# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:21:00 2020
#   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  52  34  .  2021-08-08  2021-08-08  
;
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  -0.564   2.0859   2.1071  -1.0160
 EJ8  C1'  C  CH1    0   0.232   1.0212   2.3831  -2.0745
 EJ8  O2   O  O      0  -0.486   0.4428   4.7869  -0.9690
 EJ8  O9   O  OP    -1  -0.903  -4.1045  -3.2016   0.3360
 EJ8  P2   P  P      0   1.178  -5.2037  -2.1947  -0.0108
 EJ8  O10  O  O      0  -0.886  -5.1281  -1.6518  -1.4434
 EJ8  O11  O  OP    -1  -0.910  -6.6122  -2.6432   0.4044
 EJ8  C18  C  CH2    0  -0.823  -4.8976  -0.7266   1.1031
 EJ8  S1   S  S2     0  -0.059  -3.3008   0.1112   0.8878
 EJ8  C5   C  CR6    0  -0.160  -2.4924   2.0135  -0.8228
 EJ8  C4   C  CR16   0   0.059  -1.3074   1.7849  -1.4216
 EJ8  C6   C  CR6    0   0.561  -2.7200   3.3099  -0.2203
 EJ8  O6   O  O      0  -0.454  -3.7359   3.6603   0.3510
 EJ8  N1   N  NR16   0  -0.733  -1.6560   4.1870  -0.3563
 EJ8  C8   C  CR6    0   0.735  -0.4410   3.9526  -0.9411
 EJ8  N9   N  NR6    0  -0.569  -0.2991   2.7007  -1.4879
 EJ8  O4'  O  O2     0  -0.499   0.9098   1.2291  -2.8606
 EJ8  C3'  C  CH1    0   0.002   2.9192   1.0090  -1.6861
 EJ8  O3'  O  O2     0  -0.506   3.7332   0.2094  -0.8718
 EJ8  C4'  C  CH1    0  -0.023   1.8447   0.2392  -2.4508
 EJ8  C5'  C  CH2    0  -0.223   1.2236  -0.8067  -1.5389
 EJ8  O7   O  O2     0  -0.499   2.2614  -1.5849  -0.9874
 EJ8  CAB  C  CT     0   0.167   3.1511  -0.8726  -0.1659
 EJ8  P    P  P      0   1.173   4.5821  -2.0655   0.2480
 EJ8  OP1  O  OP    -1  -0.891   5.1366  -2.4643  -1.1193
 EJ8  OP2  O  O      0  -0.882   5.5305  -1.2156   1.0909
 EJ8  OP3  O  OP    -1  -0.883   3.8920  -3.1985   1.0041
 EJ8  C2   C  C      0   0.031   2.4963  -0.4162   1.1150
 EJ8  CAA  C  C1     0  -0.272   1.4183  -1.1091   1.6621
 EJ8  C9   C  C1     0  -0.242   0.8551  -0.7194   2.8699
 EJ8  C10  C  C1     0  -0.277   1.3827   0.3535   3.5751
 EJ8  C11  C  C1     0  -0.255   2.4799   1.0303   3.0567
 EJ8  C12  C  C1     0  -0.266   3.0336   0.6440   1.8450
 EJ8  H1   H  HCH2   0   0.280   2.6681   2.9952  -0.7799
 EJ8  H2   H  HCH2   0   0.271   1.6242   1.7546  -0.0929
 EJ8  H3   H  HCH1   0   0.271   1.2868   3.2283  -2.7123
 EJ8  H6   H  HCH2   0   0.226  -5.6867   0.0257   1.0053
 EJ8  H7   H  HCH2   0   0.237  -4.9051  -1.0449   2.1500
 EJ8  H8   H  HCH2   0   0.276  -3.4616   0.2289  -1.5225
 EJ8  H9   H  HCH2   0   0.262  -4.5316   1.3824  -0.7387
 EJ8  H10  H  HCR6   0   0.317  -1.1087   0.8356  -1.8953
 EJ8  H11  H  HNR6   0   0.425  -1.7702   5.1082   0.0492
 EJ8  H12  H  HCH1   0   0.261   3.5978   1.4813  -2.4032
 EJ8  H13  H  HCH1   0   0.262   2.2394  -0.2376  -3.3506
 EJ8  H14  H  HCH2   0   0.203   0.6151  -0.3349  -0.7543
 EJ8  H15  H  HCH2   0   0.257   0.5658  -1.4779  -2.0949
 EJ8  H18  H  H      0   0.237   1.0040  -1.9585   1.1363
 EJ8  H19  H  H      0   0.239   0.0041  -1.2615   3.2633
