# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:08:47 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: [(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](O[C@H]1CC[C@H](C1)N2C=C(C)C(=O)NC2=O)[P](O)(O)=O
#
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
 3JY  3JY  '[(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid'  ligand  41  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3JY
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
 3JY  N21  N  NR16   0  -0.732  -4.6420   0.9423   0.9377
 3JY  N6   N  NR6    0  -0.539  -3.0749  -0.4549  -0.0271
 3JY  C2   C  CR6    0   0.553  -5.5773   0.8114  -0.0717
 3JY  C22  C  CR6    0   0.731  -3.3998   0.3645   1.0256
 3JY  C7   C  CH1    0  -0.083  -1.7723  -1.1313  -0.0630
 3JY  C20  C  CH2    0  -0.471  -0.5754  -0.1884  -0.2278
 3JY  C10  C  CH1    0   0.064   0.5666  -0.9677   0.4341
 3JY  C12  C  CH1    0  -0.330   2.5212   0.1542  -0.2898
 3JY  C13  C  C      0   0.540   3.1969   1.4284   0.0805
 3JY  C9   C  CH2    0  -0.465  -0.0981  -1.5569   1.6720
 3JY  C8   C  CH2    0  -0.460  -1.4556  -2.0334   1.1584
 3JY  C5   C  CR16   0   0.056  -3.9455  -0.6243  -1.0689
 3JY  C3   C  CR6    0  -0.185  -5.1591  -0.0485  -1.1567
 3JY  C4   C  CH3    0  -0.707  -6.0817  -0.2650  -2.3112
 3JY  O1   O  O      0  -0.462  -6.6472   1.3920  -0.0061
 3JY  O11  O  O2     0  -0.510   1.6748  -0.1903   0.7908
 3JY  O14  O  O      0  -0.479   3.2654   1.8893   1.1956
 3JY  O15  O  O2     0  -0.455   3.7677   2.0097  -0.9741
 3JY  O23  O  O      0  -0.482  -2.6647   0.5742   1.9702
 3JY  P16  P  P      0   1.169   3.8729  -1.1669  -0.6070
 3JY  H1   H  HNR6   0   0.422  -4.8922   1.5398   1.7160
 3JY  H2   H  HCH1   0   0.276  -1.8305  -1.7696  -0.9433
 3JY  H3   H  HCH2   0   0.245  -0.3983   0.0509  -1.2775
 3JY  H4   H  HCH2   0   0.240  -0.7278   0.7489   0.3100
 3JY  H5   H  HCH1   0   0.209   0.8799  -1.7876  -0.2221
 3JY  H6   H  HCH1   0   0.214   1.9488   0.3037  -1.2153
 3JY  H7   H  HCH2   0   0.234   0.4909  -2.3577   2.1208
 3JY  H8   H  HCH2   0   0.225  -0.2312  -0.7715   2.4198
 3JY  H9   H  HCH2   0   0.252  -2.2278  -2.0005   1.9235
 3JY  H10  H  HCH2   0   0.244  -1.3960  -3.0683   0.8188
 3JY  H11  H  HCR6   0   0.311  -3.5899  -1.2777  -1.8543
 3JY  H12  H  HCH3   0   0.246  -7.0078  -0.7489  -1.9972
 3JY  H13  H  HCH3   0   0.245  -6.3547   0.6789  -2.7848
 3JY  H14  H  HCH3   0   0.246  -5.6159  -0.8954  -3.0670
 3JY  C1   C  CH3    0  -0.419   4.5445   3.1757  -0.7320
 3JY  H17  H  HCH3   0   0.227   3.9433   3.9882  -0.3220
 3JY  H18  H  HCH3   0   0.229   5.3754   2.9741  -0.0551
 3JY  H19  H  HCH3   0   0.242   4.9396   3.4804  -1.6974
 3JY  O18  O  O      0  -0.888   4.8839  -0.9089   0.5110
 3JY  O19  O  OP    -1  -0.868   3.1254  -2.4962  -0.4868
 3JY  O17  O  OP    -1  -0.884   4.3774  -0.8535  -2.0126

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
 3JY  O18  P16  deloc   1.529  0.020  1.529
