# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:58:24 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(NC(=O)N2[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C(=O)N1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 G8D  G8D  '[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate'  ligand  41  29  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_G8D
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 G8D  O3B  O  OP    -1  -0.894   5.7851   1.2474   1.6665
 G8D  PB   P  P      0   1.224   5.1071   1.8721   0.4579
 G8D  O2B  O  OP    -1  -0.895   4.6238   3.3002   0.6677
 G8D  O1B  O  O      0  -0.898   5.7911   1.6131  -0.8765
 G8D  O3A  O  O2     0  -0.777   3.6040   1.0237   0.3390
 G8D  PA   P  P      0   1.329   3.3611  -0.2393  -0.6177
 G8D  O1A  O  O      0  -0.835   4.3771  -1.3306  -0.4258
 G8D  O2A  O  OP    -1  -0.831   2.9965   0.1649  -2.0190
 G8D  O5'  O  O2     0  -0.632   1.9608  -0.7068   0.1581
 G8D  C5'  C  CH2    0  -0.132   1.2491  -1.7788  -0.4040
 G8D  C4'  C  CH1    0  -0.036   0.1648  -2.1963   0.5682
 G8D  O4'  O  O2     0  -0.493  -0.7541  -1.1241   0.8028
 G8D  C3'  C  CH1    0  -0.033  -0.6766  -3.3621   0.0624
 G8D  O3'  O  OH1    0  -0.673  -1.1498  -4.0952   1.1655
 G8D  C2'  C  CH1    0  -0.070  -1.8245  -2.6328  -0.6388
 G8D  O2'  O  OH1    0  -0.660  -3.0149  -3.3662  -0.7197
 G8D  C1'  C  CH1    0   0.226  -2.0214  -1.4396   0.2954
 G8D  N9   N  NR5    0  -0.625  -2.6216  -0.2802  -0.3077
 G8D  C8   C  CR5    0   0.677  -2.1585   0.3827  -1.4513
 G8D  O8   O  O      0  -0.490  -1.2319   0.0449  -2.1637
 G8D  C4   C  CR5    0   0.513  -3.6779   0.4153   0.2274
 G8D  N3   N  N      0  -0.515  -4.3515   0.0746   1.3270
 G8D  C2   C  C      0   0.702  -5.3224   0.9049   1.6359
 G8D  N2   N  NH2    0  -0.830  -6.0541   0.6920   2.7349
 G8D  N1   N  NH1    0  -0.725  -5.6102   2.0079   0.8936
 G8D  C6   C  C      0   0.519  -4.9371   2.4118  -0.2681
 G8D  O6   O  O      0  -0.488  -5.2674   3.4256  -0.8678
 G8D  C5   C  CR5    0   0.073  -3.9041   1.5026  -0.5730
 G8D  N7   N  NR15   0  -0.739  -2.9656   1.4662  -1.5924
 G8D  H4   H  HCH2   0   0.212   0.8149  -1.5039  -1.3716
 G8D  H5   H  HCH2   0   0.194   1.8974  -2.6497  -0.5704
 G8D  H6   H  HCH1   0   0.244   0.6348  -2.4599   1.5217
 G8D  H7   H  HCH1   0   0.244  -0.1147  -4.0013  -0.6313
 G8D  H8   H  HOH1   0   0.446  -1.9636  -4.5367   0.8943
 G8D  H9   H  HCH1   0   0.266  -1.4873  -2.2999  -1.6230
 G8D  H10  H  HOH1   0   0.468  -2.9879  -3.9119  -1.5118
 G8D  H11  H  HCH1   0   0.253  -2.7025  -1.7287   1.1039
 G8D  H12  H  HNH2   0   0.416  -5.9496  -0.1862   3.2132
 G8D  H13  H  HNH2   0   0.418  -6.8911   1.2179   2.9196
 G8D  H14  H  HNH1   0   0.428  -6.3648   2.6106   1.1965
 G8D  H15  H  HNR5   0   0.420  -2.8774   2.1292  -2.3451

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 G8D  O6   C6   double  1.223  0.020  1.223
 G8D  N1   C6   single  1.402  0.020  1.402
 G8D  N1   C2   single  1.360  0.020  1.360
 G8D  N2   C2   single  1.337  0.020  1.337
 G8D  C6   C5   single  1.409  0.020  1.409
 G8D  C2   N3   double  1.314  0.020  1.314
 G8D  C5   N7   single  1.386  0.020  1.386
