# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 09:42:23 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{S})-2-[3-(6-aminopurin-9-yl)propoxy]-3-phosphono-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCO[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
 1KK  1KK  "(S)-2-(3-(6-amino-9H-purin-9-yl)propoxy)-3-phosphonopropanoic acid"  ligand  36  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_1KK
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
 1KK  C02  C  CR6    0   0.450   -9.2427  -49.8917  132.3792
 1KK  C03  C  CR56   0  -0.010   -7.9295  -49.4471  132.6164
 1KK  C04  C  CR56   0   0.473   -7.1842  -49.0994  131.4974
 1KK  C07  C  CH2    0  -0.461   -4.5677  -46.7516  131.4622
 1KK  C08  C  CH2    0  -0.181   -3.2513  -46.2996  130.8437
 1KK  C10  C  CH1    0  -0.043   -3.6646  -45.3222  128.7341
 1KK  C11  C  CH2    0  -0.752   -4.1131  -45.7458  127.3400
 1KK  C16  C  C      0   0.372   -2.5677  -44.2293  128.6665
 1KK  C19  C  CR15   0   0.106   -6.0421  -48.8517  133.3345
 1KK  C22  C  CR16   0   0.038   -8.8409  -49.5800  130.1366
 1KK  N01  N  NH2    0  -0.819  -10.0681  -50.2610  133.3618
 1KK  N05  N  NR5    0  -0.495   -5.9686  -48.7186  131.9790
 1KK  N20  N  N      0  -0.453   -7.1942  -49.2853  133.7604
 1KK  N21  N  N      0  -0.451   -7.5968  -49.1495  130.2316
 1KK  N23  N  N      0  -0.473   -9.6697  -49.9451  131.1130
 1KK  O09  O  O2     0  -0.491   -3.2281  -46.4595  129.4527
 1KK  O13  O  O      0  -0.909   -6.1035  -46.5860  125.7384
 1KK  O14  O  OP    -1  -0.905   -6.6504  -46.1788  128.2249
 1KK  O15  O  OP    -1  -0.899   -5.2930  -48.2474  127.5098
 1KK  O17  O  OC    -1  -0.624   -2.9686  -43.0965  128.3200
 1KK  O18  O  O      0  -0.608   -1.3936  -44.5533  128.9314
 1KK  P12  P  P      0   1.178   -5.6751  -46.7890  127.2018
 1KK  H1   H  HCH2   0   0.266   -5.0045  -48.4366  130.1737
 1KK  H2   H  HCH2   0   0.255   -3.9509  -48.8217  131.5299
 1KK  H3   H  HCH2   0   0.231   -4.5244  -46.5477  132.5360
 1KK  H4   H  HCH2   0   0.231   -5.4016  -46.1699  131.0594
 1KK  H5   H  HCH2   0   0.208   -2.4359  -46.8997  131.2640
 1KK  H6   H  HCH2   0   0.208   -3.0545  -45.2622  131.1408
 1KK  H7   H  HCH1   0   0.166   -4.5392  -44.8784  129.2319
 1KK  H8   H  HCH2   0   0.179   -3.2792  -46.2357  126.8200
 1KK  H9   H  HCH2   0   0.186   -4.3052  -44.8230  126.7859
 1KK  H10  H  HCR5   0   0.288   -5.1966  -48.6143  133.9645
 1KK  H11  H  HCR6   0   0.246   -9.2474  -49.6479  129.1328
 1KK  H12  H  HNH2   0   0.400  -11.0003  -50.5725  133.1515
 1KK  H13  H  HNH2   0   0.408   -9.7791  -50.2287  134.3233
 1KK  C06  C  CH2    0  -0.315   -4.8220  -48.2356  131.2290

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
 1KK  O13  P12  deloc     1.538  0.020  1.538
 1KK  P12  C11  single    1.883  0.020  1.883
 1KK  P12  O15  deloc     1.539  0.020  1.539
 1KK  P12  O14  deloc     1.540  0.020  1.540
 1KK  C11  C10  single    1.525  0.020  1.525
 1KK  O18  C16  deloc     1.246  0.020  1.246
 1KK  O09  C10  single    1.414  0.020  1.414
 1KK  O09  C08  single    1.400  0.020  1.400
 1KK  C10  C16  single    1.550  0.020  1.550
 1KK  C16  O17  deloc     1.251  0.020  1.251
 1KK  C08  C07  single    1.523  0.020  1.523
 1KK  C06  C07  single    1.524  0.020  1.524
 1KK  C06  N05  single    1.453  0.020  1.453
 1KK  N21  C22  aromatic  1.320  0.020  1.320
 1KK  N21  C04  aromatic  1.332  0.020  1.332
 1KK  C22  N23  aromatic  1.332  0.020  1.332
 1KK  N05  C04  aromatic  1.362  0.020  1.362
