# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jul  6 05:16:21 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O
#
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
 CXY  CXY  '[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  55  34  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CXY
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
 CXY  O1B   O  O      0  -0.799   3.5709  -1.3504  -2.6127
 CXY  PB    P  P      0   1.355   2.8469  -0.4016  -1.7119
 CXY  O2B   O  OP    -1  -0.778   2.3552   0.9229  -2.1970
 CXY  O1'   O  O2     0  -0.628   3.7391  -0.1614  -0.3348
 CXY  O3A   O  O2     0  -0.735   1.6317  -1.1818  -0.9203
 CXY  PA    P  P      0   1.338   0.5020  -2.0866  -1.6917
 CXY  O1A   O  OP    -1  -0.788   0.7630  -3.5355  -1.4229
 CXY  O2A   O  O      0  -0.800   0.2942  -1.6030  -3.0925
 CXY  O5D   O  O2     0  -0.621  -0.7427  -1.5774  -0.7394
 CXY  C5D   C  CH2    0  -0.159  -2.0420  -1.9636  -1.1346
 CXY  C4D   C  CH1    0   0.019  -2.9503  -2.0212   0.0680
 CXY  O4D   O  O2     0  -0.491  -3.0751  -0.7341   0.6434
 CXY  C3D   C  CH1    0  -0.032  -4.3702  -2.4515  -0.2966
 CXY  O3D   O  OH1    0  -0.665  -4.4764  -3.8525  -0.2354
 CXY  C2D   C  CH1    0  -0.046  -5.2275  -1.7422   0.7672
 CXY  O2D   O  OH1    0  -0.677  -5.4168  -2.5760   1.8829
 CXY  C1D   C  CH1    0   0.208  -4.3440  -0.5618   1.2102
 CXY  N1    N  NR6    0  -0.556  -4.8343   0.7697   0.8977
 CXY  C6    C  CR16   0   0.101  -4.9591   1.6741   1.8999
 CXY  C5    C  CR16   0  -0.477  -5.3635   2.9379   1.6718
 CXY  C4    C  CR6    0   0.515  -5.6322   3.2801   0.3106
 CXY  N3    N  N      0  -0.541  -5.5027   2.4074  -0.6697
 CXY  C2    C  CR6    0   0.603  -5.1126   1.1401  -0.4287
 CXY  N4    N  NH2    0  -0.807  -6.0252   4.5158   0.0082
 CXY  O2    O  O      0  -0.508  -5.0000   0.3063  -1.3162
 CXY  C1'   C  CH1    0   0.244   5.1305  -0.1718  -0.4203
 CXY  C2'   C  CH1    0  -0.001   5.7061  -0.0150   0.9940
 CXY  C3'   C  CH1    0   0.010   5.4221   1.3760   1.5383
 CXY  C4'   C  CH1    0  -0.008   5.9295   2.4083   0.5388
 CXY  C5'   C  CH2    0  -0.224   5.3303   2.1466  -0.8370
 CXY  O2'   O  OH1    0  -0.664   5.1820  -0.9639   1.8836
 CXY  O3'   O  OH1    0  -0.672   6.0642   1.5022   2.7838
 CXY  O4'   O  OH1    0  -0.673   5.5672   3.6848   1.0182
 CXY  O5'   O  O2     0  -0.496   5.6183   0.8281  -1.2678
 CXY  H5'1  H  HCH2   0   0.212  -2.0534  -2.9576  -1.5984
 CXY  H5'2  H  HCH2   0   0.215  -2.4527  -1.2568  -1.8641
 CXY  H4D   H  HCH1   0   0.229  -2.5365  -2.7253   0.8051
 CXY  H3D   H  HCH1   0   0.258  -4.6349  -2.0770  -1.2860
 CXY  H4    H  HOH1   0   0.469  -5.1605  -4.1375  -0.8489
 CXY  H2D   H  HCH1   0   0.245  -6.1894  -1.4063   0.3665
 CXY  H7    H  HOH1   0   0.447  -5.3597  -3.4867   1.5625
 CXY  H1D   H  HCH1   0   0.251  -4.2798  -0.5908   2.3026
 CXY  H6    H  HCR6   0   0.320  -4.7195   1.3248   2.8947
