data_LWM # _chem_comp.id LWM _chem_comp.name "[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H18 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-08-07 _chem_comp.pdbx_modified_date 2013-02-15 _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 363.264 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LWM _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 2LWM _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 LWM P1 P1 P 0 1 N N N -4.245 0.002 8.676 5.791 0.420 -0.038 P1 LWM 1 LWM N1 N1 N 0 1 N N N -0.387 0.257 17.024 -5.372 -1.126 -0.039 N1 LWM 2 LWM C1 C1 C 0 1 N N N -1.645 0.791 16.927 -4.325 -1.889 0.377 C1 LWM 3 LWM N2 N2 N 0 1 N N N -2.246 1.197 18.036 -4.552 -3.185 0.763 N2 LWM 4 LWM N3 N3 N 0 1 N N N -2.284 0.923 15.778 -3.100 -1.412 0.416 N3 LWM 5 LWM C2 C2 C 0 1 N N N -1.589 0.485 14.701 -2.834 -0.153 0.048 C2 LWM 6 LWM C3 C3 C 0 1 N N N -0.317 -0.068 14.699 -3.867 0.671 -0.386 C3 LWM 7 LWM C4 C4 C 0 1 N N N 0.356 -0.202 15.956 -5.169 0.150 -0.429 C4 LWM 8 LWM O1 O1 O 0 1 N N N 1.473 -0.660 16.185 -6.103 0.841 -0.804 O1 LWM 9 LWM N4 N4 N 0 1 N N N 0.150 -0.424 13.503 -3.612 1.999 -0.779 N4 LWM 10 LWM C5 C5 C 0 1 N N N 1.242 0.104 12.962 -4.231 3.019 -0.151 C5 LWM 11 LWM O2 O2 O 0 1 N N N 1.907 0.967 13.536 -4.941 2.799 0.808 O2 LWM 12 LWM N5 N5 N 0 1 N N N -2.262 0.635 13.564 -1.538 0.327 0.098 N5 LWM 13 LWM "C1'" "C1'" C 0 1 N N R -3.628 1.222 13.518 -0.452 -0.543 0.555 "C1'" LWM 14 LWM OP3 OP3 O 0 1 N Y N -5.464 0.630 8.114 6.334 0.934 1.388 OP3 LWM 15 LWM "C2'" "C2'" C 0 1 N N N -3.778 2.298 12.447 0.108 -1.354 -0.627 "C2'" LWM 16 LWM OP2 OP2 O 0 1 N N N -2.923 0.624 8.445 6.813 -0.668 -0.641 OP2 LWM 17 LWM "C3'" "C3'" C 0 1 N N S -5.170 2.163 11.821 1.595 -0.967 -0.762 "C3'" LWM 18 LWM "O3'" "O3'" O 0 1 N N N -6.162 3.129 12.237 2.378 -2.109 -1.115 "O3'" LWM 19 LWM "C4'" "C4'" C 0 1 N N R -5.645 0.737 12.156 1.984 -0.457 0.648 "C4'" LWM 20 LWM "C5'" "C5'" C 0 1 N N N -5.711 -0.161 10.920 3.190 0.482 0.571 "C5'" LWM 21 LWM "O5'" "O5'" O 0 1 N N N -4.437 -0.171 10.264 4.341 -0.254 0.151 "O5'" LWM 22 LWM "C6'" "C6'" C 0 1 N N N -4.658 0.163 13.175 0.714 0.308 1.099 "C6'" LWM 23 LWM HN1 HN1 H 0 1 N N N 0.022 0.196 17.934 -6.266 -1.502 -0.059 HN1 LWM 24 LWM HN7 HN7 H 0 1 N N N -0.346 -1.123 12.988 -2.990 2.180 -1.501 HN7 LWM 25 LWM HN9 HN9 H 0 1 N N N 1.557 -0.235 11.986 -4.095 4.031 -0.502 HN9 LWM 26 LWM H5 H5 H 0 1 N N N -1.692 1.210 12.977 -1.348 1.240 -0.170 H5 LWM 27 LWM "H2'" "H2'" H 0 1 N N N -3.670 3.294 12.902 0.016 -2.421 -0.424 "H2'" LWM 28 LWM "H5'" "H5'" H 0 1 N N N -6.476 0.223 10.229 2.986 1.277 -0.146 "H5'" LWM 29 LWM "H6'" "H6'" H 0 1 N N N -5.199 -0.133 14.086 0.694 1.306 0.660 "H6'" LWM 30 LWM "H1'" "H2'A" H 0 1 N N N -3.873 1.657 14.498 -0.815 -1.217 1.331 "H1'" LWM 31 LWM "H2''" "H2''" H 0 0 N N N -3.008 2.163 11.674 -0.430 -1.100 -1.541 "H2''" LWM 32 LWM HN2A HN2A H 0 0 N N N -1.782 1.107 18.917 -3.813 -3.739 1.062 HN2A LWM 33 LWM "H3'" "H3'" H 0 1 N N N -3.163 1.593 17.991 -5.451 -3.549 0.738 "H3'" LWM 34 LWM H3 H3 H 0 1 N