# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 10:30:12 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{S})-2-[3-(6-aminopurin-9-yl)propylamino]-3-phosphono-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCN[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
 1IK  1IK  "(S)-2-((3-(6-amino-9H-purin-9-yl)propyl)amino)-3-phosphonopropanoic acid"  ligand  37  23  .  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_1IK
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
 1IK  C02  C  CR6    0   0.450   -8.7027  -49.6392  131.6509
 1IK  C04  C  CR16   0   0.034   -7.3486  -51.2613  130.7460
 1IK  C06  C  CR56   0   0.480   -6.3380  -49.6479  131.8399
 1IK  C07  C  CR56   0   0.011   -7.5398  -49.0295  132.1492
 1IK  C09  C  CR15   0   0.099   -6.0315  -47.8173  132.9791
 1IK  C12  C  CH2    0  -0.445   -3.2316  -47.9388  131.5652
 1IK  C13  C  CH2    0  -0.291   -3.4294  -48.0080  130.0496
 1IK  C15  C  CH1    0  -0.158   -4.4460  -45.8964  129.4003
 1IK  C16  C  C      0   0.387   -4.0286  -44.4218  129.5914
 1IK  C19  C  CH2    0  -0.744   -5.2895  -46.1378  128.1359
 1IK  N01  N  NH2    0  -0.821   -9.9224  -49.1260  131.8351
 1IK  N03  N  N      0  -0.476   -8.5695  -50.7726  130.9549
 1IK  N05  N  N      0  -0.458   -6.1876  -50.7732  131.1425
 1IK  N08  N  N      0  -0.455   -7.3273  -47.8825  132.8648
 1IK  N10  N  NR5    0  -0.490   -5.3741  -48.8543  132.3835
 1IK  N14  N  NH1    0  -0.614   -3.2101  -46.7004  129.4560
 1IK  O17  O  OC    -1  -0.623   -4.2810  -43.8925  130.6960
 1IK  O18  O  O      0  -0.623   -3.4286  -43.8797  128.6376
 1IK  O21  O  O      0  -0.912   -7.7406  -46.3034  127.0031
 1IK  O22  O  OP    -1  -0.911   -7.5916  -45.3582  129.3970
 1IK  O23  O  OP    -1  -0.898   -7.2030  -47.8643  128.9722
 1IK  P20  P  P      0   1.159   -7.1203  -46.4343  128.4046
 1IK  H1   H  HCR6   0   0.243   -7.3098  -52.1830  130.1743
 1IK  H2   H  HCR5   0   0.289   -5.4926  -47.0364  133.4963
 1IK  H3   H  HCH2   0   0.264   -3.7464  -50.0210  131.9003
 1IK  H4   H  HCH2   0   0.270   -3.5647  -49.0803  133.3697
 1IK  H5   H  HCH2   0   0.239   -2.1645  -47.9839  131.7952
 1IK  H6   H  HCH2   0   0.234   -3.5732  -46.9684  131.9365
 1IK  H7   H  HCH2   0   0.195   -4.4272  -48.4061  129.8136
 1IK  H8   H  HCH2   0   0.223   -2.7128  -48.7211  129.6341
 1IK  H9   H  HCH1   0   0.182   -5.0279  -46.1867  130.2805
 1IK  H10  H  HCH2   0   0.175   -4.9002  -47.0180  127.6079
 1IK  H11  H  HCH2   0   0.185   -5.1379  -45.3023  127.4455
 1IK  H12  H  HNH2   0   0.398  -10.7336  -49.6097  131.4913
 1IK  H13  H  HNH2   0   0.407  -10.0576  -48.2952  132.3832
 1IK  H14  H  HNH1   0   0.327   -2.8467  -46.8046  128.5180
 1IK  C11  C  CH2    0  -0.331   -3.9326  -49.0429  132.3437

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
 1IK  O21  P20  deloc     1.538  0.020  1.538
 1IK  P20  C19  single    1.874  0.020  1.874
 1IK  P20  O23  deloc     1.541  0.020  1.541
 1IK  P20  O22  deloc     1.538  0.020  1.538
 1IK  C19  C15  single    1.539  0.020  1.539
 1IK  N14  C15  single    1.475  0.020  1.475
 1IK  N14  C13  single    1.453  0.020  1.453
 1IK  C15  C16  single    1.544  0.020  1.544
 1IK  O18  C16  deloc     1.250  0.020  1.250
 1IK  C13  C12  single    1.530  0.020  1.530
 1IK  C16  O17  deloc     1.251  0.020  1.251
 1IK  C12  C11  single    1.522  0.020  1.522
 1IK  N05  C04  aromatic  1.320  0.020  1.320
 1IK  N05  C06  aromatic  1.332  0.020  1.332
 1IK  C04  N03  aromatic  1.331  0.020  1.331
 1IK  C11  N10  single    1.454  0.020  1.454
 1IK  C06  N10  aromatic  1.362  0.020  1.362
