# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:32:54 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(C[C@@H](COCC[P](O)(O)=O)OCC[P](O)(O)=O)cnc2C(=O)N1
#
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
 45T  45T  '{[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)'  ligand  49  28  .  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_45T
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
 45T  OAE  O  O     0  -0.715   6.7128  -2.8733  -0.4812
 45T  PBA  P  P     0   1.357   6.4406  -1.4183  -0.5607
 45T  OAF  O  OH1   0  -0.743   7.4256  -0.4628   0.2737
 45T  OAC  O  OH1   0  -0.749   6.5243  -0.9508  -2.0986
 45T  CAL  C  CH2   0  -0.778   4.8367  -0.8880   0.0669
 45T  CAJ  C  CH2   0  -0.130   3.6986  -1.6753  -0.5617
 45T  OAS  O  O2    0  -0.484   2.4937  -1.2250   0.0062
 45T  CAN  C  CH2   0  -0.137   1.3928  -2.0122  -0.3646
 45T  CAY  C  CH1   0  -0.002   0.1524  -1.4648   0.3094
 45T  OAT  O  O2    0  -0.491  -0.1952  -0.2198  -0.2520
 45T  CAK  C  CH2   0  -0.160  -0.3640   0.8439   0.6621
 45T  CAM  C  CH2   0  -0.773  -1.0928   1.9715  -0.0555
 45T  PBB  P  P     0   1.345  -1.6365   3.2727   1.0752
 45T  OAG  O  OH1   0  -0.747  -2.3960   4.2453   0.0442
 45T  OAH  O  OH1   0  -0.775  -2.7546   2.6696   2.0504
 45T  OAD  O  O     0  -0.717  -0.5501   3.8792   1.8829
 45T  CAO  C  CH2   0  -0.345  -1.0113  -2.4555   0.1473
 45T  N9   N  NR5   0  -0.482  -2.2418  -1.8442   0.5949
 45T  C4   C  CR56  0   0.496  -3.0430  -1.0669  -0.1789
 45T  N3   N  N     0  -0.491  -3.0900  -1.0501  -1.5146
 45T  C2   C  CR6   0   0.682  -3.9244  -0.1635  -1.9970
 45T  N2   N  NH2   0  -0.829  -4.0930  -0.0445  -3.3186
 45T  N1   N  NR16  0  -0.714  -4.6189   0.7102  -1.2026
 45T  C6   C  CR6   0   0.495  -4.5615   0.7539   0.1859
 45T  O6   O  O     0  -0.508  -5.0824   1.6850   0.8040
 45T  C5   C  CR56  0  -0.069  -3.7869  -0.3076   0.7096
 45T  N7   N  N     0  -0.426  -3.4657  -0.6214   2.0066
 45T  C8   C  CR15  0   0.077  -2.5484  -1.5308   1.8982
 45T  H1   H  HOH1  0   0.495   8.3640  -0.6708   0.1644
 45T  H2   H  HOH1  0   0.491   6.4136  -0.0031  -2.2508
 45T  H3   H  HCH2  0   0.293   4.8377  -1.0392   1.1492
 45T  H4   H  HCH2  0   0.292   4.7129   0.1825  -0.1152
 45T  H5   H  HCH2  0   0.215   3.6883  -1.5398  -1.6513
 45T  H6   H  HCH2  0   0.216   3.8362  -2.7474  -0.3721
 45T  H7   H  HCH2  0   0.213   1.2516  -2.0152  -1.4550
 45T  H8   H  HCH2  0   0.212   1.5381  -3.0579  -0.0577
 45T  H9   H  HCH1  0   0.240   0.3630  -1.3593   1.3820
 45T  H10  H  HCH2  0   0.224  -0.9385   0.5225   1.5375
 45T  H11  H  HCH2  0   0.238   0.6053   1.1978   1.0300
 45T  H12  H  HCH2  0   0.301  -0.4459   2.4334  -0.8052
 45T  H13  H  HCH2  0   0.270  -1.9615   1.5813  -0.5886
 45T  H14  H  HOH1  0   0.494  -2.7378   5.0582   0.4414
 45T  H15  H  HOH1  0   0.488  -3.6098   2.3849   1.6630
 45T  H16  H  HCH2  0   0.278  -1.1407  -2.7471  -0.8950
 45T  H17  H  HCH2  0   0.289  -0.8195  -3.3593   0.7254
 45T  H18  H  HNH2  0   0.416  -3.6928  -0.7547  -3.9081
 45T  H19  H  HNH2  0   0.418  -4.8603   0.4798  -3.7028
 45T  H20  H  HNR6  0   0.432  -5.1610   1.4414  -1.6469
 45T  H21  H  HCR5  0   0.296  -2.0512  -2.0229   2.7213

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
 45T  O6   C6   double    1.233  0.020  1.233
 45T  N1   C6   single    1.390  0.020  1.390
 45T  N1   C2   single    1.370  0.020  1.370
 45T  C6   C5   single    1.415  0.020  1.415
