# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:40:26 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(C[C@@H](CO)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
 4X7  4X7  '(2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid'  ligand  38  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 OK
;

data_comp_4X7
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
 4X7  C4   C  CR56  0   0.509   2.1742  -0.1541   0.1770
 4X7  C5   C  CR56  0  -0.093   2.6721   0.6886  -0.8026
 4X7  C6   C  CR6   0   0.498   2.9603   2.0411  -0.4640
 4X7  C8   C  CR15  0   0.087   2.3945  -1.1810  -1.7374
 4X7  N1   N  NR16  0  -0.726   2.6744   2.2823   0.8853
 4X7  N3   N  N     0  -0.505   1.9289   0.1285   1.4643
 4X7  OAE  O  OH1   0  -0.743  -3.6795   2.4996   0.2775
 4X7  PAV  P  P     0   1.355  -3.5050   1.1630  -0.5955
 4X7  OAF  O  OH1   0  -0.749  -4.8201   0.2673  -0.3513
 4X7  OAC  O  O     0  -0.715  -3.3149   1.3501  -2.0538
 4X7  CAJ  C  CH2   0  -0.774  -2.1464   0.3597   0.2723
 4X7  OAO  O  O2    0  -0.481  -0.6848  -1.4880   0.3536
 4X7  CAT  C  CH1   0   0.013  -0.0766  -2.6192  -0.2196
 4X7  CAH  C  CH2   0  -0.172  -0.7049  -3.9220   0.2408
 4X7  OAD  O  OH1   0  -0.670  -0.5233  -4.0649   1.6281
 4X7  N9   N  NR5   0  -0.492   2.0079  -1.3548  -0.4346
 4X7  C2   C  CR6   0   0.676   2.1974   1.3680   1.7818
 4X7  O6   O  O     0  -0.479   3.3934   2.9332  -1.1756
 4X7  N7   N  N     0  -0.446   2.8024   0.0242  -1.9947
 4X7  H1   H  HCR5  0   0.287   2.3541  -1.9972  -2.4437
 4X7  H2   H  HNR6  0   0.423   2.8629   3.2217   1.2117
 4X7  H3   H  HNH2  0   0.409   1.5398   1.1806   3.6750
 4X7  H4   H  HNH2  0   0.412   2.0059   2.7693   3.2631
 4X7  H5   H  HOH1  0   0.495  -4.2799   3.1500  -0.1123
 4X7  H6   H  HOH1  0   0.490  -5.0704   0.1355   0.5725
 4X7  H7   H  HCH2  0   0.291  -1.2827   1.0279   0.2291
 4X7  H8   H  HCH2  0   0.291  -2.4105   0.2337   1.3252
 4X7  H9   H  HCH2  0   0.216  -2.6441  -1.6630  -0.3108
 4X7  H10  H  HCH2  0   0.216  -1.5350  -0.8409  -1.4123
 4X7  H11  H  HCH1  0   0.230  -0.1742  -2.5948  -1.3155
 4X7  H12  H  HCH2  0   0.216  -1.7680  -3.9198  -0.0341
 4X7  H13  H  HCH2  0   0.207  -0.2378  -4.7392  -0.3242
 4X7  H14  H  HOH1  0   0.460  -0.8984  -4.9086   1.8952
 4X7  H15  H  HCH2  0   0.277   1.5603  -2.5307   1.2020
 4X7  H16  H  HCH2  0   0.278   1.9254  -3.4184  -0.2742
 4X7  N2   N  NH2   0  -0.834   2.0428   1.7870   3.0494
 4X7  CAK  C  CH2   0  -0.330   1.4072  -2.5456   0.1244
 4X7  CAI  C  CH2   0  -0.134  -1.7873  -0.9785  -0.3532

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
 4X7  OAC  PAV  double    1.482  0.020  1.482
 4X7  PAV  OAF  single    1.610  0.020  1.610
 4X7  PAV  CAJ  single    1.801  0.020  1.801
 4X7  PAV  OAE  single    1.606  0.020  1.606
