# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 15:25:42 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: [(3~{S},4~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3CNC[C@@H]3OC[P](O)(O)=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
 6W8  6W8  '[(3~{S},4~{R})-4-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid'  ligand  35  22  .  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_6W8
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
 6W8  C4   C  CR56   0   0.566   1.4912   0.2412  -0.2553
 6W8  C5   C  CR56   0  -0.082   2.3055   0.2001   0.8616
 6W8  C6   C  CR6    0   0.478   3.2908  -0.8135   0.9516
 6W8  C8   C  CR15   0   0.095   0.9094   1.7397   1.2127
 6W8  N1   N  NR16   0  -0.723   3.2956  -1.6023  -0.2038
 6W8  N3   N  N      0  -0.499   1.5823  -0.5002  -1.3673
 6W8  OAD  O  OP    -1  -0.918  -2.4853  -2.7983   0.9823
 6W8  PAV  P  P      0   1.167  -1.5920  -1.6434   0.4899
 6W8  OAE  O  OP    -1  -0.862  -0.1581  -1.7140   1.0157
 6W8  OAC  O  O      0  -0.885  -1.7348  -1.3755  -1.0133
 6W8  CAI  C  CH2    0  -0.469  -2.4121  -0.1945   1.3460
 6W8  CAS  C  CH1    0   0.082  -1.8780   1.6136  -0.1204
 6W8  CAG  C  CH2    0  -0.355  -2.2822   3.0926  -0.1409
 6W8  NAL  N  NH1    0  -0.586  -1.6989   3.6559  -1.3475
 6W8  CAH  C  CH2    0  -0.316  -0.3803   3.0431  -1.4289
 6W8  CAT  C  CH1    0  -0.173  -0.5044   1.6091  -0.8661
 6W8  N9   N  NR5    0  -0.485   0.6058   1.2396  -0.0246
 6W8  C2   C  CR6    0   0.657   2.4854  -1.4322  -1.2897
 6W8  O6   O  O      0  -0.503   4.0698  -1.0557   1.8666
 6W8  N7   N  N      0  -0.471   1.9230   1.1517   1.7724
 6W8  H1   H  HCR5   0   0.269   0.3598   2.5634   1.6412
 6W8  H2   H  HNR6   0   0.414   3.9559  -2.3682  -0.2111
 6W8  H3   H  HNH2   0   0.399   2.1749  -2.0776  -3.1616
 6W8  H4   H  HNH2   0   0.401   3.5332  -2.7686  -2.4257
 6W8  H7   H  HCH2   0   0.162  -3.4755  -0.1691   1.0568
 6W8  H8   H  HCH2   0   0.185  -2.3967  -0.3610   2.4285
 6W8  H9   H  HCH1   0   0.223  -2.5730   1.0433  -0.7441
 6W8  H10  H  HCH2   0   0.242  -3.3632   3.2360  -0.1242
 6W8  H11  H  HCH2   0   0.220  -1.8692   3.6040   0.7371
 6W8  H12  H  HNH1   0   0.348  -2.2498   3.3607  -2.1446
 6W8  H14  H  HCH2   0   0.248  -0.0039   3.0643  -2.4513
 6W8  H15  H  HCH2   0   0.229   0.3205   3.6169  -0.8142
 6W8  H16  H  HCH1   0   0.280  -0.5372   0.8626  -1.6550
 6W8  N2   N  NH2    0  -0.840   2.6412  -2.3179  -2.3027
 6W8  OAN  O  O2     0  -0.499  -1.8560   1.1093   1.1751

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
 6W8  OAC  PAV  deloc     1.534  0.020  1.534
 6W8  NAL  CAG  single    1.454  0.020  1.454
 6W8  NAL  CAH  single    1.456  0.020  1.456
 6W8  CAG  CAS  single    1.533  0.020  1.533
 6W8  OAE  PAV  deloc     1.529  0.020  1.529
