# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:24:21 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (2-{[(2S)-1-hydroxy-3-(6-oxo-1,6-dihydro-9H-purin-9-yl)propan-2-yl]oxy}ethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](Cn1cnc2C(=O)NC=Nc12)OCC[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
 4X2  4X2  '(2-{[(2S)-1-hydroxy-3-(6-oxo-1,6-dihydro-9H-purin-9-yl)propan-2-yl]oxy}ethyl)phosphonic acid'  ligand  36  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_4X2
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
 4X2  N12  N  NR5   0  -0.482   2.1245  -1.1378  -0.4084
 4X2  C13  C  CR56  0   0.488   2.2931  -0.0459   0.3788
 4X2  C15  C  CR16  0   0.155   2.3390   1.2088   2.1821
 4X2  C17  C  CR6   0   0.507   3.0979   2.2279   0.0866
 4X2  C21  C  CR15  0   0.101   2.5081  -0.7644  -1.6625
 4X2  O01  O  OH1   0  -0.750  -3.2295   1.6294  -1.7807
 4X2  P02  P  P     0   1.357  -3.6510   1.0703  -0.3313
 4X2  O03  O  OH1   0  -0.743  -3.8651   2.3472   0.6189
 4X2  O04  O  O     0  -0.715  -4.8144   0.1642  -0.4831
 4X2  C05  C  CH2   0  -0.774  -2.1749   0.3385   0.3973
 4X2  O07  O  O2    0  -0.481  -0.5665  -1.3864   0.2680
 4X2  C08  C  CH1   0   0.012   0.0606  -2.4554  -0.3972
 4X2  C09  C  CH2   0  -0.172  -0.5560  -3.8026  -0.0634
 4X2  O10  O  OH1   0  -0.669  -0.4002  -4.0577   1.3108
 4X2  C11  C  CH2   0  -0.334   1.5383  -2.4045  -0.0265
 4X2  N14  N  N     0  -0.441   2.0570   0.0427   1.7034
 4X2  N16  N  NR16  0  -0.664   2.8181   2.2459   1.4563
 4X2  O18  O  O     0  -0.470   3.5389   3.2095  -0.4855
 4X2  C19  C  CR56  0  -0.063   2.7911   0.9398  -0.4548
 4X2  N20  N  N     0  -0.445   2.9182   0.4699  -1.7305
 4X2  H1   H  HCR6  0   0.302   2.1956   1.4095   3.2355
 4X2  H2   H  HCR5  0   0.295   2.4708  -1.4590  -2.4889
 4X2  H3   H  HOH1  0   0.491  -2.5075   2.2713  -1.7859
 4X2  H4   H  HOH1  0   0.495  -4.7221   2.7815   0.5061
 4X2  H5   H  HCH2  0   0.289  -1.3822   1.0896   0.4436
 4X2  H6   H  HCH2  0   0.294  -2.4192   0.0538   1.4236
 4X2  H7   H  HCH2  0   0.217  -2.5069  -1.6245  -0.4301
 4X2  H8   H  HCH2  0   0.216  -1.4601  -0.5999  -1.4165
 4X2  H9   H  HCH1  0   0.231  -0.0240  -2.3313  -1.4878
 4X2  H10  H  HCH2  0   0.216  -1.6130  -3.7942  -0.3601
 4X2  H11  H  HCH2  0   0.210  -0.0636  -4.5615  -0.6849
 4X2  H12  H  HOH1  0   0.460  -0.7316  -4.9413   1.4928
 4X2  H13  H  HCH2  0   0.284   2.0765  -3.2065  -0.5320
 4X2  H14  H  HCH2  0   0.281   1.6792  -2.5311   1.0452
 4X2  H15  H  HNR6  0   0.434   3.0016   3.1115   1.9471
 4X2  C06  C  CH2   0  -0.133  -1.7042  -0.8782  -0.3832

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
 4X2  O04  P02  double    1.482  0.020  1.482
