# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 26 15:10:09 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)c2n1
#
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
 CXC  CXC  "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"  ligand  49  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CXC
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
 CXC  O5'  O  O2    0  -0.579  48.6883  46.4600  -23.3305
 CXC  C5'  C  CH2   0  -0.228  49.8691  46.4928  -22.5066
 CXC  C4'  C  CH1   0  -0.002  50.3492  47.9276  -22.3989
 CXC  O4'  O  O2    0  -0.471  51.3550  47.9518  -21.3916
 CXC  C1'  C  CH1   0   0.037  52.4014  48.8070  -21.7481
 CXC  N1   N  N     0  -0.430  57.4409  49.0689  -22.3384
 CXC  C6   C  CR6   0   0.374  57.0709  47.7920  -22.3934
 CXC  C2   C  CR6   0   0.543  56.5094  50.0200  -22.1644
 CXC  N3   N  N     0  -0.627  55.1945  49.8465  -22.0260
 CXC  C4   C  CR56  0   0.491  54.8582  48.5625  -22.0845
 CXC  C5   C  CR56  0  -0.078  55.7029  47.4806  -22.2640
 CXC  C2'  C  CH1   0   0.041  51.9483  49.5537  -23.0095
 CXC  O2'  O  OH1   0  -0.604  51.1729  50.6697  -22.6745
 CXC  C3'  C  CH1   0  -0.120  51.0306  48.5119  -23.6439
 CXC  O3'  O  OH1   0  -0.694  50.1584  49.0699  -24.5773
 CXC  C8   C  CR15  0   0.073  53.7607  46.6657  -22.0867
 CXC  N6   N  NH2   0  -0.799  58.0033  46.8528  -22.5738
 CXC  N7   N  N     0  -0.479  54.9959  46.3037  -22.2617
 CXC  N9   N  NR5   0  -0.471  53.6086  48.0268  -21.9759
 CXC  O1A  O  OH1   0  -0.667  48.6582  44.2089  -24.3742
 CXC  O1B  O  OH1   0  -0.567  44.9595  46.2961  -26.2982
 CXC  O1G  O  OH1   0  -0.687  47.6870  47.8072  -29.7280
 CXC  O2A  O  O     0  -0.672  49.6926  46.1556  -25.7286
 CXC  O2B  O  O     0  -0.727  46.5633  44.2645  -26.8041
 CXC  O2G  O  OH1   0  -0.620  49.3774  47.1201  -28.1412
 CXC  O3A  O  O2    0  -0.730  47.1741  46.1540  -25.1651
 CXC  O3B  O  O2    0  -0.797  46.9437  46.7416  -27.5935
 CXC  O3G  O  O     0  -0.593  48.0448  45.2377  -29.3980
 CXC  PA   P  P     0   1.487  48.6679  45.7470  -24.7307
 CXC  PB   P  P     0   1.429  46.3965  45.6935  -26.5239
 CXC  PG   P  P     0   1.378  48.0585  46.5798  -28.8000
 CXC  H1   H  HCH2  0   0.294  49.5753  46.1102  -21.5296
 CXC  H2   H  HCH2  0   0.211  50.6560  45.8450  -22.9028
 CXC  H3   H  HCH1  0   0.239  49.5072  48.5645  -22.1012
 CXC  H4   H  HCH1  0   0.311  52.6148  49.5014  -20.9294
 CXC  H5   H  HCH1  0   0.272  52.7957  49.8159  -23.6527
 CXC  H6   H  HOH1  0   0.465  51.7509  51.3469  -22.3076
 CXC  H7   H  HCH1  0   0.253  51.6674  47.7385  -24.0939
 CXC  H8   H  HOH1  0   0.444  50.0350  48.4435  -25.2958
 CXC  H9   H  HCR5  0   0.300  52.9240  45.9888  -22.0239
 CXC  H10  H  HNH2  0   0.428  56.3556  52.0095  -21.8000
 CXC  H11  H  HNH2  0   0.430  57.9479  51.4418  -22.0157
 CXC  H12  H  HNH2  0   0.359  58.9753  47.1051  -22.6180
 CXC  H13  H  HNH2  0   0.372  57.7623  45.8776  -22.5704
 CXC  H14  H  HOH1  0   0.518  48.9430  43.6081  -25.0794
 CXC  H15  H  HOH1  0   0.562  44.3337  45.7076  -25.8495
