data_VQV
#
_chem_comp.id VQV
_chem_comp.name "1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H14 N2 O12 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-08
_chem_comp.pdbx_modified_date 2020-09-18
_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 404.161
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VQV
_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 7K1O
_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
VQV O2 O1 O 0 1 N N N 33.757 1.712 -19.237 -4.037 -0.580 -2.179 O2 VQV 1
VQV N1 N1 N 0 1 N N N 34.996 2.101 -21.070 -2.753 -0.073 -0.448 N1 VQV 2
VQV C4 C1 C 0 1 N N N 35.791 -0.515 -20.976 -4.765 -0.930 1.165 C4 VQV 3
VQV C2 C2 C 0 1 N N N 34.548 1.280 -20.104 -3.901 -0.541 -0.971 C2 VQV 4
VQV C6 C3 C 0 1 N N N 35.840 1.641 -22.004 -2.576 -0.018 0.907 C6 VQV 5
VQV C5 C4 C 0 1 N N N 36.262 0.317 -21.980 -3.562 -0.439 1.728 C5 VQV 6
VQV "C1'" C5 C 0 1 N N R 34.558 3.507 -21.113 -1.681 0.378 -1.339 "C1'" VQV 7
VQV "C2'" C6 C 0 1 N N S 35.332 4.389 -20.131 -1.137 1.748 -0.875 "C2'" VQV 8
VQV "C3'" C7 C 0 1 N N S 35.578 5.676 -20.888 0.084 1.389 0.002 "C3'" VQV 9
VQV "C4'" C8 C 0 1 N N S 35.628 5.199 -22.328 0.132 -0.154 -0.035 "C4'" VQV 10
VQV "C5'" C9 C 0 1 N N N 35.210 6.258 -23.332 1.583 -0.641 -0.068 "C5'" VQV 11
VQV N3 N2 N 0 1 N N N 34.939 -0.017 -20.053 -4.900 -0.967 -0.176 N3 VQV 12
VQV O1P O2 O 0 1 N N N 37.487 4.116 -24.712 2.623 -4.492 -0.017 O1P VQV 13
VQV "O2'" O3 O 0 1 N N N 36.609 3.805 -19.844 -2.120 2.443 -0.106 "O2'" VQV 14
VQV O2A O4 O 0 1 N N N 33.467 8.200 -19.054 2.870 2.217 1.522 O2A VQV 15
VQV O2B O5 O 0 1 N N N 34.680 9.072 -21.011 1.426 4.121 0.711 O2B VQV 16
VQV O2C O6 O 0 1 N N N 35.940 7.998 -19.177 3.404 3.481 -0.721 O2C VQV 17
VQV O2P O7 O 0 1 N N N 37.971 6.488 -24.257 3.826 -2.582 1.330 O2P VQV 18
VQV "O3'" O8 O 0 1 N N N 34.479 6.558 -20.688 1.279 1.941 -0.553 "O3'" VQV 19
VQV O3P O9 O 0 1 N N N 37.236 5.785 -26.520 3.766 -2.574 -1.193 O3P VQV 20
VQV O4 O10 O 0 1 N N N 36.187 -1.818 -20.925 -5.668 -1.314 1.885 O4 VQV 21
VQV "O4'" O11 O 0 1 N N N 34.759 4.068 -22.417 -0.549 -0.516 -1.256 "O4'" VQV 22
VQV "O5'" O12 O 0 1 N N N 35.556 5.792 -24.632 1.609 -2.067 0.015 "O5'" VQV 23
VQV P P1 P 0 1 N N N 37.096 5.535 -25.037 2.974 -2.921 0.007 P VQV 24
VQV P2 P2 P 0 1 N N N 34.650 7.988 -19.965 2.227 2.966 0.250 P2 VQV 25
VQV H1 H1 H 0 1 N N N 36.194 2.303 -22.780 -1.651 0.359 1.319 H1 VQV 26
VQV H2 H2 H 0 1 N N N 36.944 -0.057 -22.729 -3.435 -0.401 2.800 H2 VQV 27
VQV H3 H3 H 0 1 N N N 33.490 3.557 -20.852 -2.042 0.441 -2.365 H3 VQV 28
VQV H4 H4 H 0 1 N N N 34.742 4.572 -19.221 -0.830 2.347 -1.733 H4 VQV 29
VQV H5 H5 H 0 1 N N N 36.536 6.129 -20.592 -0.062 1.744 1.022 H5 VQV 30
VQV H6 H6 H 0 1 N N N 36.659 4.891 -22.557 -0.387 -0.571 0.827 H6 VQV 31
