# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 23:37:39 2021
#   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  44  29  .  2022-07-25  2022-11-17
;
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  OH1   0  -0.722  18.4365  16.3052  24.1151
 G8D  PB   P  P     0   1.459  19.4772  17.0960  25.0100
 G8D  O2B  O  OH1   0  -0.717  19.1671  16.5736  26.4757
 G8D  O1B  O  O     0  -0.690  19.6056  18.5503  24.8283
 G8D  O3A  O  O2    0  -0.688  20.8210  16.2620  24.6453
 G8D  PA   P  P     0   1.481  21.8446  16.6055  23.4391
 G8D  O1A  O  O     0  -0.690  21.2019  17.0854  22.1978
 G8D  O2A  O  OH1   0  -0.754  22.6075  15.2331  23.3937
 G8D  O5'  O  O2    0  -0.574  22.8245  17.7126  24.0160
 G8D  C5'  C  CH2   0  -0.245  23.6746  17.5014  25.1503
 G8D  C4'  C  CH1   0   0.016  25.1247  17.4429  24.7408
 G8D  O4'  O  O2    0  -0.497  25.3959  16.2324  24.0365
 G8D  C3'  C  CH1   0  -0.065  25.5966  18.6106  23.8359
 G8D  O3'  O  OH1   0  -0.663  26.8006  19.1769  24.2816
 G8D  C2'  C  CH1   0   0.011  25.8679  17.8912  22.5080
 G8D  O2'  O  OH1   0  -0.655  26.8541  18.4372  21.6938
 G8D  C1'  C  CH1   0   0.211  26.3238  16.5328  23.0285
 G8D  N9   N  NR5   0  -0.634  26.4031  15.4778  22.0634
 G8D  C8   C  CR5   0   0.672  27.6336  14.8731  21.7503
 G8D  O8   O  O     0  -0.494  28.6841  15.0481  22.3368
 G8D  C4   C  CR56  0   0.561  25.4453  15.0320  21.1858
 G8D  N3   N  N     0  -0.654  24.1420  15.3553  21.1940
 G8D  C2   C  CR6   0   0.758  23.4409  14.8406  20.1915
 G8D  N2   N  NH2   0  -0.849  22.1530  15.1374  20.0665
 G8D  N1   N  NR16  0  -0.723  23.9945  13.9998  19.2833
 G8D  C6   C  CR6   0   0.529  25.3264  13.5625  19.2713
 G8D  O6   O  O     0  -0.471  25.7230  12.7757  18.4278
 G8D  C5   C  CR56  0   0.092  26.0546  14.1731  20.3163
 G8D  N7   N  NR15  0  -0.739  27.3883  14.0851  20.6769
 G8D  H1   H  HOH1  0   0.510  17.5618  16.7153  24.0572
 G8D  H2   H  HOH1  0   0.509  19.4800  17.1550  27.1827
 G8D  H3   H  HOH1  0   0.524  23.2885  15.2350  22.6556
 G8D  H4   H  HCH2  0   0.272  23.5333  18.3525  25.8166
 G8D  H5   H  HCH2  0   0.266  23.3990  16.6016  25.7051
 G8D  H6   H  HCH1  0   0.259  25.7069  17.4620  25.6710
 G8D  H7   H  HCH1  0   0.253  24.8188  19.3753  23.7305
 G8D  H8   H  HOH1  0   0.458  26.6309  19.6323  25.1121
 G8D  H9   H  HCH1  0   0.244  24.9131  17.7771  21.9802
 G8D  H10  H  HOH1  0   0.463  26.5072  19.2284  21.2705
 G8D  H11  H  HCH1  0   0.262  27.3370  16.6287  23.4362
 G8D  H12  H  HNH2  0   0.430  21.7351  15.8489  20.6541
 G8D  H13  H  HNH2  0   0.424  21.5942  14.7537  19.3238
 G8D  H14  H  HNR6  0   0.435  23.4063  13.6331  18.5450
 G8D  H15  H  HNR5  0   0.425  28.0880  13.5125  20.2330

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  1.220  0.020  1.220
 G8D  N1   C6   single  1.402  0.020  1.402
 G8D  N1   C2   single  1.356  0.020  1.356
 G8D  N2   C2   single  1.328  0.020  1.328
 G8D  C6   C5   single  1.412  0.020  1.412
 G8D  C2   N3   double  1.327  0.020  1.327
 G8D  C5   N7   single  1.384  0.020  1.384
 G8D  C5   C4   double  1.366  0.020  1.366
 G8D  N3   C4   single  1.343  0.020  1.343
 G8D  N7   C8   single  1.354  0.020  1.354
 G8D  C4   N9   single  1.373  0.020  1.373
 G8D  O2'  C2'  single  1.391  0.020  1.391
 G8D  C8   N9   single  1.406  0.020  1.406
 G8D  C8   O8   double  1.216  0.020  1.216
 G8D  N9   C1'  single  1.432  0.020  1.432
 G8D  C2'  C1'  single  1.524  0.020  1.524
 G8D  C2'  C3'  single  1.534  0.020  1.534
 G8D  O1A  PA   double  1.478  0.020  1.478
 G8D  C1'  O4'  single  1.403  0.020  1.403
 G8D  C3'  O3'  single  1.403  0.020  1.403
