# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 15:39:51 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  33  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 PERFECT
;

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   0.538   1.5596   0.2282  -0.3933
 6W7  C5   C  CR56   0  -0.045   2.3710  -0.1064   0.6739
 6W7  C6   C  CR6    0   0.482   3.4072  -1.0648   0.4942
 6W7  C8   C  CR15   0   0.106   0.9422   1.2492   1.4189
 6W7  N1   N  NR16   0  -0.664   3.4397  -1.4896  -0.8349
 6W7  N3   N  N      0  -0.440   1.6746  -0.1927  -1.6669
 6W7  OAC  O  OP    -1  -0.914  -2.3565  -3.0281   0.0101
 6W7  PAU  P  P      0   1.170  -1.4523  -1.7870  -0.1023
 6W7  OAD  O  O      0  -0.868  -0.0567  -1.9921   0.4898
 6W7  OAB  O  OP    -1  -0.884  -1.4850  -1.1408  -1.4927
 6W7  CAI  C  CH2    0  -0.470  -2.3562  -0.6026   1.0302
 6W7  CAR  C  CH1    0   0.093  -1.8323   1.5209   0.0757
 6W7  CAG  C  CH2    0  -0.322  -2.2306   2.9541   0.4228
 6W7  NAL  N  NH1    0  -0.615  -1.6576   3.7040  -0.6776
 6W7  CAH  C  CH2    0  -0.279  -0.2911   3.2236  -0.7803
 6W7  CAS  C  CH1    0  -0.168  -0.4446   1.7016  -0.6291
 6W7  N9   N  NR5    0  -0.477   0.6521   1.1075   0.0946
 6W7  C2   C  CR16   0   0.138   2.6203  -1.0545  -1.8224
 6W7  O6   O  O      0  -0.496   4.1948  -1.5082   1.3201
 6W7  N7   N  N      0  -0.469   1.9697   0.5475   1.8033
 6W7  H1   H  HCR5   0   0.275   0.3781   1.9097   2.0578
 6W7  H2   H  HNR6   0   0.424   4.1465  -2.1701  -1.0800
 6W7  H5   H  HCH2   0   0.166  -3.4024  -0.5219   0.6947
 6W7  H6   H  HCH2   0   0.188  -2.3929  -1.0237   2.0406
 6W7  H7   H  HCH1   0   0.226  -2.5166   1.1270  -0.6810
 6W7  H8   H  HCH2   0   0.234  -3.3127   3.0870   0.4782
 6W7  H9   H  HCH2   0   0.196  -1.8066   3.2243   1.4046
 6W7  H10  H  HNH1   0   0.356  -1.6941   4.7022  -0.5229
 6W7  H12  H  HCH2   0   0.239   0.1618   3.5054  -1.7323
 6W7  H13  H  HCH2   0   0.209   0.3577   3.6093   0.0209
 6W7  H14  H  HCH1   0   0.281  -0.4755   1.1960  -1.5892
 6W7  H15  H  HCR6   0   0.288   2.8155  -1.4757  -2.8001
 6W7  OAN  O  O2     0  -0.500  -1.8269   0.7125   1.2054

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    1.224  0.020  1.224
 6W7  N1   C6   single    1.396  0.020  1.396
 6W7  N1   C2   single    1.355  0.020  1.355
 6W7  C6   C5   single    1.423  0.020  1.423
 6W7  C2   N3   double    1.289  0.020  1.289
 6W7  C5   N7   aromatic  1.365  0.020  1.365
 6W7  C5   C4   aromatic  1.382  0.020  1.382
 6W7  N7   C8   aromatic  1.302  0.020  1.302
 6W7  N3   C4   single    1.346  0.020  1.346
 6W7  C4   N9   aromatic  1.355  0.020  1.355
 6W7  C8   N9   aromatic  1.363  0.020  1.363
 6W7  N9   CAS  single    1.442  0.020  1.442
 6W7  CAS  CAR  single    1.567  0.020  1.567
 6W7  CAS  CAH  single    1.537  0.020  1.537
 6W7  CAI  OAN  single    1.428  0.020  1.428
