# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 22:21:38 2021
#   Inital geometry file: a 141 line input string
#   Ligand name: [(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CSCC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=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
 EJ8  EJ8  '[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid'  ligand  56  34  .  2021-08-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EJ8
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
 EJ8  C2'  C  CH2   0  -0.542  -4.7489  27.8717  28.4795
 EJ8  C1'  C  CH1   0   0.174  -3.3240  27.6442  27.9383
 EJ8  O2   O  O     0  -0.468  -2.4614  28.3907  25.3944
 EJ8  O9   O  OH1   0  -0.739  -2.6024  19.2018  23.3390
 EJ8  P2   P  P     0   1.364  -3.1221  20.6168  23.8860
 EJ8  O10  O  O     0  -0.716  -4.5515  20.9246  23.6176
 EJ8  O11  O  OH1   0  -0.780  -2.0792  21.6400  23.2467
 EJ8  C18  C  CH2   0  -0.842  -2.7106  20.5061  25.6537
 EJ8  S1   S  S2    0   0.012  -2.2642  22.0998  26.3811
 EJ8  C5   C  CR6   0  -0.143  -3.4206  24.5074  25.9621
 EJ8  C4   C  CR16  0   0.087  -3.5441  25.4299  26.9349
 EJ8  C6   C  CR6   0   0.628  -2.8925  24.9325  24.6880
 EJ8  O6   O  O     0  -0.494  -2.6963  24.2143  23.7142
 EJ8  N1   N  NR16  0  -0.729  -2.6144  26.2760  24.6084
 EJ8  C8   C  CR6   0   0.742  -2.7472  27.2297  25.5881
 EJ8  N9   N  NR6   0  -0.566  -3.2290  26.7462  26.7870
 EJ8  O4'  O  O2    0  -0.488  -2.5851  27.0717  28.9831
 EJ8  C3'  C  CH1   0  -0.019  -4.7516  27.1877  29.8348
 EJ8  O3'  O  O2    0  -0.502  -5.1882  25.8468  29.6367
 EJ8  C4'  C  CH1   0   0.003  -3.2778  27.2376  30.2117
 EJ8  C5'  C  CH2   0  -0.225  -2.8755  26.1571  31.1836
 EJ8  O7   O  O2    0  -0.487  -3.4513  24.9037  30.8502
 EJ8  CAB  C  CT    0   0.268  -4.8056  24.8742  30.5624
 EJ8  P    P  P     0   1.365  -5.8840  24.9655  32.0969
 EJ8  OP1  O  OH1   0  -0.739  -5.4132  26.2716  32.8960
 EJ8  OP2  O  O     0  -0.689  -7.3322  24.8861  31.7983
 EJ8  OP3  O  OH1   0  -0.738  -5.2733  23.8302  33.0517
 EJ8  C2   C  CR6   0  -0.072  -5.1152  23.5303  29.9266
 EJ8  CAA  C  CR16  0  -0.244  -6.2983  23.3626  29.2064
 EJ8  C9   C  CR16  0  -0.248  -6.5912  22.1408  28.6206
 EJ8  C10  C  CR16  0  -0.258  -5.7107  21.0734  28.7465
 EJ8  C11  C  CR16  0  -0.229  -4.5364  21.2357  29.4658
 EJ8  C12  C  CR16  0  -0.274  -4.2398  22.4561  30.0601
 EJ8  H1   H  HCH2  0   0.293  -4.9131  28.9403  28.6143
 EJ8  H2   H  HCH2  0   0.295  -5.5284  27.5018  27.8140
