# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:47:56 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: [(3~{S},4~{R})-4-(6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CO[C@H]1CNC[C@H]1n2cnc3C(=O)NC=Nc23
#
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
 6W7  6W7  '[(3~{S},4~{R})-4-(6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid'  ligand  35  21  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6W7
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
 6W7  C4   C  CR56  0   0.494   1.4411   0.1948  -0.4744
 6W7  C5   C  CR56  0  -0.036   2.2488  -0.2595   0.5489
 6W7  C6   C  CR6   0   0.499   3.2807  -1.2036   0.2594
 6W7  C8   C  CR15  0   0.112   0.8819   1.0802   1.4326
 6W7  N1   N  NR16  0  -0.665   3.2863  -1.5001  -1.1070
 6W7  N3   N  N     0  -0.448   1.5168  -0.1223  -1.7818
 6W7  OAC  O  OH1   0  -0.745  -2.7758  -2.8798   0.4044
 6W7  PAU  P  P     0   1.351  -1.6668  -1.7152   0.4047
 6W7  OAD  O  O     0  -0.690  -0.4153  -1.9931   1.1419
 6W7  OAB  O  OH1   0  -0.739  -1.3372  -1.3881  -1.1350
 6W7  CAI  C  CH2   0  -0.464  -2.6928  -0.3443   1.0385
 6W7  CAR  C  CH1   0   0.046  -1.9038   1.6354  -0.0512
 6W7  CAG  C  CH2   0  -0.312  -2.3738   3.0681   0.2129
 6W7  NAL  N  NH1   0  -0.613  -1.5500   3.8525  -0.6862
 6W7  CAH  C  CH2   0  -0.279  -0.2098   3.3394  -0.4936
 6W7  CAS  C  CH1   0  -0.161  -0.4435   1.8276  -0.5822
 6W7  N9   N  NR5   0  -0.493   0.5620   1.0552   0.1037
 6W7  C2   C  CR16  0   0.153   2.4544  -0.9733  -2.0352
 6W7  O6   O  O     0  -0.477   4.0779  -1.7215   1.0243
 6W7  N7   N  N     0  -0.454   1.8866   0.3110   1.7342
 6W7  H1   H  HCR5  0   0.289   0.3478   1.6990   2.1361
 6W7  H2   H  HNR6  0   0.432   3.9838  -2.1589  -1.4283
 6W7  H3   H  HOH1  0   0.496  -2.4123  -3.7747   0.3529
 6W7  H4   H  HOH1  0   0.489  -2.1033  -1.3128  -1.7187
 6W7  H5   H  HCH2  0   0.262  -3.6078  -0.2547   0.4401
 6W7  H6   H  HCH2  0   0.289  -3.0006  -0.6111   2.0522
 6W7  H7   H  HCH1  0   0.253  -2.5043   1.1901  -0.8495
 6W7  H8   H  HCH2  0   0.245  -3.4361   3.2030   0.0062
 6W7  H9   H  HCH2  0   0.213  -2.2036   3.3030   1.2749
 6W7  H10  H  HNH1  0   0.364  -1.6114   4.8428  -0.4930
 6W7  H12  H  HCH2  0   0.252   0.4777   3.6968  -1.2607
 6W7  H13  H  HCH2  0   0.216   0.2185   3.5965   0.4877
 6W7  H14  H  HCH1  0   0.298  -0.4069   1.5160  -1.6247
 6W7  H15  H  HCR6  0   0.299   2.6186  -1.3116  -3.0496
 6W7  OAN  O  O2    0  -0.479  -1.9880   0.8646   1.1195

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
 6W7  O6   C6   double    1.220  0.020  1.220
 6W7  N1   C6   single    1.398  0.020  1.398
 6W7  N1   C2   single    1.353  0.020  1.353
 6W7  C6   C5   single    1.428  0.020  1.428