 6W7  CAI  PAU  single    1.871  0.020  1.871
 6W7  CAR  OAN  single    1.389  0.020  1.389
 6W7  CAR  CAG  single    1.528  0.020  1.528
 6W7  OAD  PAU  deloc     1.530  0.020  1.530
 6W7  CAH  NAL  single    1.452  0.020  1.452
 6W7  PAU  OAC  deloc     1.540  0.020  1.540
 6W7  PAU  OAB  deloc     1.534  0.020  1.534
 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  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   126.94  3.000
 6W7  N9   C4   C5   105.81  3.000
 6W7  N3   C4   C5   127.21  3.000
 6W7  N7   C5   C6   129.87  3.000
 6W7  N7   C5   C4   110.51  3.000
 6W7  C6   C5   C4   119.55  3.000
 6W7  O6   C6   N1   121.14  3.000
 6W7  N1   C6   C5   110.01  3.000
 6W7  O6   C6   C5   128.85  3.000
 6W7  H1   C8   N7   124.61  3.000
 6W7  H1   C8   N9   121.87  3.000
 6W7  N7   C8   N9   113.50  3.000
 6W7  H2   N1   C2   117.53  3.000
 6W7  H2   N1   C6   116.86  3.000
 6W7  C2   N1   C6   125.60  3.000
 6W7  C2   N3   C4   112.70  3.000
 6W7  CAI  PAU  OAB  105.76  3.000
 6W7  OAB  PAU  OAD  115.27  3.000
 6W7  CAI  PAU  OAD  106.93  3.000
 6W7  OAB  PAU  OAC  113.16  3.000
 6W7  OAD  PAU  OAC  113.54  3.000
 6W7  CAI  PAU  OAC  100.50  3.000
 6W7  H6   CAI  H5   106.10  3.000
 6W7  H6   CAI  OAN  104.67  3.000
 6W7  H5   CAI  OAN  108.77  3.000
 6W7  H6   CAI  PAU  109.34  3.000
 6W7  H5   CAI  PAU  108.71  3.000
 6W7  OAN  CAI  PAU  118.55  3.000
 6W7  H7   CAR  CAS  106.53  3.000
 6W7  H7   CAR  CAG  109.39  3.000
 6W7  CAS  CAR  CAG  103.00  3.000
 6W7  H7   CAR  OAN  110.82  3.000
 6W7  CAG  CAR  OAN  111.24  3.000
 6W7  CAS  CAR  OAN  115.44  3.000
 6W7  H9   CAG  H8   107.82  3.000
 6W7  H9   CAG  NAL  113.39  3.000
 6W7  H8   CAG  NAL  111.55  3.000
 6W7  H9   CAG  CAR  109.38  3.000
 6W7  H8   CAG  CAR  112.60  3.000
 6W7  NAL  CAG  CAR  102.11  3.000
 6W7  H10  NAL  CAH  111.81  3.000
 6W7  H10  NAL  CAG  112.36  3.000
 6W7  CAH  NAL  CAG  104.75  3.000
 6W7  H13  CAH  H12  107.45  3.000
 6W7  H13  CAH  CAS  109.52  3.000
 6W7  H12  CAH  CAS  112.51  3.000
 6W7  H13  CAH  NAL  112.79  3.000
 6W7  H12  CAH  NAL  111.52  3.000
 6W7  CAS  CAH  NAL  103.10  3.000
 6W7  H14  CAS  N9   105.88  3.000
 6W7  H14  CAS  CAH  112.15  3.000
 6W7  N9   CAS  CAH  112.42  3.000
 6W7  H14  CAS  CAR  108.60  3.000
 6W7  CAH  CAS  CAR  104.29  3.000
 6W7  N9   CAS  CAR  113.59  3.000
 6W7  CAS  N9   C8   127.34  3.000
 6W7  CAS  N9   C4   126.60  3.000
 6W7  C8   N9   C4   105.95  3.000
 6W7  H15  C2   N3   120.10  3.000
 6W7  H15  C2   N1   115.11  3.000
 6W7  N3   C2   N1   124.78  3.000
 6W7  C8   N7   C5   104.23  3.000
 6W7  CAR  OAN  CAI  115.76  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   -48.60  30.0  1
 6W7  Var_02    CAS  CAH  NAL  CAG    43.44  30.0  1
 6W7  Var_03    H5   CAI  OAN  CAR   -59.41  30.0  1
 6W7  Var_04    OAN  CAI  PAU  OAC  -179.76  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