 EJ8  H3   H  HCH1  0   0.282  -2.8828  28.5873  27.6195
 EJ8  H4   H  HOH1  0   0.495  -3.0104  18.9340  22.5039
 EJ8  H5   H  HOH1  0   0.505  -2.2852  22.5851  23.4469
 EJ8  H6   H  HCH2  0   0.308  -3.5348  20.0392  26.1950
 EJ8  H7   H  HCH2  0   0.326  -1.8304  19.8752  25.7908
 EJ8  H8   H  HCH2  0   0.302  -4.3796  22.6964  25.3578
 EJ8  H9   H  HCH2  0   0.310  -4.4016  22.9888  27.0880
 EJ8  H10  H  HCR6  0   0.330  -3.9230  25.1460  27.9044
 EJ8  H11  H  HNR6  0   0.435  -2.2531  26.6155  23.7244
 EJ8  H12  H  HCH1  0   0.276  -5.3830  27.7014  30.5634
 EJ8  H13  H  HCH1  0   0.269  -3.0489  28.2157  30.6516
 EJ8  H14  H  HCH2  0   0.273  -1.7963  26.0063  31.1611
 EJ8  H15  H  HCH2  0   0.249  -3.1402  26.4697  32.1946
 EJ8  H16  H  HOH1  0   0.504  -6.1451  26.8443  33.1655
 EJ8  H17  H  HOH1  0   0.498  -5.5377  22.9289  32.8246
 EJ8  H18  H  HCR6  0   0.261  -6.9946  24.1810  29.0914
 EJ8  H19  H  HCR6  0   0.262  -7.5090  22.0243  28.0593
 EJ8  H20  H  HCR6  0   0.262  -5.9410  20.1216  28.2857
 EJ8  H21  H  HCR6  0   0.260  -3.8405  20.4130  29.5628
 EJ8  H22  H  HCR6  0   0.264  -3.3172  22.5596  30.6135
 EJ8  C17  C  CH2   0  -0.672  -3.7930  23.0848  26.1898

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
 EJ8  O10  P2   double    1.487  0.020  1.487
 EJ8  O9   P2   single    1.604  0.020  1.604
 EJ8  P2   O11  single    1.595  0.020  1.595
 EJ8  P2   C18  single    1.818  0.020  1.818
 EJ8  O6   C6   double    1.226  0.020  1.226
 EJ8  C6   N1   single    1.374  0.020  1.374
 EJ8  C6   C5   single    1.443  0.020  1.443
 EJ8  C17  S1   single    1.829  0.020  1.829
 EJ8  C17  C5   single    1.488  0.020  1.488
 EJ8  C18  S1   single    1.808  0.020  1.808
 EJ8  N1   C8   single    1.374  0.020  1.374
 EJ8  C5   C4   double    1.346  0.020  1.346
 EJ8  C8   O2   double    1.211  0.020  1.211
 EJ8  C8   N9   single    1.380  0.020  1.380
 EJ8  C4   N9   single    1.362  0.020  1.362
 EJ8  N9   C1'  single    1.463  0.020  1.463
 EJ8  C1'  C2'  single    1.541  0.020  1.541
 EJ8  C1'  O4'  single    1.402  0.020  1.402
 EJ8  C2'  C3'  single    1.518  0.020  1.518
 EJ8  C9   CAA  aromatic  1.386  0.020  1.386
 EJ8  C9   C10  aromatic  1.389  0.020  1.389
 EJ8  O4'  C4'  single    1.420  0.020  1.420
 EJ8  CAA  C2   aromatic  1.395  0.020  1.395
 EJ8  O3'  C3'  single    1.424  0.020  1.424
 EJ8  O3'  CAB  single    1.396  0.020  1.396
 EJ8  C3'  C4'  single    1.522  0.020  1.522
 EJ8  C10  C11  aromatic  1.387  0.020  1.387
