871 ETKDGv3 74
VDA H29 -8.614 0.728 2.769 ETKDGv3 75
VDA H29A -7.568 -0.173 3.915 ETKDGv3 76
VDA H29B -8.636 -1.086 2.791 ETKDGv3 77
VDA H28 -6.916 2.304 -0.815 ETKDGv3 78
VDA H28A -8.515 2.893 -0.285 ETKDGv3 79
VDA H28B -7.312 2.432 0.957 ETKDGv3 80
#