 45T  N2   C2   single    1.338  0.020  1.338
 45T  C2   N3   double    1.310  0.020  1.310
 45T  C5   N7   aromatic  1.372  0.020  1.372
 45T  C5   C4   aromatic  1.385  0.020  1.385
 45T  N7   C8   aromatic  1.296  0.020  1.296
 45T  N3   C4   single    1.337  0.020  1.337
 45T  C4   N9   aromatic  1.358  0.020  1.358
 45T  C8   N9   aromatic  1.375  0.020  1.375
 45T  N9   CAO  single    1.445  0.020  1.445
 45T  CAN  OAS  single    1.403  0.020  1.403
 45T  CAN  CAY  single    1.514  0.020  1.514
 45T  OAS  CAJ  single    1.406  0.020  1.406
 45T  OAT  CAY  single    1.409  0.020  1.409
 45T  OAT  CAK  single    1.413  0.020  1.413
 45T  CAY  CAO  single    1.537  0.020  1.537
 45T  CAJ  CAL  single    1.520  0.020  1.520
 45T  CAL  PBA  single    1.802  0.020  1.802
 45T  CAM  CAK  single    1.522  0.020  1.522
 45T  CAM  PBB  single    1.808  0.020  1.808
 45T  OAE  PBA  double    1.482  0.020  1.482
 45T  OAD  PBB  double    1.483  0.020  1.483
 45T  OAC  PBA  single    1.610  0.020  1.610
 45T  PBA  OAF  single    1.606  0.020  1.606
 45T  OAG  PBB  single    1.608  0.020  1.608
 45T  PBB  OAH  single    1.601  0.020  1.601
 45T  OAF  H1   single    0.850  0.020  0.980
 45T  OAC  H2   single    0.850  0.020  0.980
 45T  CAL  H3   single    0.970  0.020  1.090
 45T  CAL  H4   single    0.970  0.020  1.090
 45T  CAJ  H5   single    0.970  0.020  1.090
 45T  CAJ  H6   single    0.970  0.020  1.090
 45T  CAN  H7   single    0.970  0.020  1.090
 45T  CAN  H8   single    0.970  0.020  1.090
 45T  CAY  H9   single    0.970  0.020  1.090
 45T  CAK  H10  single    0.970  0.020  1.090
 45T  CAK  H11  single    0.970  0.020  1.090
 45T  CAM  H12  single    0.970  0.020  1.090
 45T  CAM  H13  single    0.970  0.020  1.090
 45T  OAG  H14  single    0.850  0.020  0.980
 45T  OAH  H15  single    0.850  0.020  0.980
 45T  CAO  H16  single    0.970  0.020  1.090
 45T  CAO  H17  single    0.970  0.020  1.090
 45T  N2   H18  single    0.890  0.020  1.040
 45T  N2   H19  single    0.890  0.020  1.040
 45T  N1   H20  single    0.860  0.020  1.020
 45T  C8   H21  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
 45T  CAL  PBA  OAC  107.07  3.000
 45T  OAC  PBA  OAF  106.96  3.000
 45T  CAL  PBA  OAF  100.95  3.000
 45T  OAF  PBA  OAE  116.33  3.000
 45T  OAC  PBA  OAE  109.07  3.000
 45T  CAL  PBA  OAE  115.69  3.000
 45T  H1   OAF  PBA  114.10  3.000
 45T  H2   OAC  PBA  115.43  3.000
 45T  H4   CAL  H3   107.50  3.000
 45T  H4   CAL  CAJ  110.71  3.000
 45T  H3   CAL  CAJ  109.79  3.000
 45T  H4   CAL  PBA  109.33  3.000
 45T  H3   CAL  PBA  107.66  3.000
 45T  CAJ  CAL  PBA  111.71  3.000
 45T  H6   CAJ  H5   107.05  3.000
 45T  H6   CAJ  OAS  110.52  3.000
 45T  H5   CAJ  OAS  110.68  3.000
 45T  H6   CAJ  CAL  109.92  3.000
 45T  H5   CAJ  CAL  110.70  3.000
 45T  OAS  CAJ  CAL  107.98  3.000
 45T  CAN  OAS  CAJ  112.70  3.000
 45T  H8   CAN  H7   106.93  3.000
 45T  H8   CAN  CAY  109.14  3.000
 45T  H7   CAN  CAY  109.71  3.000
 45T  H8   CAN  OAS  110.86  3.000
 45T  H7   CAN  OAS  111.36  3.000
 45T  CAY  CAN  OAS  108.81  3.000
 45T  H9   CAY  CAO  108.07  3.000
 45T  H9   CAY  OAT  110.58  3.000
 45T  CAO  CAY  OAT  109.92  3.000
 45T  H9   CAY  CAN  108.21  3.000
 45T  CAO  CAY  CAN  109.90  3.000
 45T  OAT  CAY  CAN  110.13  3.000
 45T  CAK  OAT  CAY  115.91  3.000
 45T  H11  CAK  H10  106.88  3.000
 45T  H11  CAK  CAM  110.04  3.000
 45T  H10  CAK  CAM  110.06  3.000
 45T  H11  CAK  OAT  110.78  3.000
 45T  H10  CAK  OAT  111.03  3.000