 EJ8  C4'  C5'  single    1.508  0.020  1.508
 EJ8  C2   CAB  single    1.519  0.020  1.519
 EJ8  C2   C12  aromatic  1.392  0.020  1.392
 EJ8  C11  C12  aromatic  1.389  0.020  1.389
 EJ8  CAB  O7   single    1.385  0.020  1.385
 EJ8  CAB  P    single    1.878  0.020  1.878
 EJ8  O7   C5'  single    1.419  0.020  1.419
 EJ8  OP2  P    double    1.481  0.020  1.481
 EJ8  P    OP1  single    1.602  0.020  1.602
 EJ8  P    OP3  single    1.604  0.020  1.604
 EJ8  C2'  H1   single    0.970  0.020  1.090
 EJ8  C2'  H2   single    0.970  0.020  1.090
 EJ8  C1'  H3   single    0.970  0.020  1.090
 EJ8  O9   H4   single    0.850  0.020  0.980
 EJ8  O11  H5   single    0.850  0.020  0.980
 EJ8  C18  H6   single    0.970  0.020  1.090
 EJ8  C18  H7   single    0.970  0.020  1.090
 EJ8  C17  H8   single    0.970  0.020  1.090
 EJ8  C17  H9   single    0.970  0.020  1.090
 EJ8  C4   H10  single    0.930  0.020  1.080
 EJ8  N1   H11  single    0.860  0.020  1.020
 EJ8  C3'  H12  single    0.970  0.020  1.090
 EJ8  C4'  H13  single    0.970  0.020  1.090
 EJ8  C5'  H14  single    0.970  0.020  1.090
 EJ8  C5'  H15  single    0.970  0.020  1.090
 EJ8  OP1  H16  single    0.850  0.020  0.980
 EJ8  OP3  H17  single    0.850  0.020  0.980
 EJ8  CAA  H18  single    0.930  0.020  1.080
 EJ8  C9   H19  single    0.930  0.020  1.080
 EJ8  C10  H20  single    0.930  0.020  1.080
 EJ8  C11  H21  single    0.930  0.020  1.080
 EJ8  C12  H22  single    0.930  0.020  1.080

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
 EJ8  H2   C2'  H1   107.50  3.000
 EJ8  H2   C2'  C3'  113.02  3.000
 EJ8  H1   C2'  C3'  109.34  3.000
 EJ8  H2   C2'  C1'  113.38  3.000
 EJ8  H1   C2'  C1'  109.12  3.000
 EJ8  C3'  C2'  C1'  104.40  3.000
 EJ8  H3   C1'  O4'  111.00  3.000
 EJ8  H3   C1'  N9   105.96  3.000
 EJ8  O4'  C1'  N9   107.56  3.000
 EJ8  H3   C1'  C2'  110.46  3.000
 EJ8  O4'  C1'  C2'  106.61  3.000
 EJ8  N9   C1'  C2'  115.27  3.000
 EJ8  H4   O9   P2   113.71  3.000
 EJ8  C18  P2   O11  106.31  3.000
 EJ8  C18  P2   O10  113.94  3.000
 EJ8  O11  P2   O10  115.06  3.000
 EJ8  C18  P2   O9   101.80  3.000
 EJ8  O11  P2   O9   102.56  3.000
 EJ8  O10  P2   O9   115.64  3.000
 EJ8  H5   O11  P2   113.34  3.000
 EJ8  H7   C18  H6   107.42  3.000
 EJ8  H7   C18  S1   105.06  3.000
 EJ8  H6   C18  S1   111.36  3.000
 EJ8  H7   C18  P2   109.87  3.000
 EJ8  H6   C18  P2   109.72  3.000
 EJ8  S1   C18  P2   113.16  3.000
 EJ8  C17  S1   C18  103.08  3.000
