data_VA7
#
_chem_comp.id VA7
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 Cl2 N5 O11 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-22
_chem_comp.pdbx_modified_date 2018-07-20
_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 558.099
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VA7
_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 6CRC
_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
VA7 N1 N1 N 0 1 Y N N 68.034 8.099 7.531 -8.458 -2.309 -0.709 N1 VA7 1
VA7 C2 C1 C 0 1 Y N N 66.870 7.813 6.961 -7.975 -1.574 -1.694 C2 VA7 2
VA7 N3 N2 N 0 1 Y N N 65.870 7.317 7.653 -6.894 -0.834 -1.559 N3 VA7 3
VA7 C4 C2 C 0 1 Y N N 66.006 7.082 8.994 -6.237 -0.799 -0.404 C4 VA7 4
VA7 C5 C3 C 0 1 Y N N 67.212 7.363 9.666 -6.711 -1.564 0.675 C5 VA7 5
VA7 C6 C4 C 0 1 Y N N 68.261 7.893 8.861 -7.868 -2.338 0.482 C6 VA7 6
VA7 N6 N3 N 0 1 N N N 69.552 8.224 9.435 -8.382 -3.111 1.508 N6 VA7 7
VA7 N7 N4 N 0 1 Y N N 67.022 7.024 10.981 -5.871 -1.350 1.716 N7 VA7 8
VA7 C8 C5 C 0 1 Y N N 65.765 6.559 11.131 -4.933 -0.523 1.353 C8 VA7 9
VA7 N9 N5 N 0 1 Y N N 65.153 6.590 9.943 -5.116 -0.154 0.053 N9 VA7 10
VA7 PA P1 P 0 1 N N N 63.971 4.016 14.306 1.285 1.744 0.878 PA VA7 11
VA7 PB P2 P 0 1 N N N 63.496 1.308 13.514 3.926 0.464 0.467 PB VA7 12
VA7 PG P3 P 0 1 N N N 63.455 -0.145 16.143 6.244 -1.251 -0.275 PG VA7 13
VA7 "C1'" C6 C 0 1 N N R 63.805 6.168 9.647 -4.269 0.762 -0.715 "C1'" VA7 14
VA7 O1A O1 O 0 1 N N N 62.926 3.842 15.396 1.039 1.518 2.454 O1A VA7 15
VA7 O2B O2 O 0 1 N N N 63.484 0.684 12.154 4.294 0.342 1.896 O2B VA7 16
VA7 O1G O3 O 0 1 N N N 63.503 1.072 17.049 6.644 -1.383 1.279 O1G VA7 17
VA7 "C2'" C7 C 0 1 N N N 63.820 4.942 9.317 -4.802 2.208 -0.603 "C2'" VA7 18
VA7 O2A O4 O 0 1 N N N 65.294 4.414 14.938 1.831 3.101 0.654 O2A VA7 19
VA7 O1B O5 O 0 1 N N N 62.085 1.435 14.024 4.668 1.742 -0.171 O1B VA7 20
VA7 O2G O6 O 0 1 N N N 64.163 -1.350 16.706 6.697 -2.581 -1.061 O2G VA7 21
VA7 "C3'" C8 C 0 1 N N S 63.480 4.209 10.576 -3.525 3.076 -0.544 "C3'" VA7 22
VA7 "O3'" O7 O 0 1 N N N 63.021 2.937 10.314 -3.478 3.974 -1.654 "O3'" VA7 23
VA7 O3A O8 O 0 1 N N N 64.190 2.716 13.391 2.332 0.648 0.336 O3A VA7 24
VA7 C3B C9 C 0 1 N N N 64.441 0.271 14.672 4.439 -1.043 -0.423 C3B VA7 25
VA7 CL1 CL1 CL 0 0 N N N 64.897 -1.279 13.965 3.609 -2.474 0.292 CL1B VA7 26
VA7 CL2 CL2 CL 0 0 N N N 65.799 1.167 15.300 3.992 -0.894 -2.163 CL2B VA7 27
VA7 O3G O9 O 0 1 N N N 62.016 -0.540 15.802 6.926 -0.075 -0.861 O3G VA7 28
VA7 "C4'" C10 C 0 1 N N R 62.413 5.160 11.172 -2.371 2.052 -0.627 "C4'" VA7 29
VA7 "O4'" O10 O 0 1 N N N 62.896 6.295 10.968 -2.941 0.814 -0.148 "O4'" VA7 30
VA7 "C5'" C11 C 0 1 N N N 62.202 4.962 12.708 -1.209 2.484 0.269 "C5'" VA7 31
VA7 "O5'" O11 O 0 1 N N N 63.479 5.136 13.307 -0.110 1.589 0.090 "O5'" VA7 32
VA7 H1 H1 H 0 1 N N N 66.742 7.992 5.904 -8.485 -1.580 -2.645 H1 VA7 33
VA7 H2 H2 H 0 1 N N N 70.151 8.588 8.722 -9.181 -3.641 1.362 H2 VA7 34
VA7 H3 H3 H 0 1 N N N 69.432 8.911 10.152 -7.943 -3.124 2.373 H3 VA7 35