 CXC  H16  H  HOH1  0   0.488  47.1141  47.5817  -30.4743
 CXC  H17  H  HOH1  0   0.531  49.5932  46.7426  -27.2460
 CXC  N2   N  NH2   0  -0.692  56.9643  51.2978  -22.1664

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
 CXC  O3G  PG   double    1.469  0.020  1.469
 CXC  O1G  PG   single    1.583  0.020  1.583
 CXC  PG   O3B  single    1.651  0.020  1.651
 CXC  PG   O2G  single    1.570  0.020  1.570
 CXC  O3B  PB   single    1.594  0.020  1.594
 CXC  O2B  PB   double    1.466  0.020  1.466
 CXC  PB   O1B  single    1.575  0.020  1.575
 CXC  PB   O3A  single    1.632  0.020  1.632
 CXC  O2A  PA   double    1.488  0.020  1.488
 CXC  O3'  C3'  single    1.394  0.020  1.394
 CXC  O3A  PA   single    1.608  0.020  1.608
 CXC  PA   O1A  single    1.579  0.020  1.579
 CXC  PA   O5'  single    1.571  0.020  1.571
 CXC  O2'  C2'  single    1.400  0.020  1.400
 CXC  C3'  C2'  single    1.526  0.020  1.526
 CXC  C3'  C4'  single    1.535  0.020  1.535
 CXC  C2'  C1'  single    1.534  0.020  1.534
 CXC  O5'  C5'  single    1.440  0.020  1.440
 CXC  C4'  C5'  single    1.517  0.020  1.517
 CXC  C4'  O4'  single    1.424  0.020  1.424
 CXC  C1'  O4'  single    1.398  0.020  1.398
 CXC  C1'  N9   single    1.455  0.020  1.455
 CXC  N9   C8   aromatic  1.374  0.020  1.374
 CXC  N9   C4   aromatic  1.364  0.020  1.364
 CXC  C8   N7   aromatic  1.299  0.020  1.299
 CXC  C4   N3   aromatic  1.329  0.020  1.329
 CXC  C4   C5   aromatic  1.384  0.020  1.384
 CXC  N7   C5   aromatic  1.373  0.020  1.373
 CXC  N3   C2   aromatic  1.333  0.020  1.333
 CXC  C5   C6   aromatic  1.409  0.020  1.409
 CXC  C2   N2   single    1.356  0.020  1.356
 CXC  C2   N1   aromatic  1.343  0.020  1.343
 CXC  C6   N1   aromatic  1.331  0.020  1.331
 CXC  C6   N6   single    1.336  0.020  1.336
 CXC  C5'  H1   single    0.970  0.020  1.090
 CXC  C5'  H2   single    0.970  0.020  1.090
 CXC  C4'  H3   single    0.970  0.020  1.090
 CXC  C1'  H4   single    0.970  0.020  1.090
 CXC  C2'  H5   single    0.970  0.020  1.090
 CXC  O2'  H6   single    0.850  0.020  0.980
 CXC  C3'  H7   single    0.970  0.020  1.090
 CXC  O3'  H8   single    0.850  0.020  0.980
 CXC  C8   H9   single    0.930  0.020  1.080
 CXC  N2   H10  single    0.890  0.020  1.040
 CXC  N2   H11  single    0.890  0.020  1.040
 CXC  N6   H12  single    0.860  0.020  1.020
 CXC  N6   H13  single    0.860  0.020  1.020
 CXC  O1A  H14  single    0.850  0.020  0.980
 CXC  O1B  H15  single    0.850  0.020  0.980
 CXC  O1G  H16  single    0.850  0.020  0.980
 CXC  O2G  H17  single    0.850  0.020  0.980

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
 CXC  PA   O5'  C5'  122.05  3.000
 CXC  H2   C5'  H1   108.11  3.000
 CXC  H2   C5'  C4'  110.99  3.000
 CXC  H1   C5'  C4'  110.72  3.000
 CXC  H2   C5'  O5'  111.67  3.000
 CXC  H1   C5'  O5'  106.49  3.000
 CXC  C4'  C5'  O5'  108.76  3.000
 CXC  H3   C4'  C3'  109.87  3.000
 CXC  H3   C4'  O4'  109.90  3.000
 CXC  C3'  C4'  O4'  104.70  3.000
 CXC  H3   C4'  C5'  109.00  3.000
 CXC  O4'  C4'  C5'  106.86  3.000
 CXC  C3'  C4'  C5'  116.30  3.000