 G8D  C3'  C4'  single  1.551  0.020  1.551
 G8D  PA   O5'  single  1.587  0.020  1.587
 G8D  PA   O2A  single  1.571  0.020  1.571
 G8D  PA   O3A  single  1.619  0.020  1.619
 G8D  O5'  C5'  single  1.433  0.020  1.433
 G8D  O4'  C4'  single  1.427  0.020  1.427
 G8D  O1B  PB   double  1.471  0.020  1.471
 G8D  C4'  C5'  single  1.508  0.020  1.508
 G8D  O3A  PB   single  1.623  0.020  1.623
 G8D  O3B  PB   single  1.584  0.020  1.584
 G8D  PB   O2B  single  1.587  0.020  1.587
 G8D  O3B  H1   single  0.850  0.020  0.980
 G8D  O2B  H2   single  0.850  0.020  0.980
 G8D  O2A  H3   single  0.850  0.020  0.980
 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  H1   O3B  PB   114.58  3.000
 G8D  O3A  PB   O1B  114.07  3.000
 G8D  O3A  PB   O2B  101.55  3.000
 G8D  O1B  PB   O2B  117.17  3.000
 G8D  O2B  PB   O3B  103.24  3.000
 G8D  O3A  PB   O3B   99.24  3.000
 G8D  O1B  PB   O3B  118.76  3.000
 G8D  H2   O2B  PB   114.47  3.000
 G8D  PA   O3A  PB   125.58  3.000
 G8D  O5'  PA   O2A  108.67  3.000
 G8D  O2A  PA   O1A  118.07  3.000
 G8D  O5'  PA   O1A  110.32  3.000
 G8D  O2A  PA   O3A   98.23  3.000
 G8D  O5'  PA   O3A  105.52  3.000
 G8D  O1A  PA   O3A  114.82  3.000
 G8D  H3   O2A  PA   110.42  3.000
 G8D  C5'  O5'  PA   123.45  3.000
 G8D  H5   C5'  H4   107.46  3.000
 G8D  H5   C5'  C4'  110.40  3.000
 G8D  H4   C5'  C4'  108.72  3.000
 G8D  H5   C5'  O5'  111.94  3.000
 G8D  H4   C5'  O5'  106.96  3.000
 G8D  C4'  C5'  O5'  111.17  3.000
 G8D  H6   C4'  C3'  108.66  3.000
 G8D  H6   C4'  O4'  109.41  3.000
 G8D  C3'  C4'  O4'  107.04  3.000
 G8D  H6   C4'  C5'  106.21  3.000
 G8D  O4'  C4'  C5'  110.48  3.000
 G8D  C3'  C4'  C5'  114.96  3.000
 G8D  C1'  O4'  C4'  107.39  3.000
 G8D  H7   C3'  C2'  111.68  3.000
 G8D  H7   C3'  O3'  110.97  3.000
 G8D  C2'  C3'  O3'  108.21  3.000
 G8D  H7   C3'  C4'  111.44  3.000
 G8D  O3'  C3'  C4'  112.31  3.000
 G8D  C2'  C3'  C4'  101.87  3.000
 G8D  H8   O3'  C3'  108.29  3.000
 G8D  H9   C2'  C1'  109.38  3.000
 G8D  H9   C2'  O2'  112.11  3.000
 G8D  C1'  C2'  O2'  109.73  3.000
 G8D  H9   C2'  C3'  108.14  3.000
 G8D  C1'  C2'  C3'  100.09  3.000
 G8D  O2'  C2'  C3'  116.62  3.000
 G8D  H10  O2'  C2'  108.95  3.000
 G8D  H11  C1'  N9   105.30  3.000
 G8D  H11  C1'  C2'  108.99  3.000
 G8D  N9   C1'  C2'  116.29  3.000
 G8D  H11  C1'  O4'  111.28  3.000
 G8D  C2'  C1'  O4'  103.79  3.000
 G8D  N9   C1'  O4'  111.29  3.000
 G8D  C4   N9   C8   109.17  3.000
 G8D  C8   N9   C1'  121.02  3.000
 G8D  C4   N9   C1'  129.13  3.000
 G8D  N7   C8   O8   128.52  3.000
 G8D  O8   C8   N9   125.92  3.000
 G8D  N7   C8   N9   105.56  3.000
 G8D  C5   C4   N3   126.04  3.000
 G8D  N3   C4   N9   126.50  3.000
 G8D  C5   C4   N9   107.45  3.000
 G8D  C2   N3   C4   114.51  3.000
 G8D  N1   C2   N2   118.14  3.000
 G8D  N2   C2   N3   119.80  3.000
 G8D  N1   C2   N3   122.05  3.000
 G8D  H13  N2   H12  117.85  3.000
 G8D  H13  N2   C2   121.56  3.000
 G8D  H12  N2   C2   120.17  3.000
 G8D  H14  N1   C6   115.64  3.000
 G8D  H14  N1   C2   118.40  3.000
 G8D  C6   N1   C2   125.95  3.000
 G8D  C5   C6   O6   128.52  3.000
 G8D  C5   C6   N1   110.41  3.000
 G8D  O6   C6   N1   121.06  3.000
 G8D  N7   C5   C6   131.44  3.000
 G8D  N7   C5   C4   107.70  3.000
 G8D  C6   C5   C4   120.86  3.000
 G8D  H15  N7   C5   126.20  3.000
 G8D  H15  N7   C8   123.67  3.000
 G8D  C5   N7   C8   110.12  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   110.22  30.0  3
 G8D  Var_02    O1A  PA   O3A  PB   -37.90  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
 G8D  chir_06  PA   O5'  O2A  O3A  both

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