 CXY  H5    H  HCR6   0   0.289  -5.4636   3.6485   2.4777
 CXY  HN41  H  HNH2   0   0.403  -6.1972   4.7727  -0.9488
 CXY  HN42  H  HNH2   0   0.414  -6.1321   5.2229   0.7139
 CXY  H1'   H  HCH1   0   0.234   5.4829  -1.1131  -0.8576
 CXY  H2'   H  HCH1   0   0.219   6.7973  -0.1231   0.8980
 CXY  H3'   H  HCH1   0   0.211   4.3332   1.5048   1.6462
 CXY  H4'   H  HCH1   0   0.217   7.0224   2.3095   0.4740
 CXY  H5D   H  HCH2   0   0.238   5.7732   2.8150  -1.5778
 CXY  H5B   H  HCH2   0   0.221   4.2518   2.3350  -0.8230
 CXY  H3    H  HOH1   0   0.453   5.4861  -1.8362   1.6139
 CXY  H2    H  HOH1   0   0.448   5.9328   2.4063   3.0878
 CXY  H1    H  HOH1   0   0.459   6.1510   4.3389   0.6234

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
 CXY  O1B  PB    deloc   1.495  0.020  1.495
 CXY  PB   O2B   deloc   1.494  0.020  1.494
 CXY  PB   O1'   single  1.658  0.020  1.658
 CXY  PB   O3A   single  1.647  0.020  1.647
 CXY  O1'  C1'   single  1.394  0.020  1.394
 CXY  O3A  PA    single  1.640  0.020  1.640
 CXY  PA   O1A   deloc   1.497  0.020  1.497
 CXY  PA   O2A   deloc   1.496  0.020  1.496
 CXY  PA   O5D   single  1.648  0.020  1.648
 CXY  O5D  C5D   single  1.412  0.020  1.412
 CXY  C5D  C4D   single  1.508  0.020  1.508
 CXY  C5D  H5'1  single  0.970  0.020  1.090
 CXY  C5D  H5'2  single  0.970  0.020  1.090
 CXY  C4D  O4D   single  1.415  0.020  1.415
 CXY  C4D  C3D   single  1.528  0.020  1.528
 CXY  C4D  H4D   single  0.970  0.020  1.090
 CXY  O4D  C1D   single  1.400  0.020  1.400
 CXY  C3D  O3D   single  1.406  0.020  1.406
 CXY  C3D  C2D   single  1.539  0.020  1.539
 CXY  C3D  H3D   single  0.970  0.020  1.090
 CXY  O3D  H4    single  0.850  0.020  0.980
 CXY  C2D  O2D   single  1.406  0.020  1.406
 CXY  C2D  C1D   single  1.540  0.020  1.540
 CXY  C2D  H2D   single  0.970  0.020  1.090
 CXY  O2D  H7    single  0.850  0.020  0.980
 CXY  C1D  N1    single  1.453  0.020  1.453
 CXY  C1D  H1D   single  0.970  0.020  1.090
 CXY  N1   C6    single  1.356  0.020  1.356
 CXY  N1   C2    single  1.405  0.020  1.405
 CXY  C6   C5    double  1.346  0.020  1.346
 CXY  C6   H6    single  0.930  0.020  1.080
 CXY  C5   C4    single  1.429  0.020  1.429
 CXY  C5   H5    single  0.930  0.020  1.080
 CXY  C4   N3    double  1.319  0.020  1.319
 CXY  C4   N4    single  1.332  0.020  1.332
 CXY  N3   C2    single  1.348  0.020  1.348
 CXY  C2   O2    double  1.223  0.020  1.223
 CXY  N4   HN41  single  0.860  0.020  1.020
 CXY  N4   HN42  single  0.860  0.020  1.020
 CXY  C1'  C2'   single  1.535  0.020  1.535
 CXY  C1'  O5'   single  1.399  0.020  1.399
 CXY  C1'  H1'   single  0.970  0.020  1.090
 CXY  C2'  C3'   single  1.520  0.020  1.520
 CXY  C2'  O2'   single  1.402  0.020  1.402
 CXY  C2'  H2'   single  0.970  0.020  1.090
 CXY  C3'  C4'   single  1.524  0.020  1.524