 6W8  CAH  CAT  single    1.545  0.020  1.545
 6W8  PAV  OAD  deloc     1.541  0.020  1.541
 6W8  PAV  CAI  single    1.872  0.020  1.872
 6W8  CAS  OAN  single    1.390  0.020  1.390
 6W8  CAS  CAT  single    1.563  0.020  1.563
 6W8  OAN  CAI  single    1.428  0.020  1.428
 6W8  CAT  N9   single    1.441  0.020  1.441
 6W8  N9   C8   aromatic  1.369  0.020  1.369
 6W8  N9   C4   aromatic  1.354  0.020  1.354
 6W8  C8   N7   aromatic  1.299  0.020  1.299
 6W8  C4   N3   single    1.340  0.020  1.340
 6W8  C4   C5   aromatic  1.383  0.020  1.383
 6W8  N3   C2   double    1.300  0.020  1.300
 6W8  N7   C5   aromatic  1.372  0.020  1.372
 6W8  C5   C6   single    1.416  0.020  1.416
 6W8  C2   N2   single    1.355  0.020  1.355
 6W8  C2   N1   single    1.365  0.020  1.365
 6W8  C6   N1   single    1.399  0.020  1.399
 6W8  C6   O6   double    1.226  0.020  1.226
 6W8  C8   H1   single    0.930  0.020  1.080
 6W8  N1   H2   single    0.860  0.020  1.020
 6W8  N2   H3   single    0.890  0.020  1.040
 6W8  N2   H4   single    0.890  0.020  1.040
 6W8  CAI  H7   single    0.970  0.020  1.090
 6W8  CAI  H8   single    0.970  0.020  1.090
 6W8  CAS  H9   single    0.970  0.020  1.090
 6W8  CAG  H10  single    0.970  0.020  1.090
 6W8  CAG  H11  single    0.970  0.020  1.090
 6W8  NAL  H12  single    0.890  0.020  1.040
 6W8  CAH  H14  single    0.970  0.020  1.090
 6W8  CAH  H15  single    0.970  0.020  1.090
 6W8  CAT  H16  single    0.970  0.020  1.090

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
 6W8  N9   C4   N3   126.43  3.000
 6W8  N3   C4   C5   127.88  3.000
 6W8  N9   C4   C5   105.63  3.000
 6W8  N7   C5   C6   130.41  3.000
 6W8  C6   C5   C4   118.83  3.000
 6W8  N7   C5   C4   110.58  3.000
 6W8  O6   C6   N1   120.19  3.000
 6W8  O6   C6   C5   129.12  3.000
 6W8  N1   C6   C5   110.69  3.000
 6W8  H1   C8   N7   124.90  3.000
 6W8  H1   C8   N9   121.67  3.000
 6W8  N7   C8   N9   113.41  3.000
 6W8  H2   N1   C2   118.43  3.000
 6W8  H2   N1   C6   115.80  3.000
 6W8  C2   N1   C6   125.77  3.000
 6W8  C2   N3   C4   113.23  3.000
 6W8  CAI  PAV  OAC  105.80  3.000
 6W8  CAI  PAV  OAE  106.82  3.000
 6W8  OAC  PAV  OAE  115.63  3.000
 6W8  CAI  PAV  OAD  100.37  3.000
 6W8  OAE  PAV  OAD  113.53  3.000
 6W8  OAC  PAV  OAD  112.97  3.000
 6W8  H8   CAI  H7   106.04  3.000
 6W8  H8   CAI  OAN  104.57  3.000
 6W8  H7   CAI  OAN  108.86  3.000
 6W8  H8   CAI  PAV  109.16  3.000
 6W8  H7   CAI  PAV  108.69  3.000
 6W8  OAN  CAI  PAV  118.78  3.000
 6W8  H9   CAS  CAT  106.55  3.000
 6W8  H9   CAS  CAG  109.12  3.000
 6W8  CAT  CAS  CAG  103.18  3.000
 6W8  H9   CAS  OAN  110.62  3.000
 6W8  CAT  CAS  OAN  115.44  3.000
 6W8  CAG  CAS  OAN  111.50  3.000
 6W8  H11  CAG  H10  107.43  3.000
 6W8  H11  CAG  NAL  109.43  3.000