 G8D  C5   C4   double  1.369  0.020  1.369
 G8D  N3   C4   single  1.334  0.020  1.334
 G8D  N7   C8   single  1.358  0.020  1.358
 G8D  C4   N9   single  1.373  0.020  1.373
 G8D  O2'  C2'  single  1.401  0.020  1.401
 G8D  C8   N9   single  1.401  0.020  1.401
 G8D  C8   O8   double  1.217  0.020  1.217
 G8D  N9   C1'  single  1.438  0.020  1.438
 G8D  C2'  C1'  single  1.528  0.020  1.528
 G8D  C2'  C3'  single  1.530  0.020  1.530
 G8D  O1A  PA   deloc   1.503  0.020  1.503
 G8D  C1'  O4'  single  1.401  0.020  1.401
 G8D  C3'  O3'  single  1.406  0.020  1.406
 G8D  C3'  C4'  single  1.524  0.020  1.524
 G8D  PA   O5'  single  1.668  0.020  1.668
 G8D  PA   O2A  deloc   1.503  0.020  1.503
 G8D  PA   O3A  single  1.603  0.020  1.603
 G8D  O5'  C5'  single  1.404  0.020  1.404
 G8D  O4'  C4'  single  1.431  0.020  1.431
 G8D  O1B  PB   deloc   1.522  0.020  1.522
 G8D  C4'  C5'  single  1.515  0.020  1.515
 G8D  O3A  PB   single  1.730  0.020  1.730
 G8D  O3B  PB   deloc   1.520  0.020  1.520
 G8D  PB   O2B  deloc   1.522  0.020  1.522
 G8D  C5'  H4   single  0.970  0.020  1.090
 G8D  C5'  H5   single  0.970  0.020  1.090
 G8D  C4'  H6   single  0.970  0.020  1.090
 G8D  C3'  H7   single  0.970  0.020  1.090
 G8D  O3'  H8   single  0.850  0.020  0.980
 G8D  C2'  H9   single  0.970  0.020  1.090
 G8D  O2'  H10  single  0.850  0.020  0.980
 G8D  C1'  H11  single  0.970  0.020  1.090
 G8D  N2   H12  single  0.860  0.020  1.020
 G8D  N2   H13  single  0.860  0.020  1.020
 G8D  N1   H14  single  0.860  0.020  1.020
 G8D  N7   H15  single  0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 G8D  O3A  PB   O1B  104.29  3.000
 G8D  O3A  PB   O2B  101.17  3.000
 G8D  O1B  PB   O2B  115.04  3.000
 G8D  O2B  PB   O3B  114.68  3.000
 G8D  O3A  PB   O3B  103.92  3.000
 G8D  O1B  PB   O3B  115.26  3.000
 G8D  PA   O3A  PB   123.98  3.000
 G8D  O5'  PA   O2A  107.78  3.000
 G8D  O2A  PA   O1A  118.56  3.000
 G8D  O5'  PA   O1A  107.74  3.000
 G8D  O2A  PA   O3A  112.41  3.000
 G8D  O5'  PA   O3A   94.04  3.000
 G8D  O1A  PA   O3A  113.17  3.000
 G8D  C5'  O5'  PA   116.96  3.000
 G8D  H5   C5'  H4   107.40  3.000
 G8D  H5   C5'  C4'  107.52  3.000
 G8D  H4   C5'  C4'  110.62  3.000
 G8D  H5   C5'  O5'  111.52  3.000
 G8D  H4   C5'  O5'  111.28  3.000
 G8D  C4'  C5'  O5'  108.43  3.000
 G8D  H6   C4'  C3'  109.98  3.000
 G8D  H6   C4'  O4'  108.24  3.000
 G8D  C3'  C4'  O4'  105.84  3.000
 G8D  H6   C4'  C5'  108.53  3.000
 G8D  O4'  C4'  C5'  110.98  3.000
 G8D  C3'  C4'  C5'  113.14  3.000
 G8D  C1'  O4'  C4'  110.64  3.000
 G8D  H7   C3'  C2'  111.82  3.000
 G8D  H7   C3'  O3'  111.36  3.000
 G8D  C2'  C3'  O3'  110.82  3.000
 G8D  H7   C3'  C4'  111.87  3.000
 G8D  O3'  C3'  C4'  108.92  3.000
 G8D  C2'  C3'  C4'  101.64  3.000
 G8D  H8   O3'  C3'  107.57  3.000
 G8D  H9   C2'  C1'  110.65  3.000
 G8D  H9   C2'  O2'  111.71  3.000
 G8D  C1'  C2'  O2'  109.55  3.000
 G8D  H9   C2'  C3'  109.07  3.000
 G8D  C1'  C2'  C3'  100.88  3.000
 G8D  O2'  C2'  C3'  114.49  3.000
 G8D  H10  O2'  C2'  108.70  3.000
 G8D  H11  C1'  N9   105.23  3.000
 G8D  H11  C1'  C2'  108.97  3.000
 G8D  N9   C1'  C2'  115.27  3.000