 6W7  C2   N3   double    1.291  0.020  1.291
 6W7  C5   N7   aromatic  1.364  0.020  1.364
 6W7  C5   C4   aromatic  1.381  0.020  1.381
 6W7  N7   C8   aromatic  1.301  0.020  1.301
 6W7  N3   C4   single    1.347  0.020  1.347
 6W7  C4   N9   aromatic  1.359  0.020  1.359
 6W7  C8   N9   aromatic  1.367  0.020  1.367
 6W7  N9   CAS  single    1.442  0.020  1.442
 6W7  CAS  CAR  single    1.566  0.020  1.566
 6W7  CAS  CAH  single    1.532  0.020  1.532
 6W7  CAI  OAN  single    1.402  0.020  1.402
 6W7  CAI  PAU  single    1.826  0.020  1.826
 6W7  CAR  OAN  single    1.404  0.020  1.404
 6W7  CAR  CAG  single    1.531  0.020  1.531
 6W7  OAD  PAU  double    1.479  0.020  1.479
 6W7  CAH  NAL  single    1.448  0.020  1.448
 6W7  PAU  OAC  single    1.608  0.020  1.608
 6W7  PAU  OAB  single    1.608  0.020  1.608
 6W7  CAG  NAL  single    1.450  0.020  1.450
 6W7  C8   H1   single    0.930  0.020  1.080
 6W7  N1   H2   single    0.860  0.020  1.020
 6W7  OAC  H3   single    0.850  0.020  0.980
 6W7  OAB  H4   single    0.850  0.020  0.980
 6W7  CAI  H5   single    0.970  0.020  1.090
 6W7  CAI  H6   single    0.970  0.020  1.090
 6W7  CAR  H7   single    0.970  0.020  1.090
 6W7  CAG  H8   single    0.970  0.020  1.090
 6W7  CAG  H9   single    0.970  0.020  1.090
 6W7  NAL  H10  single    0.890  0.020  1.040
 6W7  CAH  H12  single    0.970  0.020  1.090
 6W7  CAH  H13  single    0.970  0.020  1.090
 6W7  CAS  H14  single    0.970  0.020  1.090
 6W7  C2   H15  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
 6W7  N9   C4   N3   126.73  3.000
 6W7  N9   C4   C5   105.75  3.000
 6W7  N3   C4   C5   127.51  3.000
 6W7  N7   C5   C6   130.11  3.000
 6W7  N7   C5   C4   110.55  3.000
 6W7  C6   C5   C4   119.34  3.000
 6W7  O6   C6   N1   121.33  3.000
 6W7  N1   C6   C5   109.95  3.000
 6W7  O6   C6   C5   128.72  3.000
 6W7  H1   C8   N7   124.79  3.000
 6W7  H1   C8   N9   121.91  3.000
 6W7  N7   C8   N9   113.29  3.000
 6W7  H2   N1   C2   117.35  3.000
 6W7  H2   N1   C6   116.82  3.000
 6W7  C2   N1   C6   125.82  3.000
 6W7  C2   N3   C4   112.73  3.000
 6W7  H3   OAC  PAU  114.26  3.000
 6W7  CAI  PAU  OAB  107.14  3.000
 6W7  OAB  PAU  OAD  110.00  3.000
 6W7  CAI  PAU  OAD  116.34  3.000
 6W7  OAB  PAU  OAC  106.76  3.000
 6W7  OAD  PAU  OAC  116.59  3.000
 6W7  CAI  PAU  OAC   98.99  3.000
 6W7  H4   OAB  PAU  115.58  3.000
 6W7  H6   CAI  H5   106.92  3.000
 6W7  H6   CAI  OAN  107.37  3.000
 6W7  H5   CAI  OAN  112.36  3.000
 6W7  H6   CAI  PAU  107.28  3.000
 6W7  H5   CAI  PAU  109.92  3.000
 6W7  OAN  CAI  PAU  112.65  3.000
 6W7  H7   CAR  CAS  108.34  3.000
 6W7  H7   CAR  CAG  109.78  3.000
 6W7  CAS  CAR  CAG  103.29  3.000
 6W7  H7   CAR  OAN  110.62  3.000
