# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 09:34:57 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: [[(2~{S})-2-[2-(6-aminopurin-9-yl)ethylamino]-3-oxidanyl-propanoyl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCN[C@@H](CO)C(=O)N[P](O)(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
 1I1  1I1  "((2-(6-amino-9H-purin-9-yl)ethyl)-L-seryl)phosphoramidic 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 OK
;

data_comp_1I1
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
 1I1  C02  C  CR6    0   0.446  -6.3801  -49.5065  130.6907
 1I1  C04  C  CR16   0   0.034  -4.8845  -51.0696  129.9072
 1I1  C06  C  CR56   0   0.472  -4.1000  -49.0434  130.2287
 1I1  C07  C  CR56   0  -0.005  -5.3306  -48.5713  130.6637
 1I1  C09  C  CR15   0   0.115  -4.0134  -46.9271  130.7339
 1I1  C12  C  CH2    0  -0.289  -1.8635  -47.5473  128.3158
 1I1  C14  C  CH1    0  -0.223  -1.8186  -45.0703  128.3654
 1I1  C15  C  CH2    0  -0.151  -0.7451  -44.6128  127.3745
 1I1  C17  C  C      0   0.487  -2.8522  -43.9713  128.6211
 1I1  N01  N  NH2    0  -0.819  -7.6200  -49.1900  131.0745
 1I1  N03  N  N      0  -0.474  -6.1173  -50.7598  130.3029
 1I1  N05  N  N      0  -0.457  -3.8230  -50.2870  129.8364
 1I1  N08  N  N      0  -0.461  -5.2550  -47.2392  130.9796
 1I1  N10  N  NR5    0  -0.472  -3.2597  -47.9748  130.2957
 1I1  N13  N  NH1    0  -0.642  -2.5253  -46.2958  128.0570
 1I1  N18  N  NH1    0  -0.794  -3.6440  -43.5720  127.6192
 1I1  O16  O  OH1    0  -0.668   0.4025  -45.4256  127.5326
 1I1  O20  O  O      0  -0.860  -5.2928  -43.4148  125.6681
 1I1  O21  O  OP    -1  -0.858  -2.7937  -43.0994  125.1390
 1I1  O22  O  OP    -1  -0.846  -3.6947  -45.4316  125.7023
 1I1  O23  O  O      0  -0.534  -2.9453  -43.4980  129.7598
 1I1  P19  P  P      0   1.244  -3.8698  -43.9177  125.8305
 1I1  H1   H  HCR6   0   0.245  -4.7396  -52.1016  129.6041
 1I1  H2   H  HCR5   0   0.276  -3.5826  -45.9443  130.8576
 1I1  H3   H  HCH2   0   0.265  -1.4306  -48.8793  129.9657
 1I1  H4   H  HCH2   0   0.265  -1.3593  -47.1814  130.3989
 1I1  H5   H  HCH2   0   0.230  -2.3904  -48.3263  127.7592
 1I1  H6   H  HCH2   0   0.214  -0.8162  -47.5956  127.9957
 1I1  H7   H  HCH1   0   0.232  -1.3147  -45.1924  129.3290
 1I1  H8   H  HCH2   0   0.179  -0.5028  -43.5586  127.5768
 1I1  H9   H  HCH2   0   0.201  -1.1332  -44.6591  126.3554
 1I1  H10  H  HNH2   0   0.399  -8.3344  -49.8962  131.1139
 1I1  H11  H  HNH2   0   0.407  -7.8404  -48.2688  131.4094
 1I1  H12  H  HNH1   0   0.380  -2.9407  -46.2206  127.1239
 1I1  H14  H  HNH1   0   0.351  -4.2967  -42.8652  127.9355
 1I1  H15  H  HOH1   0   0.448   1.0044  -45.2333  126.8083
 1I1  C11  C  CH2    0  -0.338  -1.9034  -47.9117  129.7990

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
 1I1  O20  P19  deloc     1.518  0.020  1.518
 1I1  O21  P19  deloc     1.519  0.020  1.519
 1I1  O22  P19  deloc     1.529  0.020  1.529
 1I1  P19  N18  single    1.836  0.020  1.836
 1I1  O16  C15  single    1.415  0.020  1.415
 1I1  N18  C17  single    1.338  0.020  1.338
 1I1  C15  C14  single    1.531  0.020  1.531
 1I1  N13  C12  single    1.439  0.020  1.439
 1I1  N13  C14  single    1.448  0.020  1.448
 1I1  C12  C11  single    1.528  0.020  1.528
 1I1  C14  C17  single    1.530  0.020  1.530
 1I1  C17  O23  double    1.237  0.020  1.237
 1I1  C11  N10  single    1.446  0.020  1.446
 1I1  N05  C06  aromatic  1.333  0.020  1.333
 1I1  N05  C04  aromatic  1.321  0.020  1.321
 1I1  N10  C06  aromatic  1.361  0.020  1.361