 3JY  O19  P16  deloc   1.530  0.020  1.530
 3JY  P16  O17  deloc   1.526  0.020  1.526
 3JY  P16  C12  single  1.917  0.020  1.917
 3JY  C20  C10  single  1.533  0.020  1.533
 3JY  C20  C7   single  1.533  0.020  1.533
 3JY  O11  C10  single  1.400  0.020  1.400
 3JY  O11  C12  single  1.415  0.020  1.415
 3JY  C10  C9   single  1.524  0.020  1.524
 3JY  C12  C13  single  1.489  0.020  1.489
 3JY  C7   N6   single  1.468  0.020  1.468
 3JY  C7   C8   single  1.551  0.020  1.551
 3JY  O14  C13  double  1.209  0.020  1.209
 3JY  O23  C22  double  1.215  0.020  1.215
 3JY  C13  O15  single  1.333  0.020  1.333
 3JY  N6   C22  single  1.373  0.020  1.373
 3JY  N6   C5   single  1.368  0.020  1.368
 3JY  C22  N21  single  1.373  0.020  1.373
 3JY  C9   C8   single  1.528  0.020  1.528
 3JY  C5   C3   double  1.346  0.020  1.346
 3JY  N21  C2   single  1.382  0.020  1.382
 3JY  C3   C2   single  1.446  0.020  1.446
 3JY  C3   C4   single  1.494  0.020  1.494
 3JY  C2   O1   double  1.219  0.020  1.219
 3JY  N21  H1   single  0.860  0.020  1.020
 3JY  C7   H2   single  0.970  0.020  1.090
 3JY  C20  H3   single  0.970  0.020  1.090
 3JY  C20  H4   single  0.970  0.020  1.090
 3JY  C10  H5   single  0.970  0.020  1.090
 3JY  C12  H6   single  0.970  0.020  1.090
 3JY  C9   H7   single  0.970  0.020  1.090
 3JY  C9   H8   single  0.970  0.020  1.090
 3JY  C8   H9   single  0.970  0.020  1.090
 3JY  C8   H10  single  0.970  0.020  1.090
 3JY  C5   H11  single  0.930  0.020  1.080
 3JY  C4   H12  single  0.970  0.020  1.090
 3JY  C4   H13  single  0.970  0.020  1.090
 3JY  C4   H14  single  0.970  0.020  1.090
 3JY  O15  C1   single  1.422  0.020  1.422
 3JY  C1   H17  single  0.970  0.020  1.090
 3JY  C1   H18  single  0.970  0.020  1.090
 3JY  C1   H19  single  0.970  0.020  1.090

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
 3JY  H1   N21  C22  115.01  3.000
 3JY  H1   N21  C2   116.75  3.000
 3JY  C22  N21  C2   128.25  3.000
 3JY  C5   N6   C7   119.27  3.000
 3JY  C5   N6   C22  120.47  3.000
 3JY  C7   N6   C22  120.24  3.000
 3JY  O1   C2   C3   125.27  3.000
 3JY  O1   C2   N21  120.62  3.000
 3JY  C3   C2   N21  114.11  3.000
 3JY  O23  C22  N6   123.77  3.000
 3JY  N6   C22  N21  114.60  3.000
 3JY  O23  C22  N21  121.63  3.000
 3JY  H2   C7   C8   107.85  3.000
 3JY  H2   C7   C20  108.39  3.000
 3JY  C8   C7   C20  106.44  3.000
 3JY  H2   C7   N6   104.03  3.000
 3JY  C8   C7   N6   115.46  3.000
 3JY  C20  C7   N6   114.33  3.000
 3JY  H4   C20  H3   107.96  3.000
 3JY  H4   C20  C10  109.14  3.000
 3JY  H3   C20  C10  113.96  3.000
 3JY  H4   C20  C7   111.49  3.000
 3JY  H3   C20  C7   111.42  3.000
 3JY  C10  C20  C7   102.87  3.000
 3JY  H5   C10  O11  109.98  3.000
 3JY  H5   C10  C9   108.78  3.000
 3JY  O11  C10  C9   110.68  3.000
 3JY  H5   C10  C20  109.55  3.000
 3JY  C9   C10  C20  102.85  3.000
 3JY  O11  C10  C20  114.68  3.000
