data_LDG
# 
_chem_comp.id                                    LDG 
_chem_comp.name                                  
;2'-deoxy-N-[(1,3-dimethoxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)methyl]guanosine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H26 N5 O11 P" 
_chem_comp.mon_nstd_parent_comp_id               DG 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2017-06-15 
_chem_comp.pdbx_modified_date                    2017-10-13 
_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                        627.496 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LDG 
_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        5W2A 
_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 
LDG O19   O1  O 0 1 N N N -12.000 -31.220 30.069 -5.676  1.054  2.391  O19   LDG 1  
LDG C19   C1  C 0 1 N N N -12.142 -31.201 31.292 -6.109  0.882  1.268  C19   LDG 2  
LDG C18   C2  C 0 1 Y N N -13.471 -31.120 31.880 -5.188  0.620  0.148  C18   LDG 3  
LDG C17   C3  C 0 1 Y N N -14.640 -31.074 31.007 -3.853  0.279  0.390  C17   LDG 4  
LDG O17   O2  O 0 1 N N N -14.495 -31.069 29.664 -3.394  0.187  1.662  O17   LDG 5  
LDG C16   C4  C 0 1 Y N N -15.939 -30.966 31.677 -2.999  0.035  -0.679 C16   LDG 6  
LDG C9    C5  C 0 1 Y N N -15.970 -30.960 33.145 -3.464  0.128  -1.981 C9    LDG 7  
LDG C81   C6  C 0 1 Y N N -14.835 -31.018 33.906 -4.792  0.466  -2.235 C81   LDG 8  
LDG C7    C7  C 0 1 Y N N -13.615 -31.086 33.335 -5.657  0.711  -1.179 C7    LDG 9  
LDG C61   C8  C 0 1 N N N -12.460 -31.140 34.206 -7.070  1.068  -1.432 C61   LDG 10 
LDG O61   O3  O 0 1 N N N -12.600 -31.127 35.422 -7.433  1.392  -2.546 O61   LDG 11 
LDG C20   C9  C 0 1 Y N N -10.966 -31.241 32.177 -7.565  0.928  1.011  C20   LDG 12 
LDG C1    C10 C 0 1 Y N N -9.710  -31.311 31.640 -8.471  0.882  2.065  C1    LDG 13 
LDG C51   C11 C 0 1 Y N N -11.128 -31.222 33.624 -8.036  1.025  -0.312 C51   LDG 14 
LDG C41   C12 C 0 1 Y N N -10.029 -31.279 34.426 -9.405  1.068  -0.557 C41   LDG 15 
LDG C3    C13 C 0 1 Y N N -8.789  -31.333 33.848 -10.295 1.015  0.503  C3    LDG 16 
LDG C71   C14 C 0 1 Y N N -8.630  -31.367 32.483 -9.830  0.926  1.807  C71   LDG 17 
LDG O1    O4  O 0 1 N N N -17.191 -30.906 33.710 -2.620  -0.112 -3.016 O1    LDG 18 
LDG C14   C15 C 0 1 N N N -17.386 -30.481 35.044 -3.161  -0.000 -4.334 C14   LDG 19 
LDG C15   C16 C 0 1 N N N -14.251 -32.290 29.029 -2.855  1.375  2.245  C15   LDG 20 
LDG C2R   C17 C 0 1 N N N -17.270 -30.940 30.985 -1.561  -0.332 -0.421 C2R   LDG 21 
LDG P     P1  P 0 1 N N N -22.308 -23.293 34.840 9.117   1.606  -0.734 P     LDG 22 
LDG OP1   O5  O 0 1 N N N -22.262 -23.017 36.249 9.469   1.693  -2.302 OP1   LDG 23 
