data_VC6
#
_chem_comp.id VC6
_chem_comp.name "4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 Cl F N3 O12 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 517.620
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VC6
_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 6CTU
_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
VC6 C4 C1 C 0 1 N N N 9.305 7.554 10.929 -6.450 -3.047 -0.219 C4 VC6 1
VC6 N4 N1 N 0 1 N N N 10.736 7.526 11.131 -7.069 -4.271 -0.108 N4 VC6 2
VC6 C5 C2 C 0 1 N N N 8.482 7.194 11.977 -6.344 -2.417 -1.476 C5 VC6 3
VC6 C6 C3 C 0 1 N N N 7.116 7.223 11.744 -5.729 -1.213 -1.556 C6 VC6 4
VC6 N3 N2 N 0 1 N N N 8.787 7.893 9.757 -5.955 -2.451 0.858 N3 VC6 5
VC6 C2 C4 C 0 1 N N N 7.475 7.907 9.586 -5.353 -1.266 0.762 C2 VC6 6
VC6 O2 O1 O 0 1 N N N 7.027 8.217 8.522 -4.905 -0.739 1.767 O2 VC6 7
VC6 N1 N3 N 0 1 N N N 6.639 7.589 10.561 -5.231 -0.643 -0.424 N1 VC6 8
VC6 "C1'" C5 C 0 1 N N R 5.193 7.583 10.278 -4.564 0.660 -0.497 "C1'" VC6 9
VC6 "C2'" C6 C 0 1 N N N 4.823 6.176 9.675 -5.339 1.709 0.340 "C2'" VC6 10
VC6 "C3'" C7 C 0 1 N N S 4.481 5.283 10.896 -4.209 2.725 0.658 "C3'" VC6 11
VC6 "O3'" O2 O 0 1 N N N 3.348 4.357 10.682 -4.039 3.650 -0.417 "O3'" VC6 12
VC6 "O4'" O3 O 0 1 N N N 4.442 7.668 11.348 -3.262 0.587 0.106 "O4'" VC6 13
VC6 "C4'" C8 C 0 1 N N S 4.398 6.163 11.884 -2.974 1.809 0.796 "C4'" VC6 14
VC6 "C5'" C9 C 0 1 N N N 3.504 6.059 13.075 -1.754 2.485 0.167 "C5'" VC6 15
VC6 "O5'" O4 O 0 1 N N N 4.614 6.172 13.923 -0.593 1.685 0.401 "O5'" VC6 16
VC6 PA P1 P 0 1 N N N 4.997 4.899 14.869 0.874 2.094 -0.123 PA VC6 17
VC6 O1A O5 O 0 1 N N N 3.967 4.876 15.957 1.351 3.442 0.618 O1A VC6 18
VC6 O2A O6 O 0 1 N N N 6.398 4.997 15.361 0.830 2.323 -1.584 O2A VC6 19
VC6 O3A O7 O 0 1 N N N 4.904 3.592 13.888 1.911 0.907 0.204 O3A VC6 20
VC6 PB P2 P 0 1 N N N 3.762 2.427 13.857 3.397 0.550 -0.301 PB VC6 21
VC6 O1B O8 O 0 1 N N N 2.435 2.938 14.387 3.385 0.336 -1.897 O1B VC6 22
VC6 O2B O9 O 0 1 N N N 3.669 2.053 12.411 4.314 1.660 0.041 O2B VC6 23
VC6 C3B C10 C 0 1 N N S 4.366 0.941 14.820 3.964 -0.980 0.513 C3B VC6 24
VC6 CL1 CL1 CL 0 0 N N N 6.093 1.144 15.068 2.847 -2.332 0.096 CL1 VC6 25
VC6 F4B F1 F 0 1 N N N 4.196 -0.250 14.126 3.975 -0.794 1.899 F4B VC6 26
VC6 PG P3 P 0 1 N N N 3.556 0.898 16.507 5.648 -1.384 -0.059 PG VC6 27
VC6 O2G O10 O 0 1 N N N 3.495 2.324 17.026 6.645 -0.176 0.313 O2G VC6 28
VC6 O1G O11 O 0 1 N N N 4.384 0.057 17.439 6.149 -2.734 0.660 O1G VC6 29
VC6 O3G O12 O 0 1 N N N 2.183 0.339 16.365 5.637 -1.581 -1.526 O3G VC6 30
VC6 H1 H1 H 0 1 N N N 11.352 7.765 10.380 -7.434 -4.703 -0.897 H1 VC6 31
VC6 H2 H2 H 0 1 N N N 11.110 7.268 12.022 -7.141 -4.702 0.758 H2 VC6 32
VC6 H3 H3 H 0 1 N N N 8.885 6.903 12.936 -6.746 -2.888 -2.361 H3 VC6 33
VC6 H4 H4 H 0 1 N N N 6.433 6.945 12.533 -5.635 -0.711 -2.508 H4 VC6 34
VC6 H5 H5 H 0 1 N N N 4.954 8.357 9.534 -4.483 0.985 -1.534 H5 VC6 35
VC6 H6 H6 H 0 1 N N N 3.955 6.261 9.005 -6.131 2.173 -0.249 H6 VC6 36