 3JY  H6   C12  P16  108.78  3.000
 3JY  H6   C12  O11  111.40  3.000
 3JY  P16  C12  O11  112.36  3.000
 3JY  H6   C12  C13  109.24  3.000
 3JY  O11  C12  C13  106.84  3.000
 3JY  P16  C12  C13  108.11  3.000
 3JY  O15  C13  O14  122.65  3.000
 3JY  O15  C13  C12  111.77  3.000
 3JY  O14  C13  C12  125.56  3.000
 3JY  H8   C9   H7   108.18  3.000
 3JY  H8   C9   C8   110.25  3.000
 3JY  H7   C9   C8   112.90  3.000
 3JY  H8   C9   C10  109.34  3.000
 3JY  H7   C9   C10  112.49  3.000
 3JY  C8   C9   C10  103.60  3.000
 3JY  H10  C8   H9   106.65  3.000
 3JY  H10  C8   C9   110.62  3.000
 3JY  H9   C8   C9   112.64  3.000
 3JY  H10  C8   C7   108.53  3.000
 3JY  H9   C8   C7   113.04  3.000
 3JY  C9   C8   C7   105.35  3.000
 3JY  H11  C5   C3   120.49  3.000
 3JY  H11  C5   N6   114.74  3.000
 3JY  C3   C5   N6   124.77  3.000
 3JY  C4   C3   C5   123.04  3.000
 3JY  C4   C3   C2   119.17  3.000
 3JY  C5   C3   C2   117.78  3.000
 3JY  H14  C4   H13  107.86  3.000
 3JY  H14  C4   H12  107.82  3.000
 3JY  H13  C4   H12  107.23  3.000
 3JY  H14  C4   C3   110.87  3.000
 3JY  H13  C4   C3   111.39  3.000
 3JY  H12  C4   C3   111.48  3.000
 3JY  C12  O11  C10  114.46  3.000
 3JY  C1   O15  C13  117.19  3.000
 3JY  O17  P16  O19  114.36  3.000
 3JY  O17  P16  O18  114.85  3.000
 3JY  O19  P16  O18  114.34  3.000
 3JY  O17  P16  C12  104.13  3.000
 3JY  O19  P16  C12  103.96  3.000
 3JY  O18  P16  C12  103.24  3.000
 3JY  H19  C1   H18  109.04  3.000
 3JY  H19  C1   H17  108.99  3.000
 3JY  H18  C1   H17  108.93  3.000
 3JY  H19  C1   O15  106.10  3.000
 3JY  H18  C1   O15  111.74  3.000
 3JY  H17  C1   O15  111.94  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
 3JY  CONST_01  C7   N6   C22  N21  180.00   0.0  0
 3JY  CONST_02  C5   N6   C22  N21    0.00   0.0  0
 3JY  CONST_03  C2   N21  C22  N6     0.00   0.0  0
 3JY  CONST_04  C3   C2   N21  C22    0.00   0.0  0
 3JY  CONST_05  O23  C22  N21  C2   180.00   0.0  0
 3JY  CONST_06  O1   C2   N21  C22  180.00   0.0  0
 3JY  CONST_07  O23  C22  N6   C7     0.00   0.0  0
 3JY  CONST_08  O23  C22  N6   C5   180.00   0.0  0
 3JY  CONST_09  H1   N21  C22  N6   180.00   0.0  0
 3JY  Var_01    C10  C9   C8   C7   -26.63  30.0  1
 3JY  Var_02    H12  C4   C3   C2   -62.43  30.0  3
 3JY  Var_03    H17  C1   O15  C13  -62.63  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
 3JY  chir_01  C7   C20  N6   C8   positiv
 3JY  chir_02  C10  O11  C9   C20  negativ
 3JY  chir_03  C12  P16  O11  C13  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
 3JY  plan-1  N21  0.020
 3JY  plan-1  N6   0.020
 3JY  plan-1  C2   0.020
 3JY  plan-1  C22  0.020
 3JY  plan-1  C7   0.020
 3JY  plan-1  C5   0.020
 3JY  plan-1  C3   0.020
 3JY  plan-1  C4   0.020
 3JY  plan-1  O1   0.020
 3JY  plan-1  O23  0.020
 3JY  plan-1  H1   0.020
 3JY  plan-1  H11  0.020
 3JY  plan-2  C12  0.020
 3JY  plan-2  C13  0.020
 3JY  plan-2  O14  0.020
 3JY  plan-2  O15  0.020