 EJ8  C6   C5   C4   118.01  3.000
 EJ8  C4   C5   C17  121.43  3.000
 EJ8  C6   C5   C17  120.55  3.000
 EJ8  H10  C4   N9   115.67  3.000
 EJ8  H10  C4   C5   120.08  3.000
 EJ8  N9   C4   C5   124.24  3.000
 EJ8  N1   C6   O6   119.63  3.000
 EJ8  N1   C6   C5   114.40  3.000
 EJ8  O6   C6   C5   125.96  3.000
 EJ8  H11  N1   C8   115.09  3.000
 EJ8  H11  N1   C6   116.75  3.000
 EJ8  C8   N1   C6   128.16  3.000
 EJ8  N9   C8   N1   114.22  3.000
 EJ8  N9   C8   O2   123.87  3.000
 EJ8  N1   C8   O2   121.91  3.000
 EJ8  C8   N9   C4   120.93  3.000
 EJ8  C4   N9   C1'  119.53  3.000
 EJ8  C8   N9   C1'  119.43  3.000
 EJ8  C4'  O4'  C1'  109.88  3.000
 EJ8  H12  C3'  C4'  112.28  3.000
 EJ8  H12  C3'  O3'  111.00  3.000
 EJ8  C4'  C3'  O3'  111.23  3.000
 EJ8  H12  C3'  C2'  112.62  3.000
 EJ8  C4'  C3'  C2'  101.81  3.000
 EJ8  O3'  C3'  C2'  107.49  3.000
 EJ8  CAB  O3'  C3'  118.67  3.000
 EJ8  H13  C4'  C5'  108.96  3.000
 EJ8  H13  C4'  C3'  109.31  3.000
 EJ8  C5'  C4'  C3'  113.23  3.000
 EJ8  H13  C4'  O4'  110.45  3.000
 EJ8  C5'  C4'  O4'  110.11  3.000
 EJ8  C3'  C4'  O4'  104.73  3.000
 EJ8  H15  C5'  H14  107.40  3.000
 EJ8  H15  C5'  O7   111.86  3.000
 EJ8  H14  C5'  O7   105.95  3.000
 EJ8  H15  C5'  C4'  109.10  3.000
 EJ8  H14  C5'  C4'  110.49  3.000
 EJ8  O7   C5'  C4'  111.92  3.000
 EJ8  CAB  O7   C5'  117.67  3.000
 EJ8  C2   CAB  P    105.55  3.000
 EJ8  P    CAB  O7   113.00  3.000
 EJ8  C2   CAB  O7   107.77  3.000
 EJ8  P    CAB  O3'  110.52  3.000
 EJ8  O7   CAB  O3'  113.01  3.000
 EJ8  C2   CAB  O3'  106.45  3.000
 EJ8  OP3  P    OP2  117.03  3.000
 EJ8  OP3  P    OP1   99.69  3.000
 EJ8  OP2  P    OP1  115.58  3.000
 EJ8  OP3  P    CAB  103.49  3.000
 EJ8  OP1  P    CAB  106.17  3.000
 EJ8  OP2  P    CAB  113.22  3.000
 EJ8  H16  OP1  P    113.53  3.000
 EJ8  H17  OP3  P    114.58  3.000
 EJ8  C12  C2   CAA  119.34  3.000
 EJ8  C12  C2   CAB  120.97  3.000
 EJ8  CAA  C2   CAB  119.69  3.000
 EJ8  H18  CAA  C9   119.10  3.000
 EJ8  H18  CAA  C2   120.69  3.000
 EJ8  C9   CAA  C2   120.21  3.000
 EJ8  H19  C9   C10  120.12  3.000
 EJ8  H19  C9   CAA  119.56  3.000
 EJ8  C10  C9   CAA  120.32  3.000
 EJ8  H20  C10  C11  120.27  3.000
 EJ8  H20  C10  C9   120.14  3.000
 EJ8  C11  C10  C9   119.59  3.000
 EJ8  H21  C11  C12  119.49  3.000
 EJ8  H21  C11  C10  120.15  3.000
 EJ8  C12  C11  C10  120.36  3.000
 EJ8  H22  C12  C11  119.03  3.000
 EJ8  H22  C12  C2   120.80  3.000
 EJ8  C11  C12  C2   120.17  3.000