VA7 H4 H4 H 0 1 N N N 65.326 6.218 12.057 -4.130 -0.180 1.988 H4 VA7 36
VA7 H5 H5 H 0 1 N N N 63.368 6.815 8.872 -4.225 0.452 -1.758 H5 VA7 37
VA7 H6 H6 H 0 1 N N N 63.319 4.018 16.243 0.681 0.647 2.675 H6 VA7 38
VA7 H7 H7 H 0 1 N N N 62.618 1.363 17.236 6.232 -2.134 1.729 H7 VA7 39
VA7 H8 H8 H 0 1 N N N 63.072 4.741 8.536 -5.398 2.464 -1.479 H8 VA7 40
VA7 H9 H9 H 0 1 N N N 64.816 4.650 8.954 -5.389 2.329 0.308 H9 VA7 41
VA7 H10 H10 H 0 1 N N N 61.481 1.092 13.375 4.473 1.884 -1.107 H10 VA7 42
VA7 H11 H11 H 0 1 N N N 63.565 -2.088 16.726 7.648 -2.755 -1.024 H11 VA7 43
VA7 H12 H12 H 0 1 N N N 64.355 4.191 11.242 -3.480 3.626 0.396 H12 VA7 44
VA7 H13 H13 H 0 1 N N N 63.271 2.357 11.024 -4.214 4.600 -1.684 H13 VA7 45
VA7 H14 H14 H 0 1 N N N 61.455 4.988 10.659 -2.034 1.942 -1.658 H14 VA7 46
VA7 H15 H15 H 0 1 N N N 61.494 5.709 13.095 -0.902 3.495 0.002 H15 VA7 47
VA7 H16 H16 H 0 1 N N N 61.818 3.952 12.914 -1.528 2.465 1.312 H16 VA7 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
VA7 C2 N1 DOUB Y N 1
VA7 C2 N3 SING Y N 2
VA7 N1 C6 SING Y N 3
VA7 N3 C4 DOUB Y N 4
VA7 C6 N6 SING N N 5
VA7 C6 C5 DOUB Y N 6
VA7 C4 C5 SING Y N 7
VA7 C4 N9 SING Y N 8
VA7 "C2'" "C1'" SING N N 9
VA7 "C2'" "C3'" SING N N 10
VA7 "C1'" N9 SING N N 11
VA7 "C1'" "O4'" SING N N 12
VA7 C5 N7 SING Y N 13
VA7 N9 C8 SING Y N 14
VA7 "O3'" "C3'" SING N N 15
VA7 "C3'" "C4'" SING N N 16
VA7 "O4'" "C4'" SING N N 17
VA7 N7 C8 DOUB Y N 18
VA7 "C4'" "C5'" SING N N 19
VA7 O2B PB DOUB N N 20
VA7 "C5'" "O5'" SING N N 21
VA7 "O5'" PA SING N N 22
VA7 O3A PB SING N N 23
VA7 O3A PA SING N N 24
VA7 PB O1B SING N N 25
VA7 PB C3B SING N N 26
VA7 CL1 C3B SING N N 27
VA7 PA O2A DOUB N N 28
VA7 PA O1A SING N N 29
VA7 C3B CL2 SING N N 30
VA7 C3B PG SING N N 31
VA7 O3G PG DOUB N N 32
VA7 PG O2G SING N N 33
VA7 PG O1G SING N N 34
VA7 C2 H1 SING N N 35
VA7 N6 H2 SING N N 36
VA7 N6 H3 SING N N 37
VA7 C8 H4 SING N N 38
VA7 "C1'" H5 SING N N 39
VA7 O1A H6 SING N N 40
VA7 O1G H7 SING N N 41
VA7 "C2'" H8 SING N N 42
VA7 "C2'" H9 SING N N 43
VA7 O1B H10 SING N N 44
VA7 O2G H11 SING N N 45
VA7 "C3'" H12 SING N N 46
VA7 "O3'" H13 SING N N 47
VA7 "C4'" H14 SING N N 48
VA7 "C5'" H15 SING N N 49
VA7 "C5'" H16 SING N N 50
#
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
VA7 SMILES ACDLabs 12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)(Cl)Cl)=O)N"
VA7 InChI InChI 1.03 "InChI=1S/C11H16Cl2N5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6+,7+/m0/s1"
VA7 InChIKey InChI 1.03 AQFODBPFKZIBHW-RRKCRQDMSA-N
VA7 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O3"
VA7 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O3"
VA7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O)N"
VA7 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O)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
VA7 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine"
VA7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(chloranyl)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
VA7 "Create component" 2018-03-22 RCSB
VA7 "Initial release" 2018-07-25 RCSB
#