# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:31:18 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [2-[(6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)COCC(COC[P](O)(O)=O)Cn1cnc2C(=O)NC=Nc12
#
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
 6WC  6WC  '[2-[(6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid'  ligand  40  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6WC
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
 6WC  C4   C  CR56   0   0.477   3.2269  -0.4987  -0.3611
 6WC  C5   C  CR56   0  -0.054   4.3194   0.3494  -0.3461
 6WC  C6   C  CR6    0   0.508   5.4333   0.0398   0.4973
 6WC  C8   C  CR15   0   0.093   2.9469   1.1792  -1.7134
 6WC  N1   N  NR16   0  -0.664   5.1859  -1.1475   1.1941
 6WC  N3   N  N      0  -0.445   3.0586  -1.6379   0.3417
 6WC  OAD  O  OP    -1  -0.915  -1.5677   5.3039   1.3960
 6WC  PAY  P  P      0   1.131  -1.8412   4.0605   0.5343
 6WC  OAE  O  OP    -1  -0.910  -3.2975   3.5843   0.5776
 6WC  OAB  O  O      0  -0.900  -1.2632   4.1575  -0.8842
 6WC  CAL  C  CH2    0  -0.454  -0.8511   2.7531   1.4250
 6WC  OAR  O  O2     0  -0.489  -0.9407   1.4222   0.9359
 6WC  CAJ  C  CH2    0  -0.085  -0.2784   1.2072  -0.2759
 6WC  CAW  C  CH1    0  -0.341   0.0023  -0.2775  -0.4783
 6WC  CAK  C  CH2    0  -0.103  -1.2199  -1.0980  -0.8718
 6WC  OAS  O  O2     0  -0.491  -2.1837  -1.0621   0.1375
 6WC  CAM  C  CH2    0  -0.453  -3.3727  -1.7752  -0.1807
 6WC  PAZ  P  P      0   1.132  -3.3159  -3.6284   0.0441
 6WC  OAF  O  OP    -1  -0.912  -4.7552  -4.0380  -0.3032
 6WC  OAG  O  OP    -1  -0.899  -2.2705  -4.1620  -0.9469
 6WC  OAC  O  O      0  -0.910  -2.9411  -3.8539   1.5132
 6WC  N9   N  NR5    0  -0.480   2.3529   0.0450  -1.2454
 6WC  C2   C  CR16   0   0.158   4.0705  -1.9071   1.0992
 6WC  O6   O  O      0  -0.469   6.4723   0.6591   0.6452
 6WC  N7   N  N      0  -0.445   4.1254   1.3954  -1.2011
 6WC  H1   H  HCR5   0   0.298   2.4561   1.8052  -2.4444
 6WC  H2   H  HNR6   0   0.435   5.9120  -1.4658   1.8231
 6WC  H5   H  HCH2   0   0.155   0.2088   3.0592   1.4673
 6WC  H6   H  HCH2   0   0.186  -1.1905   2.7006   2.4661
 6WC  H7   H  HCH2   0   0.185  -0.8458   1.5938  -1.1326
 6WC  H8   H  HCH2   0   0.172   0.6747   1.7602  -0.2764
 6WC  H9   H  HCH1   0   0.238   0.4195  -0.6909   0.4474
 6WC  H10  H  HCH2   0   0.164  -1.6288  -0.6947  -1.8165
 6WC  H11  H  HCH2   0   0.204  -0.9140  -2.1292  -1.0855
 6WC  H12  H  HCH2   0   0.187  -4.1460  -1.3645   0.4791
 6WC  H13  H  HCH2   0   0.159  -3.6927  -1.5280  -1.2071
 6WC  H16  H  HCH2   0   0.278   1.1448  -1.5249  -1.8302
 6WC  H17  H  HCH2   0   0.274   0.7260   0.0402  -2.5030
 6WC  H18  H  HCR6   0   0.303   4.0614  -2.7955   1.7165
 6WC  CAN  C  CH2    0  -0.316   1.0398  -0.4667  -1.5890

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
 6WC  OAB  PAY  deloc     1.535  0.020  1.535
 6WC  OAE  PAY  deloc     1.533  0.020  1.533
 6WC  OAC  PAZ  deloc     1.533  0.020  1.533
 6WC  PAY  CAL  single    1.866  0.020  1.866