 EJ8  H9   C17  H8   107.30  3.000
 EJ8  H9   C17  C5   110.50  3.000
 EJ8  H8   C17  C5   111.02  3.000
 EJ8  H9   C17  S1   109.47  3.000
 EJ8  H8   C17  S1   109.75  3.000
 EJ8  C5   C17  S1   108.77  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
 EJ8  CONST_01  C10  C9   CAA  C2      0.00   0.0  0
 EJ8  CONST_02  C10  C11  C12  C2      0.00   0.0  0
 EJ8  CONST_03  C11  C10  C9   CAA     0.00   0.0  0
 EJ8  CONST_04  C11  C12  C2   CAA     0.00   0.0  0
 EJ8  CONST_05  C12  C2   CAA  C9      0.00   0.0  0
 EJ8  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 EJ8  CONST_07  C9   CAA  C2   CAB   180.00   0.0  0
 EJ8  CONST_08  C11  C12  C2   CAB   180.00   0.0  0
 EJ8  CONST_09  N1   C8   N9   C1'   180.00   0.0  0
 EJ8  CONST_10  C8   N1   C6   C5      0.00   0.0  0
 EJ8  CONST_11  N1   C8   N9   C4      0.00   0.0  0
 EJ8  CONST_12  N9   C8   N1   C6      0.00   0.0  0
 EJ8  CONST_13  O2   C8   N9   C1'     0.00   0.0  0
 EJ8  CONST_14  C6   N1   C8   O2    180.00   0.0  0
 EJ8  CONST_15  C4   N9   C8   O2    180.00   0.0  0
 EJ8  CONST_16  C8   N1   C6   O6    180.00   0.0  0
 EJ8  CONST_17  H18  CAA  C2   CAB     0.00   0.0  0
 EJ8  CONST_18  H22  C12  C2   CAB     0.00   0.0  0
 EJ8  CONST_19  H19  C9   CAA  C2    180.00   0.0  0
 EJ8  CONST_20  H21  C11  C12  C2    180.00   0.0  0
 EJ8  CONST_21  H20  C10  C9   CAA   180.00   0.0  0
 EJ8  CONST_22  H11  N1   C6   C5    180.00   0.0  0
 EJ8  Var_01    H14  C5'  O7   CAB  -168.19  30.0  1
 EJ8  Var_02    C6   C5   C17  S1     74.46  30.0  3
 EJ8  Var_03    C5   C17  S1   C18  -146.63  30.0  1
 EJ8  Var_04    S1   C18  P2   O9    146.98  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
 EJ8  chir_01  C1'  N9   C2'  O4'  negativ
 EJ8  chir_02  C3'  O3'  C4'  C2'  negativ
 EJ8  chir_03  C4'  O4'  C3'  C5'  negativ
 EJ8  chir_04  CAB  O7   O3'  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
 EJ8  plan-1  C1'  0.020
 EJ8  plan-1  O2   0.020
 EJ8  plan-1  C5   0.020
 EJ8  plan-1  C4   0.020
 EJ8  plan-1  C6   0.020
 EJ8  plan-1  O6   0.020
 EJ8  plan-1  N1   0.020
 EJ8  plan-1  C8   0.020
 EJ8  plan-1  N9   0.020
 EJ8  plan-1  H10  0.020
 EJ8  plan-1  H11  0.020
 EJ8  plan-1  C17  0.020
 EJ8  plan-2  CAB  0.020
 EJ8  plan-2  C2   0.020
 EJ8  plan-2  CAA  0.020
 EJ8  plan-2  C9   0.020
 EJ8  plan-2  C10  0.020
 EJ8  plan-2  C11  0.020
 EJ8  plan-2  C12  0.020
 EJ8  plan-2  H18  0.020
 EJ8  plan-2  H19  0.020
 EJ8  plan-2  H20  0.020
 EJ8  plan-2  H21  0.020
 EJ8  plan-2  H22  0.020

