# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:50:24 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{R})-2-[2-(6-aminopurin-9-yl)ethylamino]-3-phosphono-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCN[C@@H](C[P](O)(O)=O)C(O)=O)cnc12
#
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
 1IA  1IA  "(2~{R})-2-[2-(6-aminopurin-9-yl)ethylamino]-3-phosphono-propanoic acid"  ligand  34  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1IA
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
 1IA  C02  C  CR6    0   0.450  -7.2241  -48.9250  131.8469
 1IA  C04  C  CR16   0   0.036  -6.2221  -50.3037  130.3027
 1IA  C06  C  CR56   0   0.466  -4.8764  -49.0680  131.5214
 1IA  C07  C  CR56   0  -0.005  -5.9355  -48.4984  132.2145
 1IA  C09  C  CR15   0   0.104  -4.1871  -47.6270  133.0025
 1IA  C12  C  CH2    0  -0.257  -1.8977  -47.4461  130.8218
 1IA  C14  C  CH1    0  -0.183  -2.3506  -45.9998  128.9225
 1IA  C15  C  CH2    0  -0.712  -2.9840  -46.0211  127.5219
 1IA  C20  C  C      0   0.392  -2.7182  -44.7094  129.7023
 1IA  N01  N  NH2    0  -0.818  -8.3321  -48.4473  132.4197
 1IA  N03  N  N      0  -0.473  -7.3300  -49.8387  130.8766
 1IA  N05  N  N      0  -0.451  -4.9670  -49.9831  130.5571
 1IA  N08  N  N      0  -0.452  -5.4816  -47.5981  133.1419
 1IA  N10  N  NR5    0  -0.489  -3.7559  -48.4980  132.0454
 1IA  N13  N  NH1    0  -0.607  -2.6376  -47.2524  129.6013
 1IA  O17  O  O      0  -0.909  -5.0845  -46.4293  125.8963
 1IA  O18  O  OP    -1  -0.904  -5.3021  -44.5708  127.6533
 1IA  O19  O  OP    -1  -0.894  -5.3873  -47.0420  128.3778
 1IA  O21  O  O      0  -0.616  -3.5190  -44.7952  130.6577
 1IA  O22  O  OC    -1  -0.629  -2.1618  -43.6627  129.3018
 1IA  P16  P  P      0   1.158  -4.8561  -46.0109  127.3591
 1IA  H1   H  HCR6   0   0.246  -6.3784  -51.0443  129.5251
 1IA  H2   H  HCR5   0   0.289  -3.4871  -47.0357  133.5751
 1IA  H3   H  HCH2   0   0.261  -2.3591  -49.5543  130.9604
 1IA  H4   H  HCH2   0   0.269  -1.7496  -48.8484  132.4538
 1IA  H5   H  HCH2   0   0.212  -0.8432  -47.6221  130.5800
 1IA  H6   H  HCH2   0   0.191  -1.9137  -46.5821  131.5014
 1IA  H7   H  HCH1   0   0.175  -1.2597  -45.9659  128.7831
 1IA  H8   H  HCH2   0   0.173  -2.6045  -46.9179  127.0181
 1IA  H9   H  HCH2   0   0.178  -2.5934  -45.1726  126.9504
 1IA  H10  H  HNH2   0   0.400  -9.2333  -48.8091  132.1604
 1IA  H11  H  HNH2   0   0.408  -8.2808  -47.7932  133.1806
 1IA  H12  H  HNH1   0   0.338  -3.6416  -47.2925  129.7424
 1IA  C11  C  CH2    0  -0.345  -2.3862  -48.6644  131.5883

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
 1IA  O17  P16  deloc     1.539  0.020  1.539
 1IA  C15  P16  single    1.879  0.020  1.879
 1IA  C15  C14  single    1.537  0.020  1.537
 1IA  P16  O18  deloc     1.536  0.020  1.536
 1IA  P16  O19  deloc     1.544  0.020  1.544
 1IA  C14  N13  single    1.453  0.020  1.453
 1IA  C14  C20  single    1.552  0.020  1.552
 1IA  N13  C12  single    1.440  0.020  1.440
 1IA  C20  O21  deloc     1.250  0.020  1.250
 1IA  C20  O22  deloc     1.251  0.020  1.251
 1IA  C12  C11  single    1.520  0.020  1.520
 1IA  C11  N10  single    1.453  0.020  1.453
 1IA  N05  C04  aromatic  1.320  0.020  1.320
 1IA  N05  C06  aromatic  1.332  0.020  1.332
 1IA  C04  N03  aromatic  1.332  0.020  1.332
 1IA  N10  C06  aromatic  1.362  0.020  1.362