 6WC  PAY  OAD  deloc     1.537  0.020  1.537
 6WC  CAL  OAR  single    1.421  0.020  1.421
 6WC  PAZ  CAM  single    1.868  0.020  1.868
 6WC  PAZ  OAF  deloc     1.536  0.020  1.536
 6WC  PAZ  OAG  deloc     1.536  0.020  1.536
 6WC  OAR  CAJ  single    1.398  0.020  1.398
 6WC  CAM  OAS  single    1.423  0.020  1.423
 6WC  OAS  CAK  single    1.396  0.020  1.396
 6WC  CAW  CAJ  single    1.524  0.020  1.524
 6WC  CAW  CAN  single    1.532  0.020  1.532
 6WC  CAW  CAK  single    1.524  0.020  1.524
 6WC  CAN  N9   single    1.451  0.020  1.451
 6WC  N9   C8   aromatic  1.363  0.020  1.363
 6WC  N9   C4   aromatic  1.357  0.020  1.357
 6WC  C8   N7   aromatic  1.303  0.020  1.303
 6WC  C4   N3   single    1.349  0.020  1.349
 6WC  C4   C5   aromatic  1.383  0.020  1.383
 6WC  N3   C2   double    1.292  0.020  1.292
 6WC  N7   C5   aromatic  1.365  0.020  1.365
 6WC  C5   C6   single    1.431  0.020  1.431
 6WC  C2   N1   single    1.353  0.020  1.353
 6WC  C6   N1   single    1.399  0.020  1.399
 6WC  C6   O6   double    1.219  0.020  1.219
 6WC  C8   H1   single    0.930  0.020  1.080
 6WC  N1   H2   single    0.860  0.020  1.020
 6WC  CAL  H5   single    0.970  0.020  1.090
 6WC  CAL  H6   single    0.970  0.020  1.090
 6WC  CAJ  H7   single    0.970  0.020  1.090
 6WC  CAJ  H8   single    0.970  0.020  1.090
 6WC  CAW  H9   single    0.970  0.020  1.090
 6WC  CAK  H10  single    0.970  0.020  1.090
 6WC  CAK  H11  single    0.970  0.020  1.090
 6WC  CAM  H12  single    0.970  0.020  1.090
 6WC  CAM  H13  single    0.970  0.020  1.090
 6WC  CAN  H16  single    0.970  0.020  1.090
 6WC  CAN  H17  single    0.970  0.020  1.090
 6WC  C2   H18  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
 6WC  N9   C4   N3   126.69  3.000
 6WC  N3   C4   C5   127.63  3.000
 6WC  N9   C4   C5   105.67  3.000
 6WC  N7   C5   C6   130.22  3.000
 6WC  C6   C5   C4   119.24  3.000
 6WC  N7   C5   C4   110.54  3.000
 6WC  O6   C6   N1   121.45  3.000
 6WC  O6   C6   C5   128.70  3.000
 6WC  N1   C6   C5   109.85  3.000
 6WC  H1   C8   N7   125.50  3.000
 6WC  H1   C8   N9   121.09  3.000
 6WC  N7   C8   N9   113.40  3.000
 6WC  H2   N1   C2   117.29  3.000
 6WC  H2   N1   C6   116.73  3.000
 6WC  C2   N1   C6   125.98  3.000
 6WC  C2   N3   C4   112.56  3.000
 6WC  CAL  PAY  OAB  106.59  3.000
 6WC  CAL  PAY  OAE  105.83  3.000
 6WC  OAB  PAY  OAE  113.80  3.000
 6WC  CAL  PAY  OAD  101.81  3.000
 6WC  OAE  PAY  OAD  113.86  3.000
 6WC  OAB  PAY  OAD  113.57  3.000
 6WC  H6   CAL  H5   105.91  3.000
 6WC  H6   CAL  OAR  105.23  3.000
 6WC  H5   CAL  OAR  109.48  3.000
 6WC  H6   CAL  PAY  108.81  3.000
 6WC  H5   CAL  PAY  109.47  3.000
 6WC  OAR  CAL  PAY  117.29  3.000
 6WC  CAJ  OAR  CAL  114.38  3.000
 6WC  H8   CAJ  H7   105.66  3.000
 6WC  H8   CAJ  CAW  109.23  3.000
 6WC  H7   CAJ  CAW  109.54  3.000
 6WC  H8   CAJ  OAR  109.45  3.000
 6WC  H7   CAJ  OAR  112.18  3.000
 6WC  CAW  CAJ  OAR  110.62  3.000
 6WC  H9   CAW  CAN  107.94  3.000