 CXY  C3'  O3'   single  1.407  0.020  1.407
 CXY  C3'  H3'   single  0.970  0.020  1.090
 CXY  C4'  C5'   single  1.523  0.020  1.523
 CXY  C4'  O4'   single  1.411  0.020  1.411
 CXY  C4'  H4'   single  0.970  0.020  1.090
 CXY  C5'  O5'   single  1.417  0.020  1.417
 CXY  C5'  H5D   single  0.970  0.020  1.090
 CXY  C5'  H5B   single  0.970  0.020  1.090
 CXY  O2'  H3    single  0.850  0.020  0.980
 CXY  O3'  H2    single  0.850  0.020  0.980
 CXY  O4'  H1    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
 CXY  O3A   PB   O1'    93.81  3.000
 CXY  O3A   PB   O2B   109.46  3.000
 CXY  O1'   PB   O2B   108.57  3.000
 CXY  O3A   PB   O1B   110.26  3.000
 CXY  O1'   PB   O1B   109.37  3.000
 CXY  O2B   PB   O1B   121.76  3.000
 CXY  C1'   O1'  PB    119.01  3.000
 CXY  PA    O3A  PB    122.93  3.000
 CXY  O5D   PA   O2A   109.65  3.000
 CXY  O5D   PA   O1A   109.09  3.000
 CXY  O2A   PA   O1A   120.35  3.000
 CXY  O5D   PA   O3A    94.48  3.000
 CXY  O2A   PA   O3A   110.95  3.000
 CXY  O1A   PA   O3A   109.24  3.000
 CXY  C5D   O5D  PA    116.67  3.000
 CXY  H5'2  C5D  H5'1  107.40  3.000
 CXY  H5'2  C5D  C4D   109.26  3.000
 CXY  H5'1  C5D  C4D   107.23  3.000
 CXY  H5'2  C5D  O5D   110.79  3.000
 CXY  H5'1  C5D  O5D   112.07  3.000
 CXY  C4D   C5D  O5D   109.97  3.000
 CXY  H4D   C4D  C3D   109.23  3.000
 CXY  H4D   C4D  O4D   110.05  3.000
 CXY  C3D   C4D  O4D   105.73  3.000
 CXY  H4D   C4D  C5D   109.40  3.000
 CXY  C3D   C4D  C5D   112.34  3.000
 CXY  O4D   C4D  C5D   110.03  3.000
 CXY  C1D   O4D  C4D   110.87  3.000
 CXY  H3D   C3D  C2D   109.49  3.000
 CXY  H3D   C3D  O3D   111.30  3.000
 CXY  C2D   C3D  O3D   112.76  3.000
 CXY  H3D   C3D  C4D   110.21  3.000
 CXY  C2D   C3D  C4D   102.88  3.000
 CXY  O3D   C3D  C4D   109.89  3.000
 CXY  H4    O3D  C3D   108.73  3.000
 CXY  H2D   C2D  C1D   111.98  3.000
 CXY  H2D   C2D  O2D   110.74  3.000
 CXY  C1D   C2D  O2D   107.68  3.000
 CXY  H2D   C2D  C3D   112.19  3.000
 CXY  C1D   C2D  C3D   103.45  3.000
 CXY  O2D   C2D  C3D   110.50  3.000
 CXY  H7    O2D  C2D   106.72  3.000
 CXY  H1D   C1D  N1    104.99  3.000
 CXY  H1D   C1D  C2D   107.48  3.000
 CXY  N1    C1D  C2D   116.56  3.000
 CXY  H1D   C1D  O4D   110.34  3.000
 CXY  N1    C1D  O4D   109.36  3.000
 CXY  C2D   C1D  O4D   108.01  3.000
 CXY  C2    N1   C6    120.25  3.000
 CXY  C2    N1   C1D   120.76  3.000
 CXY  C6    N1   C1D   118.91  3.000
 CXY  H6    C6   C5    121.72  3.000
 CXY  H6    C6   N1    116.37  3.000
 CXY  C5    C6   N1    121.91  3.000
 CXY  H5    C5   C4    122.44  3.000
 CXY  H5    C5   C6    121.29  3.000
 CXY  C4    C5   C6    116.27  3.000
 CXY  N4    C4   N3    118.31  3.000
 CXY  N4    C4   C5    119.60  3.000
 CXY  N3    C4   C5    122.08  3.000
 CXY  C2    N3   C4    121.18  3.000
 CXY  O2    C2   N3    122.55  3.000
 CXY  O2    C2   N1    119.15  3.000
 CXY  N3    C2   N1    118.30  3.000