 1IK  C06  C07  aromatic  1.386  0.020  1.386
 1IK  N03  C02  aromatic  1.337  0.020  1.337
 1IK  N10  C09  aromatic  1.365  0.020  1.365
 1IK  C07  C02  aromatic  1.404  0.020  1.404
 1IK  C07  N08  aromatic  1.369  0.020  1.369
 1IK  C02  N01  single    1.336  0.020  1.336
 1IK  C09  N08  aromatic  1.302  0.020  1.302
 1IK  C04  H1   single    0.930  0.020  1.080
 1IK  C09  H2   single    0.930  0.020  1.080
 1IK  C11  H3   single    0.970  0.020  1.090
 1IK  C11  H4   single    0.970  0.020  1.090
 1IK  C12  H5   single    0.970  0.020  1.090
 1IK  C12  H6   single    0.970  0.020  1.090
 1IK  C13  H7   single    0.970  0.020  1.090
 1IK  C13  H8   single    0.970  0.020  1.090
 1IK  C15  H9   single    0.970  0.020  1.090
 1IK  C19  H10  single    0.970  0.020  1.090
 1IK  C19  H11  single    0.970  0.020  1.090
 1IK  N01  H12  single    0.860  0.020  1.020
 1IK  N01  H13  single    0.860  0.020  1.020
 1IK  N14  H14  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
 1IK  N03  C02  N01  119.24  3.000
 1IK  N01  C02  C07  122.71  3.000
 1IK  N03  C02  C07  118.05  3.000
 1IK  H1   C04  N05  116.14  3.000
 1IK  H1   C04  N03  115.29  3.000
 1IK  N05  C04  N03  128.57  3.000
 1IK  N10  C06  N05  128.41  3.000
 1IK  N10  C06  C07  105.34  3.000
 1IK  N05  C06  C07  126.25  3.000
 1IK  N08  C07  C06  110.85  3.000
 1IK  N08  C07  C02  132.68  3.000
 1IK  C06  C07  C02  116.42  3.000
 1IK  H2   C09  N10  121.18  3.000
 1IK  H2   C09  N08  125.06  3.000
 1IK  N10  C09  N08  113.76  3.000
 1IK  H6   C12  H5   105.68  3.000
 1IK  H6   C12  C13  109.64  3.000
 1IK  H5   C12  C13  109.45  3.000
 1IK  H6   C12  C11  109.03  3.000
 1IK  H5   C12  C11  108.20  3.000
 1IK  C13  C12  C11  114.48  3.000
 1IK  H8   C13  H7   106.08  3.000
 1IK  H8   C13  N14  109.45  3.000
 1IK  H7   C13  N14  112.03  3.000
 1IK  H8   C13  C12  108.74  3.000
 1IK  H7   C13  C12  110.25  3.000
 1IK  N14  C13  C12  110.15  3.000
 1IK  H9   C15  N14  105.70  3.000
 1IK  H9   C15  C19  109.13  3.000
 1IK  N14  C15  C19  113.87  3.000
 1IK  H9   C15  C16  107.31  3.000
 1IK  N14  C15  C16  106.81  3.000
 1IK  C19  C15  C16  113.55  3.000
 1IK  O18  C16  O17  125.95  3.000
 1IK  O17  C16  C15  117.31  3.000
 1IK  O18  C16  C15  116.69  3.000
 1IK  H11  C19  H10  105.04  3.000
 1IK  H11  C19  P20  110.28  3.000
 1IK  H10  C19  P20  106.77  3.000
 1IK  H11  C19  C15  108.83  3.000
 1IK  H10  C19  C15  109.06  3.000
 1IK  P20  C19  C15  116.26  3.000
 1IK  H13  N01  H12  118.43  3.000
 1IK  H13  N01  C02  121.05  3.000
 1IK  H12  N01  C02  120.32  3.000
 1IK  C04  N03  C02  118.96  3.000
 1IK  C06  N05  C04  111.72  3.000
 1IK  C09  N08  C07  104.02  3.000
 1IK  C11  N10  C09  126.02  3.000
 1IK  C09  N10  C06  106.03  3.000
 1IK  C11  N10  C06  127.96  3.000
 1IK  H14  N14  C15  108.79  3.000
 1IK  H14  N14  C13  109.91  3.000
 1IK  C15  N14  C13  112.30  3.000
 1IK  O23  P20  O22  113.28  3.000
 1IK  O22  P20  O21  113.88  3.000
 1IK  O23  P20  O21  113.14  3.000
 1IK  O22  P20  C19  106.33  3.000
 1IK  O23  P20  C19  104.60  3.000
 1IK  O21  P20  C19  104.47  3.000
 1IK  H4   C11  H3   107.11  3.000
 1IK  H4   C11  N10  108.24  3.000
 1IK  H3   C11  N10  107.27  3.000
 1IK  H4   C11  C12  110.53  3.000
 1IK  H3   C11  C12  111.36  3.000
 1IK  N10  C11  C12  112.11  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
 1IK  CONST_01  N05  C04  N03  C02     0.00   0.0  0
 1IK  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 1IK  CONST_03  N10  C06  C07  C02   180.00   0.0  0
 1IK  CONST_04  C09  N08  C07  C02   180.00   0.0  0
 1IK  CONST_05  N10  C06  N05  C04   180.00   0.0  0