 CXC  C1'  O4'  C4'  111.03  3.000
 CXC  H4   C1'  N9   107.18  3.000
 CXC  H4   C1'  C2'  111.33  3.000
 CXC  N9   C1'  C2'  112.16  3.000
 CXC  H4   C1'  O4'  110.09  3.000
 CXC  N9   C1'  O4'  109.45  3.000
 CXC  C2'  C1'  O4'  106.64  3.000
 CXC  C2   N1   C6   119.49  3.000
 CXC  N6   C6   C5   122.33  3.000
 CXC  N6   C6   N1   119.09  3.000
 CXC  C5   C6   N1   118.57  3.000
 CXC  N2   C2   N3   116.97  3.000
 CXC  N2   C2   N1   115.75  3.000
 CXC  N3   C2   N1   127.25  3.000
 CXC  C4   N3   C2   111.77  3.000
 CXC  N9   C4   C5   105.21  3.000
 CXC  C5   C4   N3   127.34  3.000
 CXC  N9   C4   N3   127.45  3.000
 CXC  N7   C5   C4   110.82  3.000
 CXC  N7   C5   C6   133.60  3.000
 CXC  C4   C5   C6   115.57  3.000
 CXC  H5   C2'  C3'  112.60  3.000
 CXC  H5   C2'  O2'  112.22  3.000
 CXC  C3'  C2'  O2'  108.10  3.000
 CXC  H5   C2'  C1'  111.76  3.000
 CXC  C3'  C2'  C1'  100.78  3.000
 CXC  O2'  C2'  C1'  110.78  3.000
 CXC  H6   O2'  C2'  108.63  3.000
 CXC  H7   C3'  O3'  111.73  3.000
 CXC  H7   C3'  C2'  107.60  3.000
 CXC  O3'  C3'  C2'  112.41  3.000
 CXC  H7   C3'  C4'  108.76  3.000
 CXC  C2'  C3'  C4'  100.93  3.000
 CXC  O3'  C3'  C4'  114.70  3.000
 CXC  H8   O3'  C3'  108.66  3.000
 CXC  H9   C8   N9   122.09  3.000
 CXC  H9   C8   N7   124.81  3.000
 CXC  N9   C8   N7   113.09  3.000
 CXC  H13  N6   H12  118.40  3.000
 CXC  H13  N6   C6   120.98  3.000
 CXC  H12  N6   C6   120.31  3.000
 CXC  C8   N7   C5   104.53  3.000
 CXC  C8   N9   C4   106.33  3.000
 CXC  C4   N9   C1'  124.19  3.000
 CXC  C8   N9   C1'  129.46  3.000
 CXC  H14  O1A  PA   115.96  3.000
 CXC  H15  O1B  PB   115.04  3.000
 CXC  H16  O1G  PG   114.24  3.000
 CXC  H17  O2G  PG   115.41  3.000
 CXC  PB   O3A  PA   126.59  3.000
 CXC  PG   O3B  PB   131.12  3.000
 CXC  O3A  PA   O2A  112.90  3.000
 CXC  O3A  PA   O1A  107.57  3.000
 CXC  O2A  PA   O1A  115.04  3.000
 CXC  O1A  PA   O5'  103.94  3.000
 CXC  O3A  PA   O5'   97.92  3.000
 CXC  O2A  PA   O5'  117.65  3.000
 CXC  O3B  PB   O3A  102.10  3.000
 CXC  O3A  PB   O2B  112.34  3.000
 CXC  O3B  PB   O2B  118.27  3.000
 CXC  O3A  PB   O1B  101.97  3.000
 CXC  O2B  PB   O1B  120.29  3.000
 CXC  O3B  PB   O1B   99.08  3.000
 CXC  O3G  PG   O3B  112.38  3.000
 CXC  O3B  PG   O2G  103.12  3.000
 CXC  O3G  PG   O2G  119.53  3.000
 CXC  O2G  PG   O1G  100.15  3.000
 CXC  O3B  PG   O1G  101.19  3.000
 CXC  O3G  PG   O1G  117.87  3.000
 CXC  H11  N2   H10  115.86  3.000
 CXC  H11  N2   C2   117.57  3.000
 CXC  H10  N2   C2   117.59  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
 CXC  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 CXC  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 CXC  CONST_03  N7   C5   C6   N1    180.00   0.0  0
 CXC  CONST_04  N9   C4   C5   C6    180.00   0.0  0
 CXC  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 CXC  CONST_06  C8   N7   C5   C6    180.00   0.0  0
 CXC  CONST_07  N3   C2   N1   C6      0.00   0.0  0
 CXC  CONST_08  N9   C4   N3   C2    180.00   0.0  0
 CXC  CONST_09  C5   C4   N3   C2      0.00   0.0  0