 6WC  H9   CAW  CAK  108.67  3.000
 6WC  CAN  CAW  CAK  106.83  3.000
 6WC  H9   CAW  CAJ  108.98  3.000
 6WC  CAK  CAW  CAJ  114.27  3.000
 6WC  CAN  CAW  CAJ  109.96  3.000
 6WC  H11  CAK  H10  106.24  3.000
 6WC  H11  CAK  OAS  110.96  3.000
 6WC  H10  CAK  OAS  110.68  3.000
 6WC  H11  CAK  CAW  109.45  3.000
 6WC  H10  CAK  CAW  108.71  3.000
 6WC  OAS  CAK  CAW  110.69  3.000
 6WC  CAM  OAS  CAK  113.74  3.000
 6WC  H13  CAM  H12  105.74  3.000
 6WC  H13  CAM  PAZ  110.07  3.000
 6WC  H12  CAM  PAZ  108.71  3.000
 6WC  H13  CAM  OAS  109.77  3.000
 6WC  H12  CAM  OAS  105.50  3.000
 6WC  PAZ  CAM  OAS  116.43  3.000
 6WC  OAC  PAZ  OAG  113.63  3.000
 6WC  OAG  PAZ  OAF  113.52  3.000
 6WC  OAC  PAZ  OAF  113.99  3.000
 6WC  OAG  PAZ  CAM  106.72  3.000
 6WC  OAF  PAZ  CAM  102.05  3.000
 6WC  OAC  PAZ  CAM  105.59  3.000
 6WC  CAN  N9   C8   127.35  3.000
 6WC  C8   N9   C4   106.04  3.000
 6WC  CAN  N9   C4   126.59  3.000
 6WC  H18  C2   N3   119.93  3.000
 6WC  H18  C2   N1   115.34  3.000
 6WC  N3   C2   N1   124.73  3.000
 6WC  C8   N7   C5   104.34  3.000
 6WC  H17  CAN  H16  107.05  3.000
 6WC  H17  CAN  N9   107.15  3.000
 6WC  H16  CAN  N9   107.91  3.000
 6WC  H17  CAN  CAW  110.81  3.000
 6WC  H16  CAN  CAW  110.22  3.000
 6WC  N9   CAN  CAW  113.44  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
 6WC  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 6WC  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 6WC  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 6WC  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 6WC  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 6WC  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 6WC  CONST_07  C2   N1   C6   C5      0.00   0.0  0
 6WC  CONST_08  N3   C2   N1   C6      0.00   0.0  0
 6WC  CONST_09  CAN  N9   C4   C5    180.00   0.0  0
 6WC  CONST_10  CAN  N9   C4   N3      0.00   0.0  0
 6WC  CONST_11  N7   C8   N9   CAN   180.00   0.0  0
 6WC  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 6WC  CONST_13  H1   C8   N9   C4    180.00   0.0  0
 6WC  CONST_14  H18  C2   N3   C4    180.00   0.0  0
 6WC  CONST_15  H2   N1   C6   C5    180.00   0.0  0
 6WC  Var_01    CAW  CAN  N9   C4     72.31  30.0  2
 6WC  Var_02    N9   CAN  CAW  CAJ    66.49  30.0  3
 6WC  Var_03    OAR  CAL  PAY  OAD   176.21  30.0  3
 6WC  Var_04    CAW  CAJ  OAR  CAL   159.99  30.0  3
 6WC  Var_05    CAN  CAW  CAJ  OAR  -164.70  30.0  1
 6WC  Var_06    OAS  CAK  CAW  CAJ   -62.54  30.0  3
 6WC  Var_07    PAZ  CAM  OAS  CAK    80.26  30.0  1
 6WC  Var_08    OAC  PAZ  CAM  OAS    57.41  30.0  3

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
 6WC  plan-1  C4   0.020
 6WC  plan-1  C5   0.020
 6WC  plan-1  C6   0.020
 6WC  plan-1  C8   0.020
 6WC  plan-1  N1   0.020
 6WC  plan-1  N3   0.020
 6WC  plan-1  N9   0.020
 6WC  plan-1  C2   0.020
 6WC  plan-1  O6   0.020
 6WC  plan-1  N7   0.020
 6WC  plan-1  H1   0.020
 6WC  plan-1  H2   0.020
 6WC  plan-1  H18  0.020
 6WC  plan-1  CAN  0.020