 4X2  P02  O03  single    1.606  0.020  1.606
 4X2  P02  O01  single    1.610  0.020  1.610
 4X2  P02  C05  single    1.801  0.020  1.801
 4X2  C06  C05  single    1.520  0.020  1.520
 4X2  C06  O07  single    1.406  0.020  1.406
 4X2  O10  C09  single    1.406  0.020  1.406
 4X2  C08  C11  single    1.524  0.020  1.524
 4X2  C08  O07  single    1.407  0.020  1.407
 4X2  C08  C09  single    1.519  0.020  1.519
 4X2  C11  N12  single    1.447  0.020  1.447
 4X2  N12  C21  aromatic  1.364  0.020  1.364
 4X2  N12  C13  aromatic  1.357  0.020  1.357
 4X2  C21  N20  aromatic  1.302  0.020  1.302
 4X2  C13  N14  single    1.348  0.020  1.348
 4X2  C13  C19  aromatic  1.384  0.020  1.384
 4X2  N14  C15  double    1.292  0.020  1.292
 4X2  N20  C19  aromatic  1.365  0.020  1.365
 4X2  C19  C17  single    1.430  0.020  1.430
 4X2  C15  N16  single    1.353  0.020  1.353
 4X2  C17  N16  single    1.398  0.020  1.398
 4X2  C17  O18  double    1.219  0.020  1.219
 4X2  C15  H1   single    0.930  0.020  1.080
 4X2  C21  H2   single    0.930  0.020  1.080
 4X2  O01  H3   single    0.850  0.020  0.980
 4X2  O03  H4   single    0.850  0.020  0.980
 4X2  C05  H5   single    0.970  0.020  1.090
 4X2  C05  H6   single    0.970  0.020  1.090
 4X2  C06  H7   single    0.970  0.020  1.090
 4X2  C06  H8   single    0.970  0.020  1.090
 4X2  C08  H9   single    0.970  0.020  1.090
 4X2  C09  H10  single    0.970  0.020  1.090
 4X2  C09  H11  single    0.970  0.020  1.090
 4X2  O10  H12  single    0.850  0.020  0.980
 4X2  C11  H13  single    0.970  0.020  1.090
 4X2  C11  H14  single    0.970  0.020  1.090
 4X2  N16  H15  single    0.860  0.020  1.020

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
 4X2  C11  N12  C21  126.61  3.000
 4X2  C21  N12  C13  106.16  3.000
 4X2  C11  N12  C13  126.99  3.000
 4X2  C19  C13  N14  127.45  3.000
 4X2  C19  C13  N12  105.58  3.000
 4X2  N14  C13  N12  126.95  3.000
 4X2  H1   C15  N16  115.27  3.000
 4X2  H1   C15  N14  119.96  3.000
 4X2  N16  C15  N14  124.77  3.000
 4X2  C19  C17  O18  128.69  3.000
 4X2  O18  C17  N16  121.46  3.000
 4X2  C19  C17  N16  109.85  3.000
 4X2  H2   C21  N20  125.47  3.000
 4X2  H2   C21  N12  121.19  3.000
 4X2  N20  C21  N12  113.34  3.000
 4X2  H3   O01  P02  115.55  3.000
 4X2  C05  P02  O04  115.86  3.000
 4X2  C05  P02  O03  101.13  3.000
 4X2  O04  P02  O03  116.23  3.000
 4X2  C05  P02  O01  106.90  3.000
 4X2  O03  P02  O01  106.94  3.000
 4X2  O04  P02  O01  109.00  3.000
 4X2  H4   O03  P02  113.96  3.000
 4X2  H6   C05  H5   107.54  3.000
 4X2  H6   C05  C06  110.05  3.000
 4X2  H5   C05  C06  110.32  3.000
 4X2  H6   C05  P02  107.61  3.000
 4X2  H5   C05  P02  109.40  3.000