 6W7  CAG  CAR  OAN  110.58  3.000
 6W7  CAS  CAR  OAN  113.96  3.000
 6W7  H9   CAG  H8   107.88  3.000
 6W7  H9   CAG  NAL  113.26  3.000
 6W7  H8   CAG  NAL  111.65  3.000
 6W7  H9   CAG  CAR  108.58  3.000
 6W7  H8   CAG  CAR  112.46  3.000
 6W7  NAL  CAG  CAR  103.00  3.000
 6W7  H10  NAL  CAH  112.21  3.000
 6W7  H10  NAL  CAG  112.15  3.000
 6W7  CAH  NAL  CAG  104.58  3.000
 6W7  H13  CAH  H12  107.77  3.000
 6W7  H13  CAH  CAS  109.94  3.000
 6W7  H12  CAH  CAS  112.27  3.000
 6W7  H13  CAH  NAL  113.32  3.000
 6W7  H12  CAH  NAL  111.96  3.000
 6W7  CAS  CAH  NAL  101.58  3.000
 6W7  H14  CAS  N9   106.19  3.000
 6W7  H14  CAS  CAH  109.43  3.000
 6W7  N9   CAS  CAH  113.25  3.000
 6W7  H14  CAS  CAR  108.72  3.000
 6W7  CAH  CAS  CAR  104.11  3.000
 6W7  N9   CAS  CAR  115.05  3.000
 6W7  CAS  N9   C8   128.02  3.000
 6W7  CAS  N9   C4   126.01  3.000
 6W7  C8   N9   C4   105.88  3.000
 6W7  H15  C2   N3   120.02  3.000
 6W7  H15  C2   N1   115.35  3.000
 6W7  N3   C2   N1   124.63  3.000
 6W7  C8   N7   C5   104.53  3.000
 6W7  CAR  OAN  CAI  117.09  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
 6W7  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 6W7  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 6W7  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 6W7  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 6W7  CONST_05  N7   C5   C4   N9      0.00   0.0  0
 6W7  CONST_06  CAS  N9   C4   C5    180.00   0.0  0
 6W7  CONST_07  CAS  N9   C4   N3      0.00   0.0  0
 6W7  CONST_08  N7   C8   N9   CAS   180.00   0.0  0
 6W7  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 6W7  CONST_10  C2   N1   C6   C5      0.00   0.0  0
 6W7  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 6W7  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 6W7  CONST_13  H1   C8   N9   C4    180.00   0.0  0
 6W7  CONST_14  H15  C2   N3   C4    180.00   0.0  0
 6W7  CONST_15  H2   N1   C6   C5    180.00   0.0  0
 6W7  Var_01    CAH  NAL  CAG  CAR   -46.47  30.0  1
 6W7  Var_02    CAS  CAH  NAL  CAG    47.94  30.0  1
 6W7  Var_03    H5   CAI  OAN  CAR   -40.85  30.0  2
 6W7  Var_04    OAN  CAI  PAU  OAC  -178.32  30.0  2

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
 6W7  chir_01  CAR  CAS  OAN  CAG  negativ
 6W7  chir_02  CAS  N9   CAR  CAH  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
 6W7  plan-1  C4   0.020
 6W7  plan-1  C5   0.020
 6W7  plan-1  C6   0.020
 6W7  plan-1  C8   0.020
 6W7  plan-1  N1   0.020
 6W7  plan-1  N3   0.020
 6W7  plan-1  CAS  0.020
 6W7  plan-1  N9   0.020
 6W7  plan-1  C2   0.020
 6W7  plan-1  O6   0.020
 6W7  plan-1  N7   0.020
 6W7  plan-1  H1   0.020
 6W7  plan-1  H2   0.020
 6W7  plan-1  H15  0.020