 EJ8  H20  H  H      0   0.242   0.9467   0.6572   4.5185
 EJ8  H21  H  H      0   0.240   2.9100   1.8615   3.6021
 EJ8  H22  H  H      0   0.232   3.8873   1.1814   1.4569
 EJ8  C17  C  CH2    0  -0.609  -3.5302   0.9510  -0.7128

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   deloc     1.534  0.020  1.534
 EJ8  O9   P2   deloc     1.530  0.020  1.530
 EJ8  P2   O11  deloc     1.535  0.020  1.535
 EJ8  P2   C18  single    1.868  0.020  1.868
 EJ8  O6   C6   double    1.217  0.020  1.217
 EJ8  C6   N1   single    1.386  0.020  1.386
 EJ8  C6   C5   single    1.448  0.020  1.448
 EJ8  C17  S1   single    1.822  0.020  1.822
 EJ8  C17  C5   single    1.489  0.020  1.489
 EJ8  C18  S1   single    1.816  0.020  1.816
 EJ8  N1   C8   single    1.369  0.020  1.369
 EJ8  C5   C4   double    1.347  0.020  1.347
 EJ8  C8   O2   double    1.216  0.020  1.216
 EJ8  C8   N9   single    1.374  0.020  1.374
 EJ8  C4   N9   single    1.364  0.020  1.364
 EJ8  N9   C1'  single    1.479  0.020  1.479
 EJ8  C1'  C2'  single    1.526  0.020  1.526
 EJ8  C1'  O4'  single    1.401  0.020  1.401
 EJ8  C2'  C3'  single    1.533  0.020  1.533
 EJ8  C9   CAA  aromatic  1.389  0.020  1.389
 EJ8  C9   C10  aromatic  1.388  0.020  1.388
 EJ8  O4'  C4'  single    1.422  0.020  1.422
 EJ8  CAA  C2   aromatic  1.393  0.020  1.393
 EJ8  O3'  C3'  single    1.402  0.020  1.402
 EJ8  O3'  CAB  single    1.417  0.020  1.417
 EJ8  C3'  C4'  single    1.527  0.020  1.527
 EJ8  C10  C11  aromatic  1.390  0.020  1.390
 EJ8  C4'  C5'  single    1.520  0.020  1.520
 EJ8  C2   CAB  single    1.509  0.020  1.509
 EJ8  C2   C12  aromatic  1.395  0.020  1.395
 EJ8  C11  C12  aromatic  1.387  0.020  1.387
 EJ8  CAB  O7   single    1.405  0.020  1.405
 EJ8  CAB  P    single    1.908  0.020  1.908
 EJ8  O7   C5'  single    1.410  0.020  1.410
 EJ8  OP2  P    deloc     1.527  0.020  1.527
 EJ8  P    OP1  deloc     1.528  0.020  1.528
 EJ8  P    OP3  deloc     1.527  0.020  1.527
 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  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  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   107.86  3.000
 EJ8  H2   C2'  C3'  111.63  3.000
 EJ8  H1   C2'  C3'  112.88  3.000
 EJ8  H2   C2'  C1'  110.49  3.000
 EJ8  H1   C2'  C1'  112.10  3.000
 EJ8  C3'  C2'  C1'  101.86  3.000
 EJ8  H3   C1'  O4'  109.22  3.000
 EJ8  H3   C1'  N9   106.41  3.000
 EJ8  O4'  C1'  N9   109.17  3.000
 EJ8  H3   C1'  C2'  112.05  3.000
 EJ8  O4'  C1'  C2'  107.20  3.000
 EJ8  N9   C1'  C2'  112.73  3.000
 EJ8  C18  P2   O11  102.63  3.000
 EJ8  C18  P2   O10  105.70  3.000
 EJ8  O11  P2   O10  113.65  3.000
 EJ8  C18  P2   O9   105.32  3.000
 EJ8  O11  P2   O9   113.92  3.000
 EJ8  O10  P2   O9   114.15  3.000
 EJ8  H7   C18  H6   106.29  3.000
 EJ8  H7   C18  S1   104.69  3.000
 EJ8  H6   C18  S1   107.83  3.000
 EJ8  H7   C18  P2   109.92  3.000
 EJ8  H6   C18  P2   111.64  3.000