 1I1  N10  C09  aromatic  1.363  0.020  1.363
 1I1  C06  C07  aromatic  1.388  0.020  1.388
 1I1  C04  N03  aromatic  1.331  0.020  1.331
 1I1  C09  N08  aromatic  1.304  0.020  1.304
 1I1  N03  C02  aromatic  1.338  0.020  1.338
 1I1  C07  N08  aromatic  1.371  0.020  1.371
 1I1  C07  C02  aromatic  1.406  0.020  1.406
 1I1  C02  N01  single    1.336  0.020  1.336
 1I1  C04  H1   single    0.930  0.020  1.080
 1I1  C09  H2   single    0.930  0.020  1.080
 1I1  C11  H3   single    0.970  0.020  1.090
 1I1  C11  H4   single    0.970  0.020  1.090
 1I1  C12  H5   single    0.970  0.020  1.090
 1I1  C12  H6   single    0.970  0.020  1.090
 1I1  C14  H7   single    0.970  0.020  1.090
 1I1  C15  H8   single    0.970  0.020  1.090
 1I1  C15  H9   single    0.970  0.020  1.090
 1I1  N01  H10  single    0.860  0.020  1.020
 1I1  N01  H11  single    0.860  0.020  1.020
 1I1  N13  H12  single    0.890  0.020  1.040
 1I1  N18  H14  single    0.860  0.020  1.020
 1I1  O16  H15  single    0.850  0.020  0.980

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
 1I1  N03  C02  N01  119.18  3.000
 1I1  N01  C02  C07  122.73  3.000
 1I1  N03  C02  C07  118.09  3.000
 1I1  H1   C04  N05  116.17  3.000
 1I1  H1   C04  N03  115.34  3.000
 1I1  N05  C04  N03  128.49  3.000
 1I1  N10  C06  N05  128.21  3.000
 1I1  N10  C06  C07  105.36  3.000
 1I1  N05  C06  C07  126.43  3.000
 1I1  N08  C07  C06  110.72  3.000
 1I1  N08  C07  C02  133.08  3.000
 1I1  C06  C07  C02  116.20  3.000
 1I1  H2   C09  N10  121.04  3.000
 1I1  H2   C09  N08  125.18  3.000
 1I1  N10  C09  N08  113.78  3.000
 1I1  H6   C12  H5   106.29  3.000
 1I1  H6   C12  N13  115.16  3.000
 1I1  H5   C12  N13  107.85  3.000
 1I1  H6   C12  C11  107.33  3.000
 1I1  H5   C12  C11  108.17  3.000
 1I1  N13  C12  C11  111.71  3.000
 1I1  H7   C14  N13  108.54  3.000
 1I1  H7   C14  C17  104.12  3.000
 1I1  N13  C14  C17  108.29  3.000
 1I1  H7   C14  C15  106.28  3.000
 1I1  C17  C14  C15  111.54  3.000
 1I1  N13  C14  C15  117.22  3.000
 1I1  H9   C15  H8   106.89  3.000
 1I1  H9   C15  O16  111.61  3.000
 1I1  H8   C15  O16  110.55  3.000
 1I1  H9   C15  C14  110.02  3.000
 1I1  H8   C15  C14  108.77  3.000
 1I1  O16  C15  C14  108.95  3.000
 1I1  O23  C17  N18  122.05  3.000
 1I1  O23  C17  C14  118.67  3.000
 1I1  N18  C17  C14  119.27  3.000
 1I1  H11  N01  H10  118.37  3.000
 1I1  H11  N01  C02  121.11  3.000
 1I1  H10  N01  C02  120.29  3.000
 1I1  C04  N03  C02  119.08  3.000
 1I1  C06  N05  C04  111.71  3.000
 1I1  C09  N08  C07  103.99  3.000
 1I1  C11  N10  C09  126.56  3.000
 1I1  C09  N10  C06  106.14  3.000
 1I1  C11  N10  C06  126.62  3.000
 1I1  H12  N13  C14  109.26  3.000
 1I1  H12  N13  C12  114.47  3.000
 1I1  C14  N13  C12  118.25  3.000
 1I1  H14  N18  P19  110.88  3.000
 1I1  H14  N18  C17  110.85  3.000
 1I1  P19  N18  C17  138.26  3.000
 1I1  H15  O16  C15  107.99  3.000
 1I1  O22  P19  O21  114.46  3.000
 1I1  O22  P19  O20  115.24  3.000
 1I1  O21  P19  O20  115.92  3.000
 1I1  O22  P19  N18  104.71  3.000
 1I1  O21  P19  N18  104.78  3.000
 1I1  O20  P19  N18   99.04  3.000
 1I1  H4   C11  H3   107.10  3.000
 1I1  H4   C11  N10  107.96  3.000
 1I1  H3   C11  N10  108.40  3.000
 1I1  H4   C11  C12  111.17  3.000
 1I1  H3   C11  C12  110.42  3.000
 1I1  N10  C11  C12  111.62  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
 1I1  CONST_01  N05  C04  N03  C02     0.00   0.0  0
 1I1  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 1I1  CONST_03  N10  C06  C07  C02   180.00   0.0  0
 1I1  CONST_04  C09  N08  C07  C02   180.00   0.0  0