VC6 H7 H7 H 0 1 N N N 5.676 5.759 9.120 -5.739 1.266 1.252 H7 VC6 37
VC6 H8 H8 H 0 1 N N N 5.369 4.656 11.063 -4.410 3.248 1.593 H8 VC6 38
VC6 H9 H9 H 0 1 N N N 3.447 3.599 11.246 -4.821 4.189 -0.600 H9 VC6 39
VC6 H10 H10 H 0 1 N N N 5.390 6.090 12.355 -2.782 1.603 1.849 H10 VC6 40
VC6 H11 H11 H 0 1 N N N 2.783 6.884 13.168 -1.911 2.593 -0.906 H11 VC6 41
VC6 H12 H12 H 0 1 N N N 2.974 5.098 13.155 -1.613 3.469 0.614 H12 VC6 42
VC6 H13 H13 H 0 1 N N N 4.397 4.930 16.802 1.403 3.365 1.580 H13 VC6 43
VC6 H14 H14 H 0 1 N N N 1.789 2.923 13.691 2.804 -0.378 -2.194 H14 VC6 44
VC6 H15 H15 H 0 1 N N N 2.588 2.575 17.157 6.702 0.009 1.260 H15 VC6 45
VC6 H16 H16 H 0 1 N N N 3.863 -0.671 17.756 7.039 -3.010 0.403 H16 VC6 46
#
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
VC6 O2 C2 DOUB N N 1
VC6 C2 N3 SING N N 2
VC6 C2 N1 SING N N 3
VC6 "C2'" "C1'" SING N N 4
VC6 "C2'" "C3'" SING N N 5
VC6 N3 C4 DOUB N N 6
VC6 "C1'" N1 SING N N 7
VC6 "C1'" "O4'" SING N N 8
VC6 N1 C6 SING N N 9
VC6 "O3'" "C3'" SING N N 10
VC6 "C3'" "C4'" SING N N 11
VC6 C4 N4 SING N N 12
VC6 C4 C5 SING N N 13
VC6 "O4'" "C4'" SING N N 14
VC6 C6 C5 DOUB N N 15
VC6 "C4'" "C5'" SING N N 16
VC6 O2B PB DOUB N N 17
VC6 "C5'" "O5'" SING N N 18
VC6 PB O3A SING N N 19
VC6 PB O1B SING N N 20
VC6 PB C3B SING N N 21
VC6 O3A PA SING N N 22
VC6 "O5'" PA SING N N 23
VC6 F4B C3B SING N N 24
VC6 C3B CL1 SING N N 25
VC6 C3B PG SING N N 26
VC6 PA O2A DOUB N N 27
VC6 PA O1A SING N N 28
VC6 O3G PG DOUB N N 29
VC6 PG O2G SING N N 30
VC6 PG O1G SING N N 31
VC6 N4 H1 SING N N 32
VC6 N4 H2 SING N N 33
VC6 C5 H3 SING N N 34
VC6 C6 H4 SING N N 35
VC6 "C1'" H5 SING N N 36
VC6 "C2'" H6 SING N N 37
VC6 "C2'" H7 SING N N 38
VC6 "C3'" H8 SING N N 39
VC6 "O3'" H9 SING N N 40
VC6 "C4'" H10 SING N N 41
VC6 "C5'" H11 SING N N 42
VC6 "C5'" H12 SING N N 43
VC6 O1A H13 SING N N 44
VC6 O1B H14 SING N N 45
VC6 O2G H15 SING N N 46
VC6 O1G H16 SING N N 47
#
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
VC6 SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)(P(O)(O)=O)F)=O"
VC6 InChI InChI 1.03 "InChI=1S/C10H16ClFN3O12P3/c11-10(12,28(18,19)20)29(21,22)27-30(23,24)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,21,22)(H,23,24)(H2,13,14,17)(H2,18,19,20)/t5-,6-,8+,10+/m0/s1"
VC6 InChIKey InChI 1.03 KEKPFSDJAHISFV-VBOXYBSHSA-N
VC6 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)[C@@](F)(Cl)[P](O)(O)=O)O2"
VC6 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O2"
VC6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)([C@](F)(P(=O)(O)O)Cl)O)O"
VC6 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)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
VC6 "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"
VC6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(2~{S},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-chloranyl-fluoranyl-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
VC6 "Create component" 2018-03-26 RCSB
VC6 "Initial release" 2018-06-20 RCSB
#