 EJ8  S1   C18  P2   115.85  3.000
 EJ8  C17  S1   C18  101.89  3.000
 EJ8  C6   C5   C4   118.38  3.000
 EJ8  C4   C5   C17  121.64  3.000
 EJ8  C6   C5   C17  119.91  3.000
 EJ8  H10  C4   N9   115.67  3.000
 EJ8  H10  C4   C5   120.42  3.000
 EJ8  N9   C4   C5   123.92  3.000
 EJ8  N1   C6   O6   120.32  3.000
 EJ8  N1   C6   C5   113.91  3.000
 EJ8  O6   C6   C5   125.76  3.000
 EJ8  H11  N1   C8   115.27  3.000
 EJ8  H11  N1   C6   116.73  3.000
 EJ8  C8   N1   C6   127.97  3.000
 EJ8  N9   C8   N1   114.70  3.000
 EJ8  N9   C8   O2   122.77  3.000
 EJ8  N1   C8   O2   122.53  3.000
 EJ8  C8   N9   C4   121.09  3.000
 EJ8  C4   N9   C1'  122.35  3.000
 EJ8  C8   N9   C1'  116.47  3.000
 EJ8  C4'  O4'  C1'  111.07  3.000
 EJ8  H12  C3'  C4'  109.00  3.000
 EJ8  H12  C3'  O3'  105.47  3.000
 EJ8  C4'  C3'  O3'  114.33  3.000
 EJ8  H12  C3'  C2'  108.32  3.000
 EJ8  C4'  C3'  C2'  101.39  3.000
 EJ8  O3'  C3'  C2'  118.06  3.000
 EJ8  CAB  O3'  C3'  119.10  3.000
 EJ8  H13  C4'  C5'  109.97  3.000
 EJ8  H13  C4'  C3'  112.23  3.000
 EJ8  C5'  C4'  C3'  109.50  3.000
 EJ8  H13  C4'  O4'  107.71  3.000
 EJ8  C5'  C4'  O4'  112.53  3.000
 EJ8  C3'  C4'  O4'  104.83  3.000
 EJ8  H15  C5'  H14  107.09  3.000
 EJ8  H15  C5'  O7   107.66  3.000
 EJ8  H14  C5'  O7   111.42  3.000
 EJ8  H15  C5'  C4'  111.32  3.000
 EJ8  H14  C5'  C4'  111.04  3.000
 EJ8  O7   C5'  C4'  108.28  3.000
 EJ8  CAB  O7   C5'  114.53  3.000
 EJ8  C2   CAB  P    109.29  3.000
 EJ8  P    CAB  O7   106.54  3.000
 EJ8  C2   CAB  O7   112.01  3.000
 EJ8  P    CAB  O3'  106.10  3.000
 EJ8  O7   CAB  O3'  110.85  3.000
 EJ8  C2   CAB  O3'  111.73  3.000
 EJ8  OP3  P    OP2  114.85  3.000
 EJ8  OP3  P    OP1  114.41  3.000
 EJ8  OP2  P    OP1  114.44  3.000
 EJ8  OP3  P    CAB  103.43  3.000
 EJ8  OP1  P    CAB  103.96  3.000
 EJ8  OP2  P    CAB  103.74  3.000
 EJ8  C12  C2   CAA  118.07  3.000
 EJ8  C12  C2   CAB  120.45  3.000
 EJ8  CAA  C2   CAB  121.23  3.000
 EJ8  H18  CAA  C9   119.21  3.000
 EJ8  H18  CAA  C2   119.74  3.000
 EJ8  C9   CAA  C2   121.05  3.000
 EJ8  H19  C9   C10  120.07  3.000
 EJ8  H19  C9   CAA  119.62  3.000
 EJ8  C10  C9   CAA  120.31  3.000
 EJ8  H20  C10  C11  120.42  3.000
 EJ8  H20  C10  C9   120.43  3.000
 EJ8  C11  C10  C9   119.15  3.000
 EJ8  H21  C11  C12  119.68  3.000
 EJ8  H21  C11  C10  119.96  3.000
 EJ8  C12  C11  C10  120.36  3.000
 EJ8  H22  C12  C11  119.37  3.000
 EJ8  H22  C12  C2   119.62  3.000
 EJ8  C11  C12  C2   121.00  3.000
 EJ8  H9   C17  H8   107.64  3.000
 EJ8  H9   C17  C5   110.84  3.000
 EJ8  H8   C17  C5   112.02  3.000
 EJ8  H9   C17  S1   108.59  3.000
 EJ8  H8   C17  S1   109.89  3.000
 EJ8  C5   C17  S1   107.82  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  -59.01  30.0  1
 EJ8  Var_02    C6   C5   C17  S1   -84.05  30.0  3
 EJ8  Var_03    C5   C17  S1   C18  162.30  30.0  2
 EJ8  Var_04    S1   C18  P2   O9    61.34  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