 45T  CAM  CAK  OAT  108.05  3.000
 45T  H13  CAM  H12  106.70  3.000
 45T  H13  CAM  PBB  108.88  3.000
 45T  H12  CAM  PBB  107.64  3.000
 45T  H13  CAM  CAK  110.27  3.000
 45T  H12  CAM  CAK  110.68  3.000
 45T  PBB  CAM  CAK  112.47  3.000
 45T  OAD  PBB  OAH  109.50  3.000
 45T  OAH  PBB  OAG  106.76  3.000
 45T  OAD  PBB  OAG  116.59  3.000
 45T  OAH  PBB  CAM  108.65  3.000
 45T  OAG  PBB  CAM  100.16  3.000
 45T  OAD  PBB  CAM  114.50  3.000
 45T  H14  OAG  PBB  114.33  3.000
 45T  H15  OAH  PBB  118.52  3.000
 45T  H17  CAO  H16  107.84  3.000
 45T  H17  CAO  N9   109.65  3.000
 45T  H16  CAO  N9   107.96  3.000
 45T  H17  CAO  CAY  110.20  3.000
 45T  H16  CAO  CAY  111.30  3.000
 45T  N9   CAO  CAY  109.84  3.000
 45T  C8   N9   C4   106.14  3.000
 45T  C8   N9   CAO  125.44  3.000
 45T  C4   N9   CAO  124.61  3.000
 45T  C5   C4   N3   127.96  3.000
 45T  N3   C4   N9   126.67  3.000
 45T  C5   C4   N9   105.37  3.000
 45T  C2   N3   C4   113.52  3.000
 45T  N1   C2   N2   116.90  3.000
 45T  N2   C2   N3   120.30  3.000
 45T  N1   C2   N3   122.76  3.000
 45T  H19  N2   H18  116.60  3.000
 45T  H19  N2   C2   121.33  3.000
 45T  H18  N2   C2   117.78  3.000
 45T  H20  N1   C6   115.95  3.000
 45T  H20  N1   C2   118.51  3.000
 45T  C6   N1   C2   125.33  3.000
 45T  C5   C6   O6   127.76  3.000
 45T  C5   C6   N1   111.64  3.000
 45T  O6   C6   N1   120.46  3.000
 45T  N7   C5   C6   130.51  3.000
 45T  N7   C5   C4   110.80  3.000
 45T  C6   C5   C4   117.89  3.000
 45T  C8   N7   C5   104.30  3.000
 45T  H21  C8   N7   125.56  3.000
 45T  H21  C8   N9   121.05  3.000
 45T  N7   C8   N9   113.39  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
 45T  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 45T  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 45T  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 45T  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 45T  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 45T  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 45T  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 45T  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 45T  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 45T  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 45T  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 45T  CONST_15  H21  C8   N9   C4    180.00   0.0  0
 45T  CONST_16  H20  N1   C2   N3    180.00   0.0  0
 45T  CONST_17  H18  N2   C2   N3      0.00   0.0  0
 45T  CONST_18  H19  N2   C2   N3    180.00   0.0  0
 45T  Var_01    C4   N9   CAO  CAY    85.94  30.0  3
 45T  Var_02    CAJ  CAL  PBA  OAE   -52.54  30.0  2
 45T  Var_03    OAS  CAJ  CAL  PBA   178.48  30.0  2
 45T  Var_04    CAY  CAN  OAS  CAJ   179.14  30.0  2
 45T  Var_05    CAM  CAK  OAT  CAY  -164.68  30.0  3
 45T  Var_06    PBB  CAM  CAK  OAT   169.67  30.0  1
 45T  Var_07    OAD  PBB  CAM  CAK    56.60  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
 45T  chir_01  CAY  CAN  OAT  CAO  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
 45T  plan-1  CAO  0.020
 45T  plan-1  N9   0.020
 45T  plan-1  C4   0.020
 45T  plan-1  N3   0.020
 45T  plan-1  C2   0.020
 45T  plan-1  N2   0.020
 45T  plan-1  N1   0.020
 45T  plan-1  C6   0.020
 45T  plan-1  O6   0.020
 45T  plan-1  C5   0.020
 45T  plan-1  N7   0.020
 45T  plan-1  C8   0.020
 45T  plan-1  H18  0.020
 45T  plan-1  H19  0.020
 45T  plan-1  H20  0.020
 45T  plan-1  H21  0.020