VQV H7 H7 H 0 1 N N N 35.736 7.201 -23.121 2.052 -0.323 -1.000 H7 VQV 32
VQV H8 H8 H 0 1 N N N 34.124 6.422 -23.271 2.127 -0.218 0.776 H8 VQV 33
VQV H9 H9 H 0 1 N N N 34.594 -0.610 -19.326 -5.721 -1.301 -0.570 H9 VQV 34
VQV H10 H10 H 0 1 N N N 37.743 3.667 -25.509 3.400 -5.069 -0.023 H10 VQV 35
VQV H11 H11 H 0 1 N N N 37.081 4.359 -19.234 -2.932 2.639 -0.591 H11 VQV 36
VQV H12 H12 H 0 1 N N N 32.988 8.973 -19.330 3.410 1.447 1.294 H12 VQV 37
VQV H13 H13 H 0 1 N N N 36.506 8.687 -19.504 4.015 4.103 -0.303 H13 VQV 38
VQV H14 H14 H 0 1 N N N 38.436 7.056 -24.859 3.367 -2.785 2.157 H14 VQV 39
# #
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
VQV O3P P DOUB N N 1
VQV P O1P SING N N 2
VQV P "O5'" SING N N 3
VQV P O2P SING N N 4
VQV "O5'" "C5'" SING N N 5
VQV "C5'" "C4'" SING N N 6
VQV "O4'" "C4'" SING N N 7
VQV "O4'" "C1'" SING N N 8
VQV "C4'" "C3'" SING N N 9
VQV C6 C5 DOUB N N 10
VQV C6 N1 SING N N 11
VQV C5 C4 SING N N 12
VQV "C1'" N1 SING N N 13
VQV "C1'" "C2'" SING N N 14
VQV N1 C2 SING N N 15
VQV O2B P2 DOUB N N 16
VQV C4 O4 DOUB N N 17
VQV C4 N3 SING N N 18
VQV "C3'" "O3'" SING N N 19
VQV "C3'" "C2'" SING N N 20
VQV "O3'" P2 SING N N 21
VQV "C2'" "O2'" SING N N 22
VQV C2 N3 SING N N 23
VQV C2 O2 DOUB N N 24
VQV P2 O2C SING N N 25
VQV P2 O2A SING N N 26
VQV C6 H1 SING N N 27
VQV C5 H2 SING N N 28
VQV "C1'" H3 SING N N 29
VQV "C2'" H4 SING N N 30
VQV "C3'" H5 SING N N 31
VQV "C4'" H6 SING N N 32
VQV "C5'" H7 SING N N 33
VQV "C5'" H8 SING N N 34
VQV N3 H9 SING N N 35
VQV O1P H10 SING N N 36
VQV "O2'" H11 SING N N 37
VQV O2A H12 SING N N 38
VQV O2C H13 SING N N 39
VQV O2P H14 SING N N 40
# #
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
VQV SMILES ACDLabs 12.01 "O=C1N(C=CC(=O)N1)C2C(O)C(OP(O)(=O)O)C(COP(O)(O)=O)O2"
VQV InChI InChI 1.03 "InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(14)10-5)8-6(13)7(23-25(18,19)20)4(22-8)3-21-24(15,16)17/h1-2,4,6-8,13H,3H2,(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7+,8+/m0/s1"
VQV InChIKey InChI 1.03 ZPVPRWPOZBXDKD-ZAKLUEHWSA-N
VQV SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@H](O[P](O)(O)=O)[C@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O"
VQV SMILES CACTVS 3.385 "O[CH]1[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O"
VQV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@@H](O2)COP(=O)(O)O)OP(=O)(O)O)O"
VQV SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)OP(=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
VQV "SYSTEMATIC NAME" ACDLabs 12.01 "1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione"
VQV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VQV "Create component" 2020-09-08 RCSB
VQV "Initial release" 2020-09-23 RCSB
##