 CXC  CONST_10  C5   C6   N1   C2      0.00   0.0  0
 CXC  CONST_11  C8   N9   C4   N3    180.00   0.0  0
 CXC  CONST_12  N7   C5   C4   N3    180.00   0.0  0
 CXC  CONST_13  N7   C8   N9   C4      0.00   0.0  0
 CXC  CONST_14  C8   N7   C5   C4      0.00   0.0  0
 CXC  CONST_15  C8   N9   C4   C5      0.00   0.0  0
 CXC  CONST_16  N9   C8   N7   C5      0.00   0.0  0
 CXC  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 CXC  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 CXC  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 CXC  CONST_20  C5   C4   N9   C1'   180.00   0.0  0
 CXC  CONST_21  N2   C2   N1   C6    180.00   0.0  0
 CXC  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 CXC  CONST_23  N2   C2   N3   C4    180.00   0.0  0
 CXC  CONST_24  N6   C6   C5   C4    180.00   0.0  0
 CXC  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 CXC  CONST_26  H9   C8   N9   C1'     0.00   0.0  0
 CXC  CONST_27  H9   C8   N9   C4    180.00   0.0  0
 CXC  CONST_28  H9   C8   N7   C5    180.00   0.0  0
 CXC  CONST_31  H12  N6   C6   N1      0.00   0.0  0
 CXC  CONST_32  H13  N6   C6   N1    180.00   0.0  0
 CXC  CONST_35  H12  N6   C6   C5    180.00   0.0  0
 CXC  CONST_36  H13  N6   C6   C5      0.00   0.0  0
 CXC  Var_01    PA   O5'  C5'  C4'   113.96  30.0  1
 CXC  Var_02    PB   O3A  PA   O5'  -176.77  30.0  1
 CXC  Var_03    O2A  PA   O5'  C5'   -54.72  30.0  1
 CXC  Var_04    O3A  PA   O5'  C5'  -175.82  30.0  1
 CXC  Var_05    O1A  PA   O5'  C5'    73.78  30.0  1
 CXC  Var_06    PB   O3A  PA   O1A   -69.36  30.0  1
 CXC  Var_07    PG   O3B  PB   O1B  -151.70  30.0  1
 CXC  Var_08    PA   O3A  PB   O1B   174.88  30.0  3
 CXC  Var_09    PB   O3B  PG   O1G   160.12  30.0  3
 CXC  Var_10    PB   O3A  PA   O2A    58.65  30.0  1
 CXC  Var_11    PG   O3B  PB   O2B   -19.95  30.0  1
 CXC  Var_12    PA   O3A  PB   O2B    44.75  30.0  3
 CXC  Var_13    PB   O3B  PG   O2G   -96.55  30.0  3
 CXC  Var_14    PG   O3B  PB   O3A   103.87  30.0  1
 CXC  Var_15    PA   O3A  PB   O3B   -82.97  30.0  3
 CXC  Var_16    PB   O3B  PG   O3G    33.48  30.0  3
 CXC  Var_17    H1   C5'  O5'  PA   -126.68  30.0  3
 CXC  Var_18    H2   C5'  O5'  PA     -8.87  30.0  3

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
 CXC  chir_01  C4'  C3'  C5'  O4'  negativ
 CXC  chir_02  C1'  O4'  N9   C2'  negativ
 CXC  chir_03  C2'  O2'  C1'  C3'  negativ
 CXC  chir_04  C3'  O3'  C4'  C2'  positiv
 CXC  chir_05  PA   O3A  O1A  O5'  both
 CXC  chir_06  PB   O1B  O2B  O3B  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
 CXC  plan-1  C1'  0.020
 CXC  plan-1  N1   0.020
 CXC  plan-1  C6   0.020
 CXC  plan-1  C2   0.020
 CXC  plan-1  N3   0.020
 CXC  plan-1  C4   0.020
 CXC  plan-1  C5   0.020
 CXC  plan-1  C8   0.020
 CXC  plan-1  N6   0.020
 CXC  plan-1  N7   0.020
 CXC  plan-1  N9   0.020
 CXC  plan-1  H9   0.020
 CXC  plan-1  N2   0.020
 CXC  plan-2  C6   0.020
 CXC  plan-2  N6   0.020
 CXC  plan-2  H12  0.020
 CXC  plan-2  H13  0.020
 CXC  plan-3  C2   0.020
 CXC  plan-3  H10  0.020
 CXC  plan-3  H11  0.020
 CXC  plan-3  N2   0.020