 1IK  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 1IK  CONST_07  C07  C02  N03  C04     0.00   0.0  0
 1IK  CONST_08  N03  C04  N05  C06     0.00   0.0  0
 1IK  CONST_09  N08  C09  N10  C06     0.00   0.0  0
 1IK  CONST_10  N03  C02  C07  C06     0.00   0.0  0
 1IK  CONST_11  C09  N08  C07  C06     0.00   0.0  0
 1IK  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 1IK  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 1IK  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 1IK  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 1IK  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 1IK  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 1IK  CONST_18  N01  C02  N03  C04   180.00   0.0  0
 1IK  CONST_19  N01  C02  C07  C06   180.00   0.0  0
 1IK  CONST_20  C11  N10  C06  C07   180.00   0.0  0
 1IK  CONST_21  N05  C06  N10  C11     0.00   0.0  0
 1IK  CONST_22  N08  C09  N10  C11   180.00   0.0  0
 1IK  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 1IK  CONST_24  H1   C04  N03  C02   180.00   0.0  0
 1IK  CONST_25  H1   C04  N05  C06   180.00   0.0  0
 1IK  CONST_26  H2   C09  N10  C06   180.00   0.0  0
 1IK  CONST_27  H2   C09  N08  C07   180.00   0.0  0
 1IK  CONST_28  H12  N01  C02  C07   180.00   0.0  0
 1IK  CONST_29  H13  N01  C02  C07     0.00   0.0  0
 1IK  CONST_30  H12  N01  C02  N03     0.00   0.0  0
 1IK  CONST_31  H13  N01  C02  N03   180.00   0.0  0
 1IK  Var_01    C12  C11  N10  C06   115.38  30.0  2
 1IK  Var_02    C12  C11  N10  C09   -64.08  30.0  2
 1IK  Var_03    H3   C11  N10  C06    -7.17  30.0  2
 1IK  Var_04    H4   C11  N10  C06  -122.45  30.0  2
 1IK  Var_05    H3   C11  N10  C09   173.37  30.0  2
 1IK  Var_06    H4   C11  N10  C09    58.09  30.0  2
 1IK  Var_07    N10  C11  C12  C13   -72.68  30.0  3
 1IK  Var_08    H5   C12  C11  N10   165.00  30.0  2
 1IK  Var_09    H6   C12  C11  N10    50.53  30.0  2
 1IK  Var_10    N14  C13  C12  C11   157.39  30.0  2
 1IK  Var_11    C15  N14  C13  C12   -89.36  30.0  1
 1IK  Var_12    O21  P20  C19  C15   166.88  30.0  3
 1IK  Var_13    O23  P20  C19  C15   -74.00  30.0  3
 1IK  Var_14    O22  P20  C19  C15    46.13  30.0  3
 1IK  Var_15    H7   C13  C12  C11    33.25  30.0  2
 1IK  Var_16    H8   C13  C12  C11   -82.67  30.0  2
 1IK  Var_17    H14  N14  C13  C12   149.39  30.0  1
 1IK  Var_18    H3   C11  C12  C13    47.53  30.0  3
 1IK  Var_19    H4   C11  C12  C13   166.46  30.0  3
 1IK  Var_20    H7   C13  N14  C15    33.75  30.0  3
 1IK  Var_21    H8   C13  N14  C15   151.13  30.0  3
 1IK  Var_22    H5   C12  C13  N14   -80.97  30.0  3
 1IK  Var_23    H6   C12  C13  N14    34.52  30.0  3
 1IK  Var_24    H10  C19  P20  O21   -71.18  30.0  3
 1IK  Var_25    H11  C19  P20  O21    42.42  30.0  3
 1IK  Var_26    H10  C19  P20  O22   168.07  30.0  3
 1IK  Var_27    H11  C19  P20  O22   -78.33  30.0  3
 1IK  Var_28    H10  C19  P20  O23    47.94  30.0  3
 1IK  Var_29    H11  C19  P20  O23   161.54  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
 1IK  chir_01  C15  C19  N14  C16  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
 1IK  plan-1  C02  0.020
 1IK  plan-1  C04  0.020
 1IK  plan-1  C06  0.020
 1IK  plan-1  C07  0.020
 1IK  plan-1  C09  0.020
 1IK  plan-1  N01  0.020
 1IK  plan-1  N03  0.020
 1IK  plan-1  N05  0.020
 1IK  plan-1  N08  0.020
 1IK  plan-1  N10  0.020
 1IK  plan-1  H1   0.020
 1IK  plan-1  H2   0.020
 1IK  plan-1  C11  0.020
 1IK  plan-2  C02  0.020
 1IK  plan-2  N01  0.020
 1IK  plan-2  H12  0.020
 1IK  plan-2  H13  0.020
 1IK  plan-3  C15  0.020
 1IK  plan-3  C16  0.020
 1IK  plan-3  O17  0.020
 1IK  plan-3  O18  0.020