 CXY  HN42  N4   HN41  118.06  3.000
 CXY  HN42  N4   C4    121.68  3.000
 CXY  HN41  N4   C4    120.24  3.000
 CXY  H1'   C1'  O5'   105.07  3.000
 CXY  H1'   C1'  C2'   109.55  3.000
 CXY  O5'   C1'  C2'   110.76  3.000
 CXY  H1'   C1'  O1'   110.60  3.000
 CXY  O5'   C1'  O1'   112.33  3.000
 CXY  C2'   C1'  O1'   108.48  3.000
 CXY  H2'   C2'  O2'   111.06  3.000
 CXY  H2'   C2'  C3'   107.83  3.000
 CXY  O2'   C2'  C3'   108.80  3.000
 CXY  H2'   C2'  C1'   106.34  3.000
 CXY  O2'   C2'  C1'   112.04  3.000
 CXY  C3'   C2'  C1'   110.68  3.000
 CXY  H3'   C3'  O3'   110.72  3.000
 CXY  H3'   C3'  C4'   108.31  3.000
 CXY  O3'   C3'  C4'   111.58  3.000
 CXY  H3'   C3'  C2'   109.06  3.000
 CXY  O3'   C3'  C2'   108.28  3.000
 CXY  C4'   C3'  C2'   108.83  3.000
 CXY  H4'   C4'  O4'   110.89  3.000
 CXY  H4'   C4'  C5'   108.81  3.000
 CXY  O4'   C4'  C5'   111.18  3.000
 CXY  H4'   C4'  C3'   107.99  3.000
 CXY  O4'   C4'  C3'   107.74  3.000
 CXY  C5'   C4'  C3'   110.19  3.000
 CXY  H5B   C5'  H5D   107.64  3.000
 CXY  H5B   C5'  O5'   111.37  3.000
 CXY  H5D   C5'  O5'   106.32  3.000
 CXY  H5B   C5'  C4'   110.26  3.000
 CXY  H5D   C5'  C4'   110.37  3.000
 CXY  O5'   C5'  C4'   110.76  3.000
 CXY  H3    O2'  C2'   108.51  3.000
 CXY  H2    O3'  C3'   107.55  3.000
 CXY  H1    O4'  C4'   108.67  3.000
 CXY  C5'   O5'  C1'   114.22  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
 CXY  CONST_01  N3    C2   N1   C1D  180.00   0.0  0
 CXY  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 CXY  CONST_03  N3    C2   N1   C6     0.00   0.0  0
 CXY  CONST_04  C2    N3   C4   C5     0.00   0.0  0
 CXY  CONST_05  O2    C2   N1   C1D    0.00   0.0  0
 CXY  CONST_06  O2    C2   N1   C6   180.00   0.0  0
 CXY  CONST_07  O2    C2   N3   C4   180.00   0.0  0
 CXY  CONST_08  N4    C4   N3   C2   180.00   0.0  0
 CXY  CONST_09  HN41  N4   C4   C5   180.00   0.0  0
 CXY  CONST_10  HN42  N4   C4   C5     0.00   0.0  0
 CXY  Var_01    C4'   C5'  O5'  C1'   59.51  30.0  1
 CXY  Var_02    C4D   C5D  O5D  PA   153.35  30.0  3
 CXY  Var_03    O1A   PA   O3A  PB   107.42  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
 CXY  chir_03  C4D  C5D  O4D  C3D  negativ
 CXY  chir_04  C3D  O3D  C4D  C2D  positiv
 CXY  chir_05  C2D  O2D  C3D  C1D  positiv
 CXY  chir_06  C1D  O4D  N1   C2D  negativ
 CXY  chir_07  C1'  O1'  C2'  O5'  positiv
 CXY  chir_08  C2'  O2'  C1'  C3'  negativ
 CXY  chir_09  C3'  O3'  C2'  C4'  positiv
 CXY  chir_10  C4'  O4'  C3'  C5'  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
 CXY  plan-1  C1D   0.020
 CXY  plan-1  N1    0.020
 CXY  plan-1  C6    0.020
 CXY  plan-1  C5    0.020
 CXY  plan-1  C4    0.020
 CXY  plan-1  N3    0.020
 CXY  plan-1  C2    0.020
 CXY  plan-1  N4    0.020
 CXY  plan-1  O2    0.020
 CXY  plan-1  H6    0.020
 CXY  plan-1  H5    0.020
 CXY  plan-1  HN41  0.020
 CXY  plan-1  HN42  0.020