 1IA  N10  C09  aromatic  1.364  0.020  1.364
 1IA  C06  C07  aromatic  1.388  0.020  1.388
 1IA  N03  C02  aromatic  1.337  0.020  1.337
 1IA  C09  N08  aromatic  1.302  0.020  1.302
 1IA  C07  C02  aromatic  1.406  0.020  1.406
 1IA  C07  N08  aromatic  1.370  0.020  1.370
 1IA  C02  N01  single    1.336  0.020  1.336
 1IA  C04  H1   single    0.930  0.020  1.080
 1IA  C09  H2   single    0.930  0.020  1.080
 1IA  C11  H3   single    0.970  0.020  1.090
 1IA  C11  H4   single    0.970  0.020  1.090
 1IA  C12  H5   single    0.970  0.020  1.090
 1IA  C12  H6   single    0.970  0.020  1.090
 1IA  C14  H7   single    0.970  0.020  1.090
 1IA  C15  H8   single    0.970  0.020  1.090
 1IA  C15  H9   single    0.970  0.020  1.090
 1IA  N01  H10  single    0.860  0.020  1.020
 1IA  N01  H11  single    0.860  0.020  1.020
 1IA  N13  H12  single    0.890  0.020  1.040

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
 1IA  N03  C02  N01  119.34  3.000
 1IA  N01  C02  C07  122.65  3.000
 1IA  N03  C02  C07  118.01  3.000
 1IA  H1   C04  N05  116.15  3.000
 1IA  H1   C04  N03  115.30  3.000
 1IA  N05  C04  N03  128.55  3.000
 1IA  N10  C06  N05  128.44  3.000
 1IA  N10  C06  C07  105.30  3.000
 1IA  N05  C06  C07  126.26  3.000
 1IA  N08  C07  C06  110.79  3.000
 1IA  N08  C07  C02  132.84  3.000
 1IA  C06  C07  C02  116.37  3.000
 1IA  H2   C09  N10  121.10  3.000
 1IA  H2   C09  N08  125.10  3.000
 1IA  N10  C09  N08  113.80  3.000
 1IA  H6   C12  H5   106.05  3.000
 1IA  H6   C12  N13  114.25  3.000
 1IA  H5   C12  N13  109.20  3.000
 1IA  H6   C12  C11  108.27  3.000
 1IA  H5   C12  C11  106.97  3.000
 1IA  N13  C12  C11  111.72  3.000
 1IA  H7   C14  N13  106.35  3.000
 1IA  H7   C14  C20  105.83  3.000
 1IA  N13  C14  C20  115.79  3.000
 1IA  H7   C14  C15  107.07  3.000
 1IA  C20  C14  C15  111.82  3.000
 1IA  N13  C14  C15  109.41  3.000
 1IA  H9   C15  H8   105.69  3.000
 1IA  H9   C15  P16  107.81  3.000
 1IA  H8   C15  P16  108.03  3.000
 1IA  H9   C15  C14  108.53  3.000
 1IA  H8   C15  C14  106.70  3.000
 1IA  P16  C15  C14  119.30  3.000
 1IA  O22  C20  O21  125.95  3.000
 1IA  O22  C20  C14  115.43  3.000
 1IA  O21  C20  C14  118.61  3.000
 1IA  H11  N01  H10  118.39  3.000
 1IA  H11  N01  C02  121.02  3.000
 1IA  H10  N01  C02  120.29  3.000
 1IA  C04  N03  C02  119.04  3.000
 1IA  C06  N05  C04  111.77  3.000
 1IA  C09  N08  C07  104.02  3.000
 1IA  C11  N10  C09  126.27  3.000
 1IA  C09  N10  C06  106.08  3.000
 1IA  C11  N10  C06  127.33  3.000
 1IA  H12  N13  C14  107.12  3.000
 1IA  H12  N13  C12  112.65  3.000
 1IA  C14  N13  C12  114.23  3.000
 1IA  O19  P16  O18  113.57  3.000
 1IA  O19  P16  O17  113.25  3.000
 1IA  O18  P16  O17  113.20  3.000
 1IA  O19  P16  C15  106.38  3.000
 1IA  O18  P16  C15  106.13  3.000
 1IA  O17  P16  C15  103.22  3.000
 1IA  H4   C11  H3   107.77  3.000
 1IA  H4   C11  N10  108.66  3.000
 1IA  H3   C11  N10  107.35  3.000
 1IA  H4   C11  C12  110.37  3.000
 1IA  H3   C11  C12  110.85  3.000
 1IA  N10  C11  C12  111.70  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
 1IA  CONST_01  N05  C04  N03  C02     0.00   0.0  0
 1IA  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 1IA  CONST_03  N10  C06  C07  C02   180.00   0.0  0
 1IA  CONST_04  C09  N08  C07  C02   180.00   0.0  0
 1IA  CONST_05  N10  C06  N05  C04   180.00   0.0  0
