data_VT7
#
_chem_comp.id VT7
_chem_comp.name "5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 F2 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 516.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VT7
_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 6CTO
_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
VT7 O4 O1 O 0 1 N N N 10.876 7.731 10.924 -7.478 -3.049 1.385 O4 VT7 1
VT7 C4 C1 C 0 1 N N N 9.480 7.683 10.641 -6.765 -2.247 0.810 C4 VT7 2
VT7 C5 C2 C 0 1 N N N 8.620 7.214 11.641 -6.584 -2.326 -0.592 C5 VT7 3
VT7 C5M C3 C 0 1 N N N 9.112 6.772 13.000 -7.272 -3.403 -1.390 C5M VT7 4
VT7 C6 C4 C 0 1 N N N 7.252 7.171 11.330 -5.789 -1.423 -1.204 C6 VT7 5
VT7 N3 N1 N 0 1 N N N 8.990 8.052 9.450 -6.144 -1.270 1.503 N3 VT7 6
VT7 C2 C5 C 0 1 N N N 7.681 7.980 9.229 -5.356 -0.383 0.868 C2 VT7 7
VT7 O2 O2 O 0 1 N N N 7.259 8.295 8.146 -4.803 0.492 1.505 O2 VT7 8
VT7 N1 N2 N 0 1 N N N 6.817 7.558 10.146 -5.172 -0.451 -0.463 N1 VT7 9
VT7 "C1'" C6 C 0 1 N N R 5.397 7.438 9.854 -4.309 0.529 -1.128 "C1'" VT7 10
VT7 "C2'" C7 C 0 1 N N N 5.136 6.214 9.530 -4.876 1.955 -0.947 "C2'" VT7 11
VT7 "C3'" C8 C 0 1 N N S 4.522 5.557 10.777 -3.621 2.838 -0.770 "C3'" VT7 12
VT7 "O3'" O3 O 0 1 N N N 3.724 4.459 10.547 -3.540 3.809 -1.816 "O3'" VT7 13
VT7 "O4'" O4 O 0 1 N N N 4.535 7.748 11.179 -3.011 0.566 -0.495 "O4'" VT7 14
VT7 "C4'" C9 C 0 1 N N R 3.757 6.744 11.398 -2.444 1.842 -0.864 "C4'" VT7 15
VT7 "C5'" C10 C 0 1 N N N 3.543 6.496 12.940 -1.335 2.234 0.114 "C5'" VT7 16
VT7 "O5'" O5 O 0 1 N N N 4.850 6.410 13.589 -0.211 1.372 -0.070 "O5'" VT7 17
VT7 PA P1 P 0 1 N N N 5.092 5.241 14.671 1.142 1.498 0.794 PA VT7 18
VT7 O1A O6 O 0 1 N N N 3.993 5.270 15.712 0.826 1.164 2.337 O1A VT7 19
VT7 O2A O7 O 0 1 N N N 6.453 5.424 15.313 1.670 2.876 0.686 O2A VT7 20
VT7 O3A O8 O 0 1 N N N 5.165 3.865 13.928 2.236 0.458 0.233 O3A VT7 21
VT7 PB P2 P 0 1 N N N 4.089 2.682 13.830 3.826 0.293 0.429 PB VT7 22
VT7 O2B O9 O 0 1 N N N 4.044 2.275 12.369 4.127 0.084 1.862 O2B VT7 23
VT7 O1B O10 O 0 1 N N N 2.685 3.142 14.221 4.570 1.624 -0.087 O1B VT7 24
VT7 C3B C11 C 0 1 N N N 4.735 1.242 14.796 4.410 -1.142 -0.532 C3B VT7 25
VT7 PG P3 P 0 1 N N N 3.848 1.225 16.415 6.210 -1.328 -0.310 PG VT7 26
VT7 O3G O11 O 0 1 N N N 2.445 0.773 16.194 6.512 -1.538 1.123 O3G VT7 27
VT7 O2G O12 O 0 1 N N N 4.498 0.299 17.342 6.727 -2.595 -1.158 O2G VT7 28
VT7 O1G O13 O 0 1 N N N 3.848 2.656 16.890 6.955 0.002 -0.826 O1G VT7 29
VT7 F2B F1 F 0 1 N N N 6.091 1.323 14.908 3.763 -2.298 -0.083 F2B VT7 30
VT7 F3B F2 F 0 1 N N N 4.393 0.090 14.185 4.125 -0.943 -1.887 F3B VT7 31
VT7 H1 H1 H 0 1 N N N 8.258 6.446 13.612 -7.865 -4.028 -0.722 H1 VT7 32
VT7 H2 H2 H 0 1 N N N 9.817 5.936 12.881 -7.924 -2.944 -2.133 H2 VT7 33
VT7 H3 H3 H 0 1 N N N 9.620 7.612 13.497 -6.524 -4.016 -1.893 H3 VT7 34
VT7 H4 H4 H 0 1 N N N 6.548 6.817 12.068 -5.639 -1.468 -2.272 H4 VT7 35
VT7 H5 H5 H 0 1 N N N 9.605 8.379 8.732 -6.265 -1.207 2.464 H5 VT7 36