N N -5.052 2.225 10.729 1.717 -0.176 -1.501 H3 LWM 35 LWM "H4'" "H4'" H 0 1 N N N -6.643 0.792 12.614 2.189 -1.293 1.317 "H4'" LWM 36 LWM "H5''" "H5''" H 0 0 N N N -5.974 -1.185 11.225 3.375 0.917 1.553 "H5''" LWM 37 LWM "H6''" "H6''" H 0 0 N N N -4.154 -0.716 12.746 0.671 0.367 2.186 "H6''" LWM 38 LWM HOP3 HOP3 H 0 0 N N N -5.384 0.688 7.169 6.428 0.234 2.048 HOP3 LWM 39 LWM HOP2 HOP2 H 0 0 N N N -2.754 0.672 7.511 7.708 -0.331 -0.782 HOP2 LWM 40 LWM "HO3'" "HO3'" H 0 0 N Y N -6.982 2.954 11.791 2.137 -2.504 -1.964 "HO3'" LWM 41 LWM OP1 OP1 O 0 1 N N N -4.035 0.051 7.222 5.685 1.566 -0.968 OP1 LWM 42 # 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 LWM P1 "O5'" SING N N 1 LWM P1 OP1 DOUB N N 2 LWM N1 HN1 SING N N 3 LWM C1 N1 SING N N 4 LWM C1 N2 SING N N 5 LWM N2 "H3'" SING N N 6 LWM N3 C1 DOUB N N 7 LWM C2 N3 SING N N 8 LWM C3 C2 DOUB N N 9 LWM C3 C4 SING N N 10 LWM C4 N1 SING N N 11 LWM C4 O1 DOUB N N 12 LWM N4 C3 SING N N 13 LWM C5 N4 SING N N 14 LWM C5 O2 DOUB N N 15 LWM N5 C2 SING N N 16 LWM "C1'" N5 SING N N 17 LWM "C1'" "H1'" SING N N 18 LWM OP3 P1 SING N N 19 LWM OP3 HOP3 SING N N 20 LWM "C2'" "C1'" SING N N 21 LWM "C2'" "H2'" SING N N 22 LWM OP2 P1 SING N N 23 LWM OP2 HOP2 SING N N 24 LWM "C3'" "C2'" SING N N 25 LWM "C3'" "C4'" SING N N 26 LWM "C3'" "O3'" SING N N 27 LWM "O3'" "HO3'" SING N N 28 LWM "C4'" "H4'" SING N N 29 LWM "C4'" "C6'" SING N N 30 LWM "C5'" "C4'" SING N N 31 LWM "C5'" "H5''" SING N N 32 LWM "O5'" "C5'" SING N N 33 LWM "C6'" "C1'" SING N N 34 LWM "C6'" "H6'" SING N N 35 LWM HN7 N4 SING N N 36 LWM HN9 C5 SING N N 37 LWM H5 N5 SING N N 38 LWM "H5'" "C5'" SING N N 39 LWM "H2''" "C2'" SING N N 40 LWM HN2A N2 SING N N 41 LWM H3 "C3'" SING N N 42 LWM "H6''" "C6'" SING N N 43 # 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 LWM SMILES ACDLabs 12.01 "O=C1C(NC=O)=C(N=C(N)N1)NC2CC(COP(=O)(O)O)C(O)C2" LWM InChI InChI 1.03 "InChI=1S/C11H18N5O7P/c12-11-15-9(8(13-4-17)10(19)16-11)14-6-1-5(7(18)2-6)3-23-24(20,21)22/h4-7,18H,1-3H2,(H,13,17)(H2,20,21,22)(H4,12,14,15,16,19)/t5-,6-,7+/m1/s1" LWM InChIKey InChI 1.03 UQRLPMGPCBTFTR-QYNIQEEDSA-N LWM SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=C(NC=O)C(=O)N1)N[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)C2" LWM SMILES CACTVS 3.370 "NC1=NC(=C(NC=O)C(=O)N1)N[CH]2C[CH](O)[CH](CO[P](O)(O)=O)C2" LWM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@H](C[C@@H]([C@H]1COP(=O)(O)O)O)NC2=C(C(=O)NC(=N2)N)NC=O" LWM SMILES "OpenEye OEToolkits" 1.7.6 "C1C(CC(C1COP(=O)(O)O)O)NC2=C(C(=O)NC(=N2)N)NC=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 LWM "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl dihydrogen phosphate" LWM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1R,2S,4R)-4-[(2-azanyl-5-formamido-6-oxidanylidene-1H-pyrimidin-4-yl)amino]-2-oxidanyl-cyclopentyl]methyl 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 LWM "Create component" 2012-08-07 RCSB LWM "Modify atom id" 2013-01-18 RCSB LWM "Modify leaving atom flag" 2013-01-18 RCSB LWM "Initial release" 2013-02-15 RCSB #