LDG "O5'" O6  O 0 1 N N N -21.641 -24.690 34.590 7.523   1.488  -0.547 "O5'" LDG 24 
LDG "C5'" C18 C 0 1 N N N -21.577 -25.577 35.705 6.886   1.497  0.733  "C5'" LDG 25 
LDG "C4'" C19 C 0 1 N N R -20.437 -26.547 35.550 5.373   1.368  0.551  "C4'" LDG 26 
LDG "C3'" C20 C 0 1 N N S -19.056 -25.985 35.843 4.654   1.502  1.912  "C3'" LDG 27 
LDG "O3'" O7  O 0 1 N N N -18.374 -26.793 36.793 4.155   2.829  2.086  "O3'" LDG 28 
LDG "C2'" C21 C 0 1 N N N -18.337 -26.038 34.513 3.487   0.493  1.821  "C2'" LDG 29 
LDG "C1'" C22 C 0 1 N N R -19.164 -26.931 33.628 3.639   -0.131 0.416  "C1'" LDG 30 
LDG "O4'" O8  O 0 1 N N N -20.446 -26.885 34.160 5.034   0.045  0.083  "O4'" LDG 31 
LDG N9    N1  N 0 1 Y N N -19.215 -26.480 32.261 3.299   -1.556 0.451  N9    LDG 32 
LDG C4    C23 C 0 1 Y N N -18.782 -27.173 31.179 2.052   -2.094 0.281  C4    LDG 33 
LDG C5    C24 C 0 1 Y N N -18.971 -26.335 30.128 2.210   -3.480 0.395  C5    LDG 34 
LDG N7    N2  N 0 1 Y N N -19.488 -25.143 30.562 3.524   -3.718 0.624  N7    LDG 35 
LDG C8    C25 C 0 1 Y N N -19.613 -25.250 31.849 4.168   -2.588 0.652  C8    LDG 36 
LDG N3    N3  N 0 1 N N N -18.307 -28.426 31.188 0.838   -1.582 0.051  N3    LDG 37 
LDG C2    C26 C 0 1 N N N -17.999 -28.868 29.986 -0.215  -2.359 -0.072 C2    LDG 38 
LDG N2    N4  N 0 1 N N N -17.492 -30.116 29.846 -1.440  -1.787 -0.308 N2    LDG 39 
LDG N1    N5  N 0 1 N N N -18.138 -28.077 28.864 -0.126  -3.715 0.029  N1    LDG 40 
LDG C6    C27 C 0 1 N N N -18.633 -26.771 28.829 1.067   -4.304 0.266  C6    LDG 41 
LDG O6    O9  O 0 1 N N N -18.723 -26.133 27.747 1.158   -5.517 0.357  O6    LDG 42 
LDG OP2   O10 O 0 1 N N N -21.866 -22.250 33.977 9.830   0.311  -0.095 OP2   LDG 43 
LDG H1    H1  H 0 1 N N N -14.917 -31.009 34.983 -5.147  0.537  -3.252 H1    LDG 44 
LDG H2    H2  H 0 1 N N N -9.571  -31.322 30.569 -8.115  0.813  3.082  H2    LDG 45 
LDG H3    H3  H 0 1 N N N -10.134 -31.282 35.501 -9.772  1.142  -1.569 H3    LDG 46 
LDG H4    H4  H 0 1 N N N -7.914  -31.349 34.480 -11.357 1.049  0.313  H4    LDG 47 
LDG H5    H5  H 0 1 N N N -7.636  -31.439 32.067 -10.533 0.890  2.626  H5    LDG 48 
LDG H6    H6  H 0 1 N N N -18.458 -30.518 35.288 -2.383  -0.217 -5.066 H6    LDG 49 
LDG H7    H7  H 0 1 N N N -16.832 -31.144 35.725 -3.979  -0.711 -4.452 H7    LDG 50 
LDG H8    H8  H 0 1 N N N -17.019 -29.450 35.158 -3.534  1.013  -4.489 H8    LDG 51 
LDG H9    H9  H 0 1 N N N -14.157 -32.128 27.945 -2.525  1.163  3.262  H9    LDG 52 
LDG H10   H10 H 0 1 N N N -13.318 -32.725 29.417 -2.007  1.718  1.652  H10   LDG 53 
LDG H11   H11 H 0 1 N N N -15.086 -32.979 29.225 -3.621  2.150  2.266  H11   LDG 54 