 4X7  CAI  OAO  single    1.405  0.020  1.405
 4X7  CAI  CAJ  single    1.520  0.020  1.520
 4X7  CAT  OAO  single    1.406  0.020  1.406
 4X7  CAT  CAH  single    1.518  0.020  1.518
 4X7  CAT  CAK  single    1.525  0.020  1.525
 4X7  OAD  CAH  single    1.406  0.020  1.406
 4X7  CAK  N9   single    1.446  0.020  1.446
 4X7  N9   C8   aromatic  1.370  0.020  1.370
 4X7  N9   C4   aromatic  1.358  0.020  1.358
 4X7  N3   C4   single    1.341  0.020  1.341
 4X7  N3   C2   double    1.307  0.020  1.307
 4X7  C8   N7   aromatic  1.298  0.020  1.298
 4X7  C4   C5   aromatic  1.385  0.020  1.385
 4X7  N2   C2   single    1.344  0.020  1.344
 4X7  C2   N1   single    1.367  0.020  1.367
 4X7  N7   C5   aromatic  1.371  0.020  1.371
 4X7  C5   C6   single    1.424  0.020  1.424
 4X7  N1   C6   single    1.400  0.020  1.400
 4X7  C6   O6   double    1.221  0.020  1.221
 4X7  C8   H1   single    0.930  0.020  1.080
 4X7  N1   H2   single    0.860  0.020  1.020
 4X7  N2   H3   single    0.890  0.020  1.040
 4X7  N2   H4   single    0.890  0.020  1.040
 4X7  OAE  H5   single    0.850  0.020  0.980
 4X7  OAF  H6   single    0.850  0.020  0.980
 4X7  CAJ  H7   single    0.970  0.020  1.090
 4X7  CAJ  H8   single    0.970  0.020  1.090
 4X7  CAI  H9   single    0.970  0.020  1.090
 4X7  CAI  H10  single    0.970  0.020  1.090
 4X7  CAT  H11  single    0.970  0.020  1.090
 4X7  CAH  H12  single    0.970  0.020  1.090
 4X7  CAH  H13  single    0.970  0.020  1.090
 4X7  OAD  H14  single    0.850  0.020  0.980
 4X7  CAK  H15  single    0.970  0.020  1.090
 4X7  CAK  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
 4X7  N9   C4   N3   126.63  3.000
 4X7  N3   C4   C5   128.08  3.000
 4X7  N9   C4   C5   105.28  3.000
 4X7  N7   C5   C6   130.39  3.000
 4X7  C6   C5   C4   118.85  3.000
 4X7  N7   C5   C4   110.75  3.000
 4X7  O6   C6   N1   120.56  3.000
 4X7  O6   C6   C5   128.86  3.000
 4X7  N1   C6   C5   110.58  3.000
 4X7  H1   C8   N7   125.71  3.000
 4X7  H1   C8   N9   121.03  3.000
 4X7  N7   C8   N9   113.27  3.000
 4X7  H2   N1   C2   118.32  3.000
 4X7  H2   N1   C6   115.64  3.000
 4X7  C2   N1   C6   126.03  3.000
 4X7  C2   N3   C4   113.30  3.000
 4X7  H5   OAE  PAV  114.08  3.000
 4X7  CAJ  PAV  OAC  115.69  3.000
 4X7  CAJ  PAV  OAF  107.16  3.000
 4X7  OAC  PAV  OAF  108.92  3.000
 4X7  CAJ  PAV  OAE  101.02  3.000
 4X7  OAF  PAV  OAE  106.97  3.000
 4X7  OAC  PAV  OAE  116.33  3.000
 4X7  H6   OAF  PAV  115.63  3.000
 4X7  H8   CAJ  H7   107.43  3.000
 4X7  H8   CAJ  CAI  110.61  3.000
 4X7  H7   CAJ  CAI  109.59  3.000
 4X7  H8   CAJ  PAV  109.47  3.000
 4X7  H7   CAJ  PAV  107.72  3.000
 4X7  CAI  CAJ  PAV  111.87  3.000
 4X7  CAT  OAO  CAI  115.21  3.000
 4X7  H11  CAT  CAK  108.05  3.000
 4X7  H11  CAT  CAH  106.52  3.000
 4X7  CAK  CAT  CAH  112.08  3.000