 1KK  N05  C19  aromatic  1.364  0.020  1.364
 1KK  C04  C03  aromatic  1.389  0.020  1.389
 1KK  N23  C02  aromatic  1.337  0.020  1.337
 1KK  C19  N20  aromatic  1.303  0.020  1.303
 1KK  C03  C02  aromatic  1.407  0.020  1.407
 1KK  C03  N20  aromatic  1.370  0.020  1.370
 1KK  C02  N01  single    1.335  0.020  1.335
 1KK  C06  H1   single    0.970  0.020  1.090
 1KK  C06  H2   single    0.970  0.020  1.090
 1KK  C07  H3   single    0.970  0.020  1.090
 1KK  C07  H4   single    0.970  0.020  1.090
 1KK  C08  H5   single    0.970  0.020  1.090
 1KK  C08  H6   single    0.970  0.020  1.090
 1KK  C10  H7   single    0.970  0.020  1.090
 1KK  C11  H8   single    0.970  0.020  1.090
 1KK  C11  H9   single    0.970  0.020  1.090
 1KK  C19  H10  single    0.930  0.020  1.080
 1KK  C22  H11  single    0.930  0.020  1.080
 1KK  N01  H12  single    0.860  0.020  1.020
 1KK  N01  H13  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
 1KK  N23  C02  N01  119.23  3.000
 1KK  N01  C02  C03  122.71  3.000
 1KK  N23  C02  C03  118.06  3.000
 1KK  N20  C03  C04  110.81  3.000
 1KK  N20  C03  C02  132.80  3.000
 1KK  C04  C03  C02  116.38  3.000
 1KK  N21  C04  N05  128.52  3.000
 1KK  N05  C04  C03  105.32  3.000
 1KK  N21  C04  C03  126.15  3.000
 1KK  H4   C07  H3   107.02  3.000
 1KK  H4   C07  C08  110.58  3.000
 1KK  H3   C07  C08  108.00  3.000
 1KK  H4   C07  C06  109.54  3.000
 1KK  H3   C07  C06  109.78  3.000
 1KK  C08  C07  C06  111.78  3.000
 1KK  H6   C08  H5   106.28  3.000
 1KK  H6   C08  O09  111.96  3.000
 1KK  H5   C08  O09  107.81  3.000
 1KK  H6   C08  C07  109.02  3.000
 1KK  H5   C08  C07  108.96  3.000
 1KK  O09  C08  C07  112.57  3.000
 1KK  H7   C10  O09  109.87  3.000
 1KK  H7   C10  C16  107.34  3.000
 1KK  O09  C10  C16  111.76  3.000
 1KK  H7   C10  C11  106.98  3.000
 1KK  C16  C10  C11  111.36  3.000
 1KK  O09  C10  C11  109.39  3.000
 1KK  H9   C11  H8   105.67  3.000
 1KK  H9   C11  P12  106.54  3.000
 1KK  H8   C11  P12  110.36  3.000
 1KK  H9   C11  C10  106.29  3.000
 1KK  H8   C11  C10  109.48  3.000
 1KK  P12  C11  C10  117.71  3.000
 1KK  O18  C16  O17  126.60  3.000
 1KK  O17  C16  C10  115.08  3.000
 1KK  O18  C16  C10  118.30  3.000
 1KK  H10  C19  N20  125.06  3.000
 1KK  H10  C19  N05  121.04  3.000
 1KK  N20  C19  N05  113.90  3.000
 1KK  H11  C22  N23  115.34  3.000
 1KK  H11  C22  N21  116.11  3.000
 1KK  N23  C22  N21  128.55  3.000
 1KK  H13  N01  H12  118.49  3.000
 1KK  H13  N01  C02  121.18  3.000
 1KK  H12  N01  C02  120.33  3.000
 1KK  C19  N05  C06  126.02  3.000
 1KK  C19  N05  C04  106.02  3.000
 1KK  C06  N05  C04  127.95  3.000
 1KK  C19  N20  C03  103.95  3.000
 1KK  C22  N21  C04  111.87  3.000
 1KK  C22  N23  C02  118.98  3.000
 1KK  C10  O09  C08  114.06  3.000
 1KK  O15  P12  O14  113.57  3.000
 1KK  O14  P12  O13  113.79  3.000
 1KK  O15  P12  O13  112.63  3.000
 1KK  O14  P12  C11  104.90  3.000
 1KK  O15  P12  C11  107.72  3.000
 1KK  O13  P12  C11  103.16  3.000
 1KK  H2   C06  H1   107.54  3.000
 1KK  H2   C06  N05  107.99  3.000
 1KK  H1   C06  N05  107.84  3.000
 1KK  H2   C06  C07  110.33  3.000
 1KK  H1   C06  C07  110.85  3.000
 1KK  N05  C06  C07  112.12  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
 1KK  CONST_01  N21  C22  N23  C02     0.00   0.0  0
 1KK  CONST_02  N21  C04  C03  C02     0.00   0.0  0
 1KK  CONST_03  N05  C04  C03  C02   180.00   0.0  0
 1KK  CONST_04  C19  N20  C03  C02   180.00   0.0  0
 1KK  CONST_05  C22  N21  C04  C03     0.00   0.0  0