LDG H12   H12 H 0 1 N N N -18.008 -30.633 31.740 -0.942  0.021  -1.246 H12   LDG 55 
LDG H13   H13 H 0 1 N N N -17.477 -31.973 30.668 -1.228  0.133  0.508  H13   LDG 56 
LDG H14   H14 H 0 1 N N N -23.139 -23.067 36.611 10.414  1.766  -2.490 H14   LDG 57 
LDG H15   H15 H 0 1 N N N -21.430 -24.991 36.624 7.253   0.661  1.328  H15   LDG 58 
LDG H16   H16 H 0 1 N N N -22.521 -26.138 35.775 7.112   2.433  1.244  H16   LDG 59 
LDG H17   H17 H 0 1 N N N -20.615 -27.436 36.173 5.009   2.124  -0.146 H17   LDG 60 
LDG H18   H18 H 0 1 N N N -19.139 -24.943 36.187 5.327   1.238  2.727  H18   LDG 61 
LDG H19   H19 H 0 1 N N N -18.829 -26.756 37.626 3.694   2.969  2.925  H19   LDG 62 
LDG H20   H20 H 0 1 N N N -17.328 -26.456 34.641 3.583   -0.273 2.591  H20   LDG 63 
LDG H21   H21 H 0 1 N N N -18.264 -25.030 34.078 2.530   1.006  1.911  H21   LDG 64 
LDG H22   H22 H 0 1 N N N -18.761 -27.953 33.671 3.009   0.393  -0.303 H22   LDG 65 
LDG H23   H23 H 0 1 N N N -19.981 -24.471 32.500 5.230   -2.483 0.816  H23   LDG 66 
LDG H24   H24 H 0 1 N N N -17.272 -30.462 28.934 -2.227  -2.348 -0.401 H24   LDG 67 
LDG H25   H25 H 0 1 N N N -17.857 -28.477 27.992 -0.923  -4.260 -0.066 H25   LDG 68 
LDG H26   H26 H 0 1 N N N -22.576 -21.993 33.400 9.557   -0.525 -0.495 H26   LDG 69 
LDG OP3   OP3 O 0 1 N Y N -23.801 -23.569 34.456 9.605   2.825  -0.050 OP3   LDG 70 
# 
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 
LDG O6    C6    DOUB N N 1  
LDG C6    N1    SING N N 2  
LDG C6    C5    SING N N 3  
LDG N1    C2    SING N N 4  
LDG C15   O17   SING N N 5  
LDG O17   C17   SING N N 6  
LDG N2    C2    SING N N 7  
LDG N2    C2R   SING N N 8  
LDG C2    N3    DOUB N N 9  
LDG O19   C19   DOUB N N 10 
LDG C5    N7    SING Y N 11 
LDG C5    C4    DOUB Y N 12 
LDG N7    C8    DOUB Y N 13 
LDG C2R   C16   SING N N 14 
LDG C17   C16   DOUB Y N 15 
LDG C17   C18   SING Y N 16 
LDG C4    N3    SING N N 17 
LDG C4    N9    SING Y N 18 
LDG C19   C18   SING N N 19 
LDG C19   C20   SING N N 20 
LDG C1    C20   DOUB Y N 21 
LDG C1    C71   SING Y N 22 
LDG C16   C9    SING Y N 23 
LDG C8    N9    SING Y N 24 
LDG C18   C7    DOUB Y N 25 
LDG C20   C51   SING Y N 26 
LDG N9    "C1'" SING N N 27 
LDG C71   C3    DOUB Y N 28 
LDG C9    O1    SING N N 29 
LDG C9    C81   DOUB Y N 30 
LDG C7    C81   SING Y N 31 
LDG C7    C61   SING N N 32 
LDG C51   C61   SING N N 33 
LDG C51   C41   DOUB Y N 34 
LDG "C1'" "O4'" SING N N 35 
LDG "C1'" "C2'" SING N N 36 
LDG O1    C14   SING N N 37 
LDG C3    C41   SING Y N 38 
LDG OP2   P     SING N N 39 
LDG "O4'" "C4'" SING N N 40 
LDG C61   O61   DOUB N N 41 
LDG "C2'" "C3'" SING N N 42 