 4X7  H11  CAT  OAO  110.46  3.000
 4X7  CAK  CAT  OAO  106.86  3.000
 4X7  CAH  CAT  OAO  112.81  3.000
 4X7  H13  CAH  H12  106.54  3.000
 4X7  H13  CAH  OAD  112.15  3.000
 4X7  H12  CAH  OAD  111.85  3.000
 4X7  H13  CAH  CAT  107.86  3.000
 4X7  H12  CAH  CAT  108.86  3.000
 4X7  OAD  CAH  CAT  109.45  3.000
 4X7  H14  OAD  CAH  108.24  3.000
 4X7  CAK  N9   C8   126.11  3.000
 4X7  C8   N9   C4   106.36  3.000
 4X7  CAK  N9   C4   127.22  3.000
 4X7  N3   C2   N2   120.07  3.000
 4X7  N2   C2   N1   116.77  3.000
 4X7  N3   C2   N1   123.14  3.000
 4X7  C8   N7   C5   104.34  3.000
 4X7  H4   N2   H3   115.98  3.000
 4X7  H4   N2   C2   120.60  3.000
 4X7  H3   N2   C2   117.14  3.000
 4X7  H16  CAK  H15  107.82  3.000
 4X7  H16  CAK  N9   108.69  3.000
 4X7  H15  CAK  N9   108.24  3.000
 4X7  H16  CAK  CAT  109.95  3.000
 4X7  H15  CAK  CAT  111.15  3.000
 4X7  N9   CAK  CAT  110.90  3.000
 4X7  H10  CAI  H9   107.15  3.000
 4X7  H10  CAI  OAO  110.52  3.000
 4X7  H9   CAI  OAO  111.53  3.000
 4X7  H10  CAI  CAJ  109.94  3.000
 4X7  H9   CAI  CAJ  110.41  3.000
 4X7  OAO  CAI  CAJ  107.31  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
 4X7  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 4X7  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 4X7  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 4X7  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 4X7  CONST_05  N7   C5   C4   N9     0.00   0.0  0
 4X7  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 4X7  CONST_07  C2   N1   C6   C5     0.00   0.0  0
 4X7  CONST_08  N3   C2   N1   C6     0.00   0.0  0
 4X7  CONST_09  CAK  N9   C4   C5   180.00   0.0  0
 4X7  CONST_10  CAK  N9   C4   N3     0.00   0.0  0
 4X7  CONST_11  N7   C8   N9   CAK  180.00   0.0  0
 4X7  CONST_12  N2   C2   N3   C4   180.00   0.0  0
 4X7  CONST_13  N2   C2   N1   C6   180.00   0.0  0
 4X7  CONST_14  O6   C6   N1   C2   180.00   0.0  0
 4X7  CONST_15  H1   C8   N9   C4   180.00   0.0  0
 4X7  CONST_16  H2   N1   C6   C5   180.00   0.0  0
 4X7  CONST_17  H3   N2   C2   N1   180.00   0.0  0
 4X7  Var_01    CAT  CAK  N9   C4    93.67  30.0  2
 4X7  Var_02    CAI  CAJ  PAV  OAE  178.95  30.0  3
 4X7  Var_03    OAO  CAI  CAJ  PAV  177.28  30.0  1

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
 4X7  chir_01  CAT  OAO  CAH  CAK  positiv

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
 4X7  plan-1  C4   0.020
 4X7  plan-1  C5   0.020
 4X7  plan-1  C6   0.020
 4X7  plan-1  C8   0.020
 4X7  plan-1  N1   0.020
 4X7  plan-1  N3   0.020
 4X7  plan-1  N9   0.020
 4X7  plan-1  C2   0.020
 4X7  plan-1  O6   0.020
 4X7  plan-1  N7   0.020
 4X7  plan-1  H1   0.020
 4X7  plan-1  H2   0.020
 4X7  plan-1  H3   0.020
 4X7  plan-1  H4   0.020
 4X7  plan-1  N2   0.020
 4X7  plan-1  CAK  0.020