VT7 H6 H6 H 0 1 N N N 5.105 8.159 9.077 -4.209 0.290 -2.186 H6 VT7 37
VT7 H7 H7 H 0 1 N N N 4.421 6.186 8.694 -5.435 2.258 -1.833 H7 VT7 38
VT7 H8 H8 H 0 1 N N N 6.060 5.692 9.241 -5.508 2.005 -0.060 H8 VT7 39
VT7 H9 H9 H 0 1 N N N 5.343 5.291 11.459 -3.632 3.326 0.205 H9 VT7 40
VT7 H10 H10 H 0 1 N N N 3.904 3.794 11.201 -4.286 4.423 -1.840 H10 VT7 41
VT7 H11 H11 H 0 1 N N N 2.775 6.839 10.912 -2.058 1.806 -1.882 H11 VT7 42
VT7 H12 H12 H 0 1 N N N 2.970 7.329 13.372 -1.036 3.266 -0.071 H12 VT7 43
VT7 H13 H13 H 0 1 N N N 2.993 5.555 13.090 -1.702 2.140 1.136 H13 VT7 44
VT7 H14 H14 H 0 1 N N N 4.375 5.398 16.572 0.476 0.275 2.484 H14 VT7 45
VT7 H15 H15 H 0 1 N N N 2.107 3.070 13.470 4.417 1.824 -1.021 H15 VT7 46
VT7 H16 H16 H 0 1 N N N 3.884 -0.380 17.595 7.678 -2.755 -1.087 H16 VT7 47
VT7 H17 H17 H 0 1 N N N 2.954 2.970 16.949 6.802 0.202 -1.760 H17 VT7 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
VT7 O2 C2 DOUB N N 1
VT7 C2 N3 SING N N 2
VT7 C2 N1 SING N N 3
VT7 N3 C4 SING N N 4
VT7 "C2'" "C1'" SING N N 5
VT7 "C2'" "C3'" SING N N 6
VT7 "C1'" N1 SING N N 7
VT7 "C1'" "O4'" SING N N 8
VT7 N1 C6 SING N N 9
VT7 "O3'" "C3'" SING N N 10
VT7 C4 O4 DOUB N N 11
VT7 C4 C5 SING N N 12
VT7 "C3'" "C4'" SING N N 13
VT7 "O4'" "C4'" SING N N 14
VT7 C6 C5 DOUB N N 15
VT7 "C4'" "C5'" SING N N 16
VT7 C5 C5M SING N N 17
VT7 O2B PB DOUB N N 18
VT7 "C5'" "O5'" SING N N 19
VT7 "O5'" PA SING N N 20
VT7 PB O3A SING N N 21
VT7 PB O1B SING N N 22
VT7 PB C3B SING N N 23
VT7 O3A PA SING N N 24
VT7 F3B C3B SING N N 25
VT7 PA O2A DOUB N N 26
VT7 PA O1A SING N N 27
VT7 C3B F2B SING N N 28
VT7 C3B PG SING N N 29
VT7 O3G PG DOUB N N 30
VT7 PG O1G SING N N 31
VT7 PG O2G SING N N 32
VT7 C5M H1 SING N N 33
VT7 C5M H2 SING N N 34
VT7 C5M H3 SING N N 35
VT7 C6 H4 SING N N 36
VT7 N3 H5 SING N N 37
VT7 "C1'" H6 SING N N 38
VT7 "C2'" H7 SING N N 39
VT7 "C2'" H8 SING N N 40
VT7 "C3'" H9 SING N N 41
VT7 "O3'" H10 SING N N 42
VT7 "C4'" H11 SING N N 43
VT7 "C5'" H12 SING N N 44
VT7 "C5'" H13 SING N N 45
VT7 O1A H14 SING N N 46
VT7 O1B H15 SING N N 47
VT7 O2G H16 SING N N 48
VT7 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
VT7 SMILES ACDLabs 12.01 "O=C1C(C)=CN(C(N1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(F)(P(O)(O)=O)F)=O"
VT7 InChI InChI 1.03 "InChI=1S/C11H17F2N2O13P3/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+/m0/s1"
VT7 InChIKey InChI 1.03 PZJVGXNXDJKXPK-XLPZGREQSA-N
VT7 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)(F)[P](O)(O)=O)O2)C(=O)NC1=O"
VT7 SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O"
VT7 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)(F)P(=O)(O)O)O)O"
VT7 SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)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
VT7 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
VT7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[bis(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
VT7 "Create component" 2018-03-26 RCSB
VT7 "Initial release" 2018-06-20 RCSB
#