LDG "O5'" P     SING N N 43 
LDG "O5'" "C5'" SING N N 44 
LDG P     OP1   SING N N 45 
LDG "C4'" "C5'" SING N N 46 
LDG "C4'" "C3'" SING N N 47 
LDG "C3'" "O3'" SING N N 48 
LDG C81   H1    SING N N 49 
LDG C1    H2    SING N N 50 
LDG C41   H3    SING N N 51 
LDG C3    H4    SING N N 52 
LDG C71   H5    SING N N 53 
LDG C14   H6    SING N N 54 
LDG C14   H7    SING N N 55 
LDG C14   H8    SING N N 56 
LDG C15   H9    SING N N 57 
LDG C15   H10   SING N N 58 
LDG C15   H11   SING N N 59 
LDG C2R   H12   SING N N 60 
LDG C2R   H13   SING N N 61 
LDG OP1   H14   SING N N 62 
LDG "C5'" H15   SING N N 63 
LDG "C5'" H16   SING N N 64 
LDG "C4'" H17   SING N N 65 
LDG "C3'" H18   SING N N 66 
LDG "O3'" H19   SING N N 67 
LDG "C2'" H20   SING N N 68 
LDG "C2'" H21   SING N N 69 
LDG "C1'" H22   SING N N 70 
LDG C8    H23   SING N N 71 
LDG N2    H24   SING N N 72 
LDG N1    H25   SING N N 73 
LDG OP2   H26   SING N N 74 
LDG P     OP3   DOUB N N 75 
# 
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 
LDG SMILES           ACDLabs              12.01 "O=C5c1c(cc(c(c1OC)CNC4=Nc3n(C2CC(C(COP(O)(=O)O)O2)O)cnc3C(N4)=O)OC)C(=O)c6c5cccc6" 
LDG InChI            InChI                1.03  
"InChI=1S/C27H26N5O11P/c1-40-17-7-14-20(23(35)13-6-4-3-5-12(13)22(14)34)24(41-2)15(17)9-28-27-30-25-21(26(36)31-27)29-11-32(25)19-8-16(33)18(43-19)10-42-44(37,38)39/h3-7,11,16,18-19,33H,8-10H2,1-2H3,(H2,37,38,39)(H2,28,30,31,36)/t16-,18+,19+/m0/s1" 
LDG InChIKey         InChI                1.03  DZJXUNLGRPPLSY-QXAKKESOSA-N 
LDG SMILES_CANONICAL CACTVS               3.385 "COc1cc2C(=O)c3ccccc3C(=O)c2c(OC)c1CNC4=Nc5n(cnc5C(=O)N4)[C@H]6C[C@H](O)[C@@H](CO[P](O)(O)=O)O6" 
LDG SMILES           CACTVS               3.385 "COc1cc2C(=O)c3ccccc3C(=O)c2c(OC)c1CNC4=Nc5n(cnc5C(=O)N4)[CH]6C[CH](O)[CH](CO[P](O)(O)=O)O6" 
LDG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "COc1cc2c(c(c1CNC3=Nc4c(ncn4[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O)C(=O)N3)OC)C(=O)c6ccccc6C2=O" 
LDG SMILES           "OpenEye OEToolkits" 2.0.6 "COc1cc2c(c(c1CNC3=Nc4c(ncn4C5CC(C(O5)COP(=O)(O)O)O)C(=O)N3)OC)C(=O)c6ccccc6C2=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 
LDG "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-N-[(1,3-dimethoxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)methyl]guanosine 5'-(dihydrogen phosphate)
;
LDG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},5~{R})-5-[2-[[1,3-dimethoxy-9,10-bis(oxidanylidene)anthracen-2-yl]methylamino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]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 
LDG "Create component" 2017-06-15 RCSB 
LDG "Initial release"  2017-10-18 RCSB 
# 