 1I1  CONST_05  N10  C06  N05  C04   180.00   0.0  0
 1I1  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 1I1  CONST_07  C07  C02  N03  C04     0.00   0.0  0
 1I1  CONST_08  N03  C04  N05  C06     0.00   0.0  0
 1I1  CONST_09  N08  C09  N10  C06     0.00   0.0  0
 1I1  CONST_10  C09  N08  C07  C06     0.00   0.0  0
 1I1  CONST_11  N03  C02  C07  C06     0.00   0.0  0
 1I1  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 1I1  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 1I1  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 1I1  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 1I1  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 1I1  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 1I1  CONST_18  N01  C02  N03  C04   180.00   0.0  0
 1I1  CONST_19  N01  C02  C07  C06   180.00   0.0  0
 1I1  CONST_20  C11  N10  C06  C07   180.00   0.0  0
 1I1  CONST_21  N05  C06  N10  C11     0.00   0.0  0
 1I1  CONST_22  N08  C09  N10  C11   180.00   0.0  0
 1I1  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 1I1  CONST_24  H1   C04  N03  C02   180.00   0.0  0
 1I1  CONST_25  H1   C04  N05  C06   180.00   0.0  0
 1I1  CONST_26  H2   C09  N10  C06   180.00   0.0  0
 1I1  CONST_27  H2   C09  N08  C07   180.00   0.0  0
 1I1  CONST_28  H10  N01  C02  C07   180.00   0.0  0
 1I1  CONST_29  H11  N01  C02  C07     0.00   0.0  0
 1I1  CONST_30  H10  N01  C02  N03     0.00   0.0  0
 1I1  CONST_31  H11  N01  C02  N03   180.00   0.0  0
 1I1  CONST_32  P19  N18  C17  C14     0.00   0.0  0
 1I1  CONST_33  P19  N18  C17  O23   180.00   0.0  0
 1I1  CONST_34  H14  N18  C17  C14   180.00   0.0  0
 1I1  CONST_35  H14  N18  C17  O23     0.00   0.0  0
 1I1  Var_01    C12  C11  N10  C06    85.07  30.0  1
 1I1  Var_02    C12  C11  N10  C09   -84.14  30.0  1
 1I1  Var_03    H3   C11  N10  C06   -36.77  30.0  1
 1I1  Var_04    H4   C11  N10  C06  -152.46  30.0  1
 1I1  Var_05    H3   C11  N10  C09   154.03  30.0  1
 1I1  Var_06    H4   C11  N10  C09    38.33  30.0  1
 1I1  Var_07    N13  C12  C11  N10    57.19  30.0  1
 1I1  Var_08    H5   C12  C11  N10   -61.36  30.0  1
 1I1  Var_09    H6   C12  C11  N10  -175.68  30.0  1
 1I1  Var_10    C14  N13  C12  C11    78.21  30.0  2
 1I1  Var_11    O20  P19  N18  C17   159.67  30.0  3
 1I1  Var_12    O21  P19  N18  C17   -80.35  30.0  3
 1I1  Var_13    O22  P19  N18  C17    40.46  30.0  3
 1I1  Var_14    H12  N13  C12  C11  -150.80  30.0  2
 1I1  Var_15    H5   C12  N13  C14  -163.05  30.0  3
 1I1  Var_16    H6   C12  N13  C14   -44.57  30.0  3
 1I1  Var_17    H3   C11  C12  N13   177.85  30.0  3
 1I1  Var_18    H4   C11  C12  N13   -63.42  30.0  3
 1I1  Var_19    H14  N18  P19  O20   -21.58  30.0  3
 1I1  Var_20    H14  N18  P19  O21    98.40  30.0  3
 1I1  Var_21    H14  N18  P19  O22  -140.80  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
 1I1  chir_01  C14  C15  N13  C17  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
 1I1  plan-1  C02  0.020
 1I1  plan-1  C04  0.020
 1I1  plan-1  C06  0.020
 1I1  plan-1  C07  0.020
 1I1  plan-1  C09  0.020
 1I1  plan-1  N01  0.020
 1I1  plan-1  N03  0.020
 1I1  plan-1  N05  0.020
 1I1  plan-1  N08  0.020
 1I1  plan-1  N10  0.020
 1I1  plan-1  H1   0.020
 1I1  plan-1  H2   0.020
 1I1  plan-1  C11  0.020
 1I1  plan-2  C14  0.020
 1I1  plan-2  C17  0.020
 1I1  plan-2  N18  0.020
 1I1  plan-2  O23  0.020
 1I1  plan-2  P19  0.020
 1I1  plan-2  H14  0.020
 1I1  plan-3  C02  0.020
 1I1  plan-3  N01  0.020
 1I1  plan-3  H10  0.020
 1I1  plan-3  H11  0.020