 G8D  H11  C1'  O4'  110.75  3.000
 G8D  C2'  C1'  O4'  106.30  3.000
 G8D  N9   C1'  O4'  110.35  3.000
 G8D  C4   N9   C8   109.44  3.000
 G8D  C8   N9   C1'  125.87  3.000
 G8D  C4   N9   C1'  124.46  3.000
 G8D  N7   C8   O8   127.82  3.000
 G8D  O8   C8   N9   126.76  3.000
 G8D  N7   C8   N9   105.42  3.000
 G8D  C5   C4   N3   126.97  3.000
 G8D  N3   C4   N9   125.48  3.000
 G8D  C5   C4   N9   107.55  3.000
 G8D  C2   N3   C4   113.92  3.000
 G8D  N1   C2   N2   117.50  3.000
 G8D  N2   C2   N3   119.79  3.000
 G8D  N1   C2   N3   122.70  3.000
 G8D  H13  N2   H12  117.12  3.000
 G8D  H13  N2   C2   121.54  3.000
 G8D  H12  N2   C2   118.24  3.000
 G8D  H14  N1   C6   115.75  3.000
 G8D  H14  N1   C2   118.50  3.000
 G8D  C6   N1   C2   125.74  3.000
 G8D  C5   C6   O6   128.78  3.000
 G8D  C5   C6   N1   110.20  3.000
 G8D  O6   C6   N1   121.02  3.000
 G8D  N7   C5   C6   132.25  3.000
 G8D  N7   C5   C4   107.29  3.000
 G8D  C6   C5   C4   120.46  3.000
 G8D  H15  N7   C5   126.28  3.000
 G8D  H15  N7   C8   123.42  3.000
 G8D  C5   N7   C8   110.30  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 G8D  CONST_01  C5   C4   N9   C1'  180.00   0.0  0
 G8D  CONST_02  N3   C4   N9   C1'    0.00   0.0  0
 G8D  CONST_03  N7   C8   N9   C1'  180.00   0.0  0
 G8D  CONST_04  N7   C5   C4   N9     0.00   0.0  0
 G8D  CONST_05  C2   N3   C4   N9   180.00   0.0  0
 G8D  CONST_06  C5   N7   C8   N9     0.00   0.0  0
 G8D  CONST_07  C4   C5   N7   C8     0.00   0.0  0
 G8D  CONST_08  C5   C4   N9   C8     0.00   0.0  0
 G8D  CONST_09  N3   C4   N9   C8   180.00   0.0  0
 G8D  CONST_10  N1   C2   N3   C4     0.00   0.0  0
 G8D  CONST_11  N7   C8   N9   C4     0.00   0.0  0
 G8D  CONST_12  C6   N1   C2   N3     0.00   0.0  0
 G8D  CONST_13  C5   C6   N1   C2     0.00   0.0  0
 G8D  CONST_14  C5   C4   N3   C2     0.00   0.0  0
 G8D  CONST_15  O8   C8   N9   C1'    0.00   0.0  0
 G8D  CONST_16  C5   N7   C8   O8   180.00   0.0  0
 G8D  CONST_17  C4   N9   C8   O8   180.00   0.0  0
 G8D  CONST_18  N2   C2   N3   C4   180.00   0.0  0
 G8D  CONST_19  O6   C6   N1   C2   180.00   0.0  0
 G8D  CONST_20  C6   N1   C2   N2   180.00   0.0  0
 G8D  CONST_21  H15  N7   C8   N9   180.00   0.0  0
 G8D  CONST_22  H14  N1   C2   N3   180.00   0.0  0
 G8D  CONST_23  H12  N2   C2   N3     0.00   0.0  0
 G8D  CONST_24  H13  N2   C2   N3   180.00   0.0  0
 G8D  Var_01    C4'  C5'  O5'  PA   170.24  30.0  3
 G8D  Var_02    O1A  PA   O3A  PB    52.90  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 G8D  chir_02  C4'  C3'  O4'  C5'  positiv
 G8D  chir_03  C3'  O3'  C2'  C4'  negativ
 G8D  chir_04  C2'  O2'  C1'  C3'  negativ
 G8D  chir_05  C1'  O4'  N9   C2'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 G8D  plan-1  C1'  0.020
 G8D  plan-1  N9   0.020
 G8D  plan-1  C8   0.020
 G8D  plan-1  O8   0.020
 G8D  plan-1  C4   0.020
 G8D  plan-1  N3   0.020
 G8D  plan-1  C2   0.020
 G8D  plan-1  N2   0.020
 G8D  plan-1  N1   0.020
 G8D  plan-1  C6   0.020
 G8D  plan-1  O6   0.020
 G8D  plan-1  C5   0.020
 G8D  plan-1  N7   0.020
 G8D  plan-1  H12  0.020
 G8D  plan-1  H13  0.020
 G8D  plan-1  H14  0.020
 G8D  plan-1  H15  0.020

