data_VT6
#
_chem_comp.id VT6
_chem_comp.name "5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 Cl F N2 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 532.631
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VT6
_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 6CTN
_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.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
VT6 O4 O1 O 0 1 N N N 10.721 7.742 10.981 -7.606 -3.011 1.463 O4 VT6 1
VT6 C4 C1 C 0 1 N N N 9.366 7.669 10.712 -6.888 -2.226 0.871 C4 VT6 2
VT6 C5 C2 C 0 1 N N N 8.513 7.237 11.716 -6.686 -2.355 -0.524 C5 VT6 3
VT6 C7 C3 C 0 1 N N N 9.029 6.831 13.095 -7.355 -3.466 -1.293 C7 VT6 4
VT6 C6 C4 C 0 1 N N N 7.168 7.180 11.423 -5.885 -1.471 -1.157 C6 VT6 5
VT6 N3 N1 N 0 1 N N N 8.895 8.013 9.527 -6.283 -1.221 1.536 N3 VT6 6
VT6 C2 C5 C 0 1 N N N 7.597 7.930 9.299 -5.490 -0.353 0.881 C2 VT6 7
VT6 O2 O2 O 0 1 N N N 7.185 8.225 8.227 -4.952 0.548 1.494 O2 VT6 8
VT6 N1 N2 N 0 1 N N N 6.742 7.526 10.229 -5.286 -0.469 -0.444 N1 VT6 9
VT6 "C1'" C6 C 0 1 N N R 5.315 7.420 9.931 -4.417 0.490 -1.131 "C1'" VT6 10
VT6 "C2'" C7 C 0 1 N N N 5.045 6.204 9.582 -4.994 1.918 -1.012 "C2'" VT6 11
VT6 "C3'" C8 C 0 1 N N S 4.512 5.499 10.834 -3.747 2.815 -0.849 "C3'" VT6 12
VT6 "O3'" O3 O 0 1 N N N 3.709 4.415 10.524 -3.654 3.747 -1.928 "O3'" VT6 13
VT6 "O4'" O4 O 0 1 N N N 4.458 7.702 11.246 -3.129 0.558 -0.481 "O4'" VT6 14
VT6 "C4'" C9 C 0 1 N N R 3.739 6.652 11.491 -2.563 1.822 -0.887 "C4'" VT6 15
VT6 "C5'" C10 C 0 1 N N N 3.597 6.431 13.037 -1.471 2.257 0.092 "C5'" VT6 16
VT6 "O5'" O5 O 0 1 N N N 4.866 6.433 13.620 -0.340 1.395 -0.042 "O5'" VT6 17
VT6 PA P1 P 0 1 N N N 5.129 5.224 14.707 0.998 1.560 0.837 PA VT6 18
VT6 O1A O6 O 0 1 N N N 4.063 5.267 15.790 0.661 1.282 2.386 O1A VT6 19
VT6 O2A O7 O 0 1 N N N 6.547 5.312 15.224 1.521 2.937 0.685 O2A VT6 20
VT6 O3A O8 O 0 1 N N N 5.072 3.844 13.846 2.106 0.507 0.332 O3A VT6 21
VT6 PB P2 P 0 1 N N N 4.000 2.621 13.854 3.694 0.359 0.557 PB VT6 22
VT6 O2B O9 O 0 1 N N N 3.982 2.129 12.420 3.974 0.204 2.002 O2B VT6 23
VT6 O1B O10 O 0 1 N N N 2.634 3.038 14.321 4.440 1.673 0.004 O1B VT6 24
VT6 C3B C11 C 0 1 N N S 4.689 1.239 14.896 4.300 -1.108 -0.340 C3B VT6 25
VT6 F3B F1 F 0 1 N N N 4.470 0.021 14.296 3.652 -2.250 0.141 F3B VT6 26
VT6 CL1 CL1 CL 0 0 N N N 6.440 1.452 15.095 3.959 -0.919 -2.100 CL1 VT6 27
VT6 PG P3 P 0 1 N N N 3.906 1.252 16.572 6.098 -1.276 -0.084 PG VT6 28
VT6 O3G O11 O 0 1 N N N 2.624 0.482 16.458 6.378 -1.431 1.361 O3G VT6 29
VT6 O2G O12 O 0 1 N N N 4.892 0.659 17.563 6.634 -2.571 -0.877 O2G VT6 30
VT6 O1G O13 O 0 1 N N N 3.677 2.668 16.996 6.844 0.039 -0.638 O1G VT6 31
VT6 H1 H1 H 0 1 N N N 8.183 6.524 13.728 -7.956 -4.069 -0.612 H1 VT6 32
VT6 H2 H2 H 0 1 N N N 9.732 5.991 12.991 -7.998 -3.038 -2.062 H2 VT6 33
VT6 H3 H3 H 0 1 N N N 9.544 7.685 13.560 -6.596 -4.093 -1.761 H3 VT6 34
VT6 H4 H4 H 0 1 N N N 6.465 6.851 12.174 -5.719 -1.555 -2.221 H4 VT6 35
VT6 H5 H5 H 0 1 N N N 9.515 8.333 8.810 -6.420 -1.123 2.492 H5 VT6 36
VT6 H6 H6 H 0 1 N N N 5.031 8.158 9.166 -4.299 0.212 -2.178 H6 VT6 37