 1IA  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 1IA  CONST_07  C07  C02  N03  C04     0.00   0.0  0
 1IA  CONST_08  N03  C04  N05  C06     0.00   0.0  0
 1IA  CONST_09  N08  C09  N10  C06     0.00   0.0  0
 1IA  CONST_10  N03  C02  C07  C06     0.00   0.0  0
 1IA  CONST_11  C09  N08  C07  C06     0.00   0.0  0
 1IA  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 1IA  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 1IA  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 1IA  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 1IA  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 1IA  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 1IA  CONST_18  N01  C02  N03  C04   180.00   0.0  0
 1IA  CONST_19  N01  C02  C07  C06   180.00   0.0  0
 1IA  CONST_20  C11  N10  C06  C07   180.00   0.0  0
 1IA  CONST_21  N05  C06  N10  C11     0.00   0.0  0
 1IA  CONST_22  N08  C09  N10  C11   180.00   0.0  0
 1IA  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 1IA  CONST_24  H1   C04  N03  C02   180.00   0.0  0
 1IA  CONST_25  H1   C04  N05  C06   180.00   0.0  0
 1IA  CONST_26  H2   C09  N10  C06   180.00   0.0  0
 1IA  CONST_27  H2   C09  N08  C07   180.00   0.0  0
 1IA  CONST_28  H10  N01  C02  C07   180.00   0.0  0
 1IA  CONST_29  H11  N01  C02  C07     0.00   0.0  0
 1IA  CONST_30  H10  N01  C02  N03     0.00   0.0  0
 1IA  CONST_31  H11  N01  C02  N03   180.00   0.0  0
 1IA  Var_01    C12  C11  N10  C06   104.23  30.0  2
 1IA  Var_02    C12  C11  N10  C09   -68.45  30.0  2
 1IA  Var_03    H3   C11  N10  C06   -17.49  30.0  2
 1IA  Var_04    H4   C11  N10  C06  -133.78  30.0  2
 1IA  Var_05    H3   C11  N10  C09   169.83  30.0  2
 1IA  Var_06    H4   C11  N10  C09    53.53  30.0  2
 1IA  Var_07    N13  C12  C11  N10   -64.63  30.0  2
 1IA  Var_08    H5   C12  C11  N10   175.92  30.0  2
 1IA  Var_09    H6   C12  C11  N10    62.02  30.0  2
 1IA  Var_10    C14  N13  C12  C11   171.53  30.0  2
 1IA  Var_11    O17  P16  C15  C14  -164.79  30.0  3
 1IA  Var_12    O18  P16  C15  C14    75.92  30.0  3
 1IA  Var_13    O19  P16  C15  C14   -45.34  30.0  3
 1IA  Var_14    H12  N13  C12  C11    49.01  30.0  2
 1IA  Var_15    H5   C12  N13  C14   -70.35  30.0  3
 1IA  Var_16    H6   C12  N13  C14    48.20  30.0  3
 1IA  Var_17    H3   C11  C12  N13    55.04  30.0  3
 1IA  Var_18    H4   C11  C12  N13   174.37  30.0  3
 1IA  Var_19    H8   C15  P16  O17   -42.84  30.0  2
 1IA  Var_20    H9   C15  P16  O17    70.95  30.0  2
 1IA  Var_21    H8   C15  P16  O18  -162.13  30.0  2
 1IA  Var_22    H9   C15  P16  O18   -48.34  30.0  2
 1IA  Var_23    H8   C15  P16  O19    76.61  30.0  2
 1IA  Var_24    H9   C15  P16  O19  -169.60  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
 1IA  chir_01  C14  C15  N13  C20  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
 1IA  plan-1  C02  0.020
 1IA  plan-1  C04  0.020
 1IA  plan-1  C06  0.020
 1IA  plan-1  C07  0.020
 1IA  plan-1  C09  0.020
 1IA  plan-1  N01  0.020
 1IA  plan-1  N03  0.020
 1IA  plan-1  N05  0.020
 1IA  plan-1  N08  0.020
 1IA  plan-1  N10  0.020
 1IA  plan-1  H1   0.020
 1IA  plan-1  H2   0.020
 1IA  plan-1  C11  0.020
 1IA  plan-2  C02  0.020
 1IA  plan-2  N01  0.020
 1IA  plan-2  H10  0.020
 1IA  plan-2  H11  0.020
 1IA  plan-3  C14  0.020
 1IA  plan-3  C20  0.020
 1IA  plan-3  O21  0.020
 1IA  plan-3  O22  0.020