 4X2  C06  C05  P02  111.79  3.000
 4X2  C08  O07  C06  114.61  3.000
 4X2  H9   C08  C11  108.15  3.000
 4X2  H9   C08  C09  106.65  3.000
 4X2  C11  C08  C09  111.70  3.000
 4X2  H9   C08  O07  110.40  3.000
 4X2  C09  C08  O07  112.91  3.000
 4X2  C11  C08  O07  106.97  3.000
 4X2  H11  C09  H10  106.51  3.000
 4X2  H11  C09  O10  112.22  3.000
 4X2  H10  C09  O10  111.85  3.000
 4X2  H11  C09  C08  107.86  3.000
 4X2  H10  C09  C08  108.95  3.000
 4X2  O10  C09  C08  109.31  3.000
 4X2  H12  O10  C09  108.28  3.000
 4X2  H14  C11  H13  107.89  3.000
 4X2  H14  C11  C08  111.17  3.000
 4X2  H13  C11  C08  109.96  3.000
 4X2  H14  C11  N12  108.01  3.000
 4X2  H13  C11  N12  108.76  3.000
 4X2  C08  C11  N12  110.96  3.000
 4X2  C15  N14  C13  112.65  3.000
 4X2  H15  N16  C17  116.74  3.000
 4X2  H15  N16  C15  117.36  3.000
 4X2  C17  N16  C15  125.90  3.000
 4X2  N20  C19  C17  130.05  3.000
 4X2  C17  C19  C13  119.38  3.000
 4X2  N20  C19  C13  110.56  3.000
 4X2  C19  N20  C21  104.36  3.000
 4X2  H8   C06  H7   107.16  3.000
 4X2  H8   C06  O07  110.35  3.000
 4X2  H7   C06  O07  111.47  3.000
 4X2  H8   C06  C05  110.44  3.000
 4X2  H7   C06  C05  109.87  3.000
 4X2  O07  C06  C05  107.58  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
 4X2  CONST_01  C19  N20  C21  N12     0.00   0.0  0
 4X2  CONST_02  N20  C19  C13  N12     0.00   0.0  0
 4X2  CONST_03  N20  C21  N12  C13     0.00   0.0  0
 4X2  CONST_04  C21  N20  C19  C13     0.00   0.0  0
 4X2  CONST_05  C19  C13  N12  C21     0.00   0.0  0
 4X2  CONST_06  N16  C15  N14  C13     0.00   0.0  0
 4X2  CONST_07  C19  C17  N16  C15     0.00   0.0  0
 4X2  CONST_08  N14  C15  N16  C17     0.00   0.0  0
 4X2  CONST_09  N20  C21  N12  C11   180.00   0.0  0
 4X2  CONST_10  N14  C13  N12  C11     0.00   0.0  0
 4X2  CONST_11  C19  C13  N12  C11   180.00   0.0  0
 4X2  CONST_12  O18  C17  N16  C15   180.00   0.0  0
 4X2  CONST_13  H2   C21  N12  C13   180.00   0.0  0
 4X2  CONST_14  H1   C15  N14  C13   180.00   0.0  0
 4X2  CONST_15  H15  N16  C15  N14   180.00   0.0  0
 4X2  Var_01    C08  C11  N12  C13    95.63  30.0  2
 4X2  Var_02    C06  C05  P02  O01   -65.16  30.0  3
 4X2  Var_03    O07  C06  C05  P02  -179.22  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
 4X2  chir_01  C08  C11  O07  C09  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
 4X2  plan-1  N12  0.020
 4X2  plan-1  C13  0.020
 4X2  plan-1  C15  0.020
 4X2  plan-1  C17  0.020
 4X2  plan-1  C21  0.020
 4X2  plan-1  C11  0.020
 4X2  plan-1  N14  0.020
 4X2  plan-1  N16  0.020
 4X2  plan-1  O18  0.020
 4X2  plan-1  C19  0.020
 4X2  plan-1  N20  0.020
 4X2  plan-1  H1   0.020
 4X2  plan-1  H2   0.020
 4X2  plan-1  H15  0.020