VT6 H7 H7 H 0 1 N N N 4.283 6.197 8.789 -5.541 2.186 -1.917 H7 VT6 38
VT6 H8 H8 H 0 1 N N N 5.955 5.701 9.221 -5.640 1.998 -0.138 H8 VT6 39
VT6 H9 H9 H 0 1 N N N 5.355 5.209 11.479 -3.775 3.338 0.107 H9 VT6 40
VT6 H10 H10 H 0 1 N N N 3.845 3.726 11.164 -4.403 4.356 -1.987 H10 VT6 41
VT6 H11 H11 H 0 1 N N N 2.733 6.710 11.049 -2.161 1.751 -1.898 H11 VT6 42
VT6 H12 H12 H 0 1 N N N 2.992 7.241 13.470 -1.174 3.283 -0.126 H12 VT6 43
VT6 H13 H13 H 0 1 N N N 3.106 5.465 13.227 -1.853 2.199 1.112 H13 VT6 44
VT6 H14 H14 H 0 1 N N N 4.478 5.345 16.641 0.313 0.397 2.560 H14 VT6 45
VT6 H15 H15 H 0 1 N N N 2.007 2.913 13.619 4.300 1.838 -0.939 H15 VT6 46
VT6 H16 H16 H 0 1 N N N 4.518 -0.122 17.954 7.584 -2.722 -0.785 H16 VT6 47
VT6 H17 H17 H 0 1 N N N 2.746 2.817 17.116 6.704 0.203 -1.581 H17 VT6 48
#
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
VT6 O2 C2 DOUB N N 1
VT6 C2 N3 SING N N 2
VT6 C2 N1 SING N N 3
VT6 N3 C4 SING N N 4
VT6 "C2'" "C1'" SING N N 5
VT6 "C2'" "C3'" SING N N 6
VT6 "C1'" N1 SING N N 7
VT6 "C1'" "O4'" SING N N 8
VT6 N1 C6 SING N N 9
VT6 "O3'" "C3'" SING N N 10
VT6 C4 O4 DOUB N N 11
VT6 C4 C5 SING N N 12
VT6 "C3'" "C4'" SING N N 13
VT6 "O4'" "C4'" SING N N 14
VT6 C6 C5 DOUB N N 15
VT6 "C4'" "C5'" SING N N 16
VT6 C5 C7 SING N N 17
VT6 O2B PB DOUB N N 18
VT6 "C5'" "O5'" SING N N 19
VT6 "O5'" PA SING N N 20
VT6 O3A PB SING N N 21
VT6 O3A PA SING N N 22
VT6 PB O1B SING N N 23
VT6 PB C3B SING N N 24
VT6 F3B C3B SING N N 25
VT6 PA O2A DOUB N N 26
VT6 PA O1A SING N N 27
VT6 C3B CL1 SING N N 28
VT6 C3B PG SING N N 29
VT6 O3G PG DOUB N N 30
VT6 PG O1G SING N N 31
VT6 PG O2G SING N N 32
VT6 C7 H1 SING N N 33
VT6 C7 H2 SING N N 34
VT6 C7 H3 SING N N 35
VT6 C6 H4 SING N N 36
VT6 N3 H5 SING N N 37
VT6 "C1'" H6 SING N N 38
VT6 "C2'" H7 SING N N 39
VT6 "C2'" H8 SING N N 40
VT6 "C3'" H9 SING N N 41
VT6 "O3'" H10 SING N N 42
VT6 "C4'" H11 SING N N 43
VT6 "C5'" H12 SING N N 44
VT6 "C5'" H13 SING N N 45
VT6 O1A H14 SING N N 46
VT6 O1B H15 SING N N 47
VT6 O2G H16 SING N N 48
VT6 O1G H17 SING N N 49
#
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
VT6 SMILES ACDLabs 12.01 "O=C1C(C)=CN(C(N1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)(P(O)(O)=O)F)=O"
VT6 InChI InChI 1.03 "InChI=1S/C11H17ClFN2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-31(24,25)28-30(22,23)11(12,13)29(19,20)21/h3,6-8,16H,2,4H2,1H3,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t6-,7+,8+,11+/m0/s1"
VT6 InChIKey InChI 1.03 WBEGMIDCSWALNY-PRKAOEEVSA-N
VT6 SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@](F)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
VT6 SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
VT6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)([C@](F)(P(=O)(O)O)Cl)O)O"
VT6 SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)(P(=O)(O)O)Cl)O)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
VT6 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
VT6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-chloranyl-fluoranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VT6 "Create component" 2018-03-26 RCSB
VT6 "Initial release" 2018-06-20 RCSB
#