 1KK  CONST_06  C19  N05  C04  C03     0.00   0.0  0
 1KK  CONST_07  C22  N23  C02  C03     0.00   0.0  0
 1KK  CONST_08  N05  C19  N20  C03     0.00   0.0  0
 1KK  CONST_09  N23  C22  N21  C04     0.00   0.0  0
 1KK  CONST_10  N20  C19  N05  C04     0.00   0.0  0
 1KK  CONST_11  N23  C02  C03  C04     0.00   0.0  0
 1KK  CONST_12  C19  N20  C03  C04     0.00   0.0  0
 1KK  CONST_13  N21  C04  N05  C19   180.00   0.0  0
 1KK  CONST_14  N05  C04  N21  C22   180.00   0.0  0
 1KK  CONST_15  N20  C03  C04  N05     0.00   0.0  0
 1KK  CONST_16  N21  C04  C03  N20   180.00   0.0  0
 1KK  CONST_17  N23  C02  C03  N20   180.00   0.0  0
 1KK  CONST_18  C06  N05  C04  C03   180.00   0.0  0
 1KK  CONST_19  N01  C02  C03  C04   180.00   0.0  0
 1KK  CONST_20  N21  C04  N05  C06     0.00   0.0  0
 1KK  CONST_21  N20  C19  N05  C06   180.00   0.0  0
 1KK  CONST_22  N01  C02  N23  C22   180.00   0.0  0
 1KK  CONST_23  N20  C03  C02  N01     0.00   0.0  0
 1KK  CONST_24  H11  C22  N23  C02   180.00   0.0  0
 1KK  CONST_25  H10  C19  N20  C03   180.00   0.0  0
 1KK  CONST_26  H11  C22  N21  C04   180.00   0.0  0
 1KK  CONST_27  H10  C19  N05  C04   180.00   0.0  0
 1KK  CONST_28  H12  N01  C02  C03   180.00   0.0  0
 1KK  CONST_29  H13  N01  C02  C03     0.00   0.0  0
 1KK  CONST_30  H12  N01  C02  N23     0.00   0.0  0
 1KK  CONST_31  H13  N01  C02  N23   180.00   0.0  0
 1KK  Var_01    C07  C06  N05  C04   109.50  30.0  1
 1KK  Var_02    C19  N05  C06  C07   -68.92  30.0  2
 1KK  Var_03    H1   C06  N05  C04   -12.80  30.0  1
 1KK  Var_04    H2   C06  N05  C04  -128.74  30.0  1
 1KK  Var_05    H1   C06  N05  C19   168.77  30.0  1
 1KK  Var_06    H2   C06  N05  C19    52.83  30.0  1
 1KK  Var_07    N05  C06  C07  C08   171.48  30.0  1
 1KK  Var_08    H3   C07  C06  N05    51.64  30.0  3
 1KK  Var_09    H4   C07  C06  N05   -65.59  30.0  3
 1KK  Var_10    O09  C08  C07  C06    61.97  30.0  2
 1KK  Var_11    C10  O09  C08  C07    91.47  30.0  2
 1KK  Var_12    O13  P12  C11  C10   159.86  30.0  3
 1KK  Var_13    O15  P12  C11  C10   -80.84  30.0  3
 1KK  Var_14    O14  P12  C11  C10    40.46  30.0  3
 1KK  Var_15    H5   C08  C07  C06   -57.57  30.0  2
 1KK  Var_16    H6   C08  C07  C06  -173.16  30.0  2
 1KK  Var_17    H1   C06  C07  C08   -67.95  30.0  1
 1KK  Var_18    H2   C06  C07  C08    51.07  30.0  1
 1KK  Var_19    H5   C08  O09  C10  -148.32  30.0  3
 1KK  Var_20    H6   C08  O09  C10   -31.76  30.0  3
 1KK  Var_21    H3   C07  C08  O09  -177.16  30.0  3
 1KK  Var_22    H4   C07  C08  O09   -60.36  30.0  3
 1KK  Var_23    H8   C11  P12  O13   -73.50  30.0  3
 1KK  Var_24    H9   C11  P12  O13    40.74  30.0  3
 1KK  Var_25    H8   C11  P12  O14   167.10  30.0  3
 1KK  Var_26    H9   C11  P12  O14   -78.66  30.0  3
 1KK  Var_27    H8   C11  P12  O15    45.80  30.0  3
 1KK  Var_28    H9   C11  P12  O15   160.05  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
 1KK  chir_01  C10  C11  O09  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
 1KK  plan-1  C02  0.020
 1KK  plan-1  C03  0.020
 1KK  plan-1  C04  0.020
 1KK  plan-1  C19  0.020
 1KK  plan-1  C22  0.020
 1KK  plan-1  N01  0.020
 1KK  plan-1  N05  0.020
 1KK  plan-1  N20  0.020
 1KK  plan-1  N21  0.020
 1KK  plan-1  N23  0.020
 1KK  plan-1  H10  0.020
 1KK  plan-1  H11  0.020
 1KK  plan-1  C06  0.020
 1KK  plan-2  C02  0.020
 1KK  plan-2  N01  0.020
 1KK  plan-2  H12  0.020
 1KK  plan-2  H13  0.020
 1KK  plan-3  C10  0.020
 1KK  plan-3  C16  0.020
 1KK  plan-3  O17  0.020
 1KK  plan-3  O18  0.020