 6W8  H10  CAG  NAL  111.07  3.000
 6W8  H11  CAG  CAS  109.86  3.000
 6W8  H10  CAG  CAS  112.83  3.000
 6W8  NAL  CAG  CAS  106.20  3.000
 6W8  H12  NAL  CAH  109.01  3.000
 6W8  H12  NAL  CAG  108.78  3.000
 6W8  CAH  NAL  CAG  104.28  3.000
 6W8  H15  CAH  H14  107.19  3.000
 6W8  H15  CAH  CAT  109.47  3.000
 6W8  H14  CAH  CAT  112.79  3.000
 6W8  H15  CAH  NAL  109.13  3.000
 6W8  H14  CAH  NAL  110.92  3.000
 6W8  CAT  CAH  NAL  107.30  3.000
 6W8  H16  CAT  N9   105.73  3.000
 6W8  H16  CAT  CAH  112.06  3.000
 6W8  N9   CAT  CAH  112.87  3.000
 6W8  H16  CAT  CAS  108.77  3.000
 6W8  N9   CAT  CAS  113.52  3.000
 6W8  CAH  CAT  CAS  103.98  3.000
 6W8  CAT  N9   C8   127.23  3.000
 6W8  C8   N9   C4   106.16  3.000
 6W8  CAT  N9   C4   126.38  3.000
 6W8  N3   C2   N2   120.26  3.000
 6W8  N2   C2   N1   116.42  3.000
 6W8  N3   C2   N1   123.30  3.000
 6W8  C8   N7   C5   104.22  3.000
 6W8  H4   N2   H3   114.40  3.000
 6W8  H4   N2   C2   119.08  3.000
 6W8  H3   N2   C2   115.39  3.000
 6W8  CAS  OAN  CAI  115.89  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
 6W8  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 6W8  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 6W8  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 6W8  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 6W8  CONST_05  N7   C5   C4   N9     0.00   0.0  0
 6W8  CONST_06  CAT  N9   C4   C5   180.00   0.0  0
 6W8  CONST_07  CAT  N9   C4   N3     0.00   0.0  0
 6W8  CONST_08  N7   C8   N9   CAT  180.00   0.0  0
 6W8  CONST_09  N1   C2   N3   C4     0.00   0.0  0
 6W8  CONST_10  C2   N1   C6   C5     0.00   0.0  0
 6W8  CONST_11  N3   C2   N1   C6     0.00   0.0  0
 6W8  CONST_12  N2   C2   N3   C4   180.00   0.0  0
 6W8  CONST_13  N2   C2   N1   C6   180.00   0.0  0
 6W8  CONST_14  O6   C6   N1   C2   180.00   0.0  0
 6W8  CONST_15  H1   C8   N9   C4   180.00   0.0  0
 6W8  CONST_16  H2   N1   C6   C5   180.00   0.0  0
 6W8  CONST_17  H3   N2   C2   N1   180.00   0.0  0
 6W8  Var_01    CAH  NAL  CAG  CAS  -40.02  30.0  1
 6W8  Var_02    CAT  CAH  NAL  CAG   33.97  30.0  1
 6W8  Var_03    H7   CAI  OAN  CAS  -61.27  30.0  3
 6W8  Var_04    OAN  CAI  PAV  OAD  178.50  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
 6W8  chir_01  CAS  CAG  OAN  CAT  positiv
 6W8  chir_02  CAT  N9   CAS  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
 6W8  plan-1  C4   0.020
 6W8  plan-1  C5   0.020
 6W8  plan-1  C6   0.020
 6W8  plan-1  C8   0.020
 6W8  plan-1  N1   0.020
 6W8  plan-1  N3   0.020
 6W8  plan-1  CAT  0.020
 6W8  plan-1  N9   0.020
 6W8  plan-1  C2   0.020
 6W8  plan-1  O6   0.020
 6W8  plan-1  N7   0.020
 6W8  plan-1  H1   0.020
 6W8  plan-1  H2   0.020
 6W8  plan-1  H3   0.020
 6W8  plan-1  H4   0.020
 6W8  plan-1  N2   0.020

