# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:55:53 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1cc(nn1c2ccc(CCCF)cc2)C(O)=O)C(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
 5DY  5DY  '5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid'  ligand  40  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5DY
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
 5DY  N01  N  NH2    0  -0.779  -1.3584  -1.9466  -1.5659
 5DY  C02  C  CH1    0  -0.202  -2.2683  -2.3689  -0.5168
 5DY  C03  C  CH2    0  -0.555  -1.9964  -1.5605   0.7587
 5DY  C04  C  CR5    0   0.452  -2.1183  -0.0914   0.5470
 5DY  C05  C  CR15   0  -0.565  -3.2442   0.6975   0.5417
 5DY  C06  C  CR5    0   0.085  -2.8027   1.9901   0.2029
 5DY  N07  N  N      0  -0.305  -1.4946   1.9992   0.0151
 5DY  N08  N  NR5    0  -0.443  -1.0929   0.7435   0.2306
 5DY  C09  C  CR6    0   0.316   0.2779   0.4315   0.0812
 5DY  C10  C  CR16   0  -0.246   0.9096   0.6890  -1.1277
 5DY  C11  C  CR16   0  -0.318   2.2593   0.4108  -1.2712
 5DY  C12  C  CR6    0   0.141   2.9968  -0.1426  -0.2270
 5DY  C13  C  CH2    0  -0.527   4.4688  -0.4034  -0.3759
 5DY  C14  C  CH2    0  -0.489   5.3037   0.7480   0.1899
 5DY  C15  C  CH2    0   0.000   6.7794   0.4941  -0.0030
 5DY  F16  F  F      0  -0.383   7.5234   1.5410   0.5437
 5DY  C17  C  CR16   0  -0.312   2.3456  -0.3973   0.9767
 5DY  C18  C  CR16   0  -0.268   0.9996  -0.1037   1.1391
 5DY  C19  C  C      0   0.363  -3.6401   3.2364   0.0687
 5DY  O20  O  OC    -1  -0.604  -3.0477   4.2939  -0.2121
 5DY  O21  O  O      0  -0.600  -4.8629   3.0799   0.2571
 5DY  C22  C  C      0   0.387  -2.2747  -3.8853  -0.1886
 5DY  O23  O  O      0  -0.602  -1.5346  -4.6249  -0.8647
 5DY  O24  O  OC    -1  -0.620  -3.0465  -4.2403   0.7269
 5DY  H1   H  HNH2   0   0.326  -0.4076  -2.1438  -1.2744
 5DY  H2   H  HNH2   0   0.336  -1.5044  -2.5396  -2.3740
 5DY  H4   H  HCH1   0   0.226  -3.2846  -2.1169  -0.8458
 5DY  H5   H  HCH2   0   0.261  -2.7108  -1.8605   1.5239
 5DY  H6   H  HCH2   0   0.248  -1.0063  -1.8206   1.1420
 5DY  H7   H  HCR5   0   0.248  -4.2521   0.3772   0.7494
 5DY  H8   H  HCR6   0   0.262   0.3466   1.1025  -1.9536
 5DY  H9   H  HCR6   0   0.252   2.7444   0.6178  -2.2178
 5DY  H10  H  HCH2   0   0.250   4.7362  -1.3312   0.1372
 5DY  H11  H  HCH2   0   0.249   4.7118  -0.5490  -1.4317
 5DY  H12  H  HCH2   0   0.242   5.0216   1.6818  -0.3037
 5DY  H13  H  HCH2   0   0.241   5.0876   0.8664   1.2551
 5DY  H14  H  HCH2   0   0.203   7.0884  -0.4299   0.4903
 5DY  H15  H  HCH2   0   0.204   7.0307   0.4217  -1.0635
 5DY  H16  H  HCR6   0   0.253   2.8967  -0.8201   1.8085
 5DY  H17  H  HCR6   0   0.273   0.5207  -0.2790   2.0939

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
 5DY  C13  C12  single    1.502  0.020  1.502
 5DY  C13  C14  single    1.531  0.020  1.531
 5DY  C11  C12  aromatic  1.393  0.020  1.393
 5DY  C11  C10  aromatic  1.385  0.020  1.385
 5DY  C12  C17  aromatic  1.392  0.020  1.392
 5DY  C14  C15  single    1.510  0.020  1.510
 5DY  F16  C15  single    1.396  0.020  1.396
 5DY  C10  C09  aromatic  1.388  0.020  1.388
 5DY  C17  C18  aromatic  1.387  0.020  1.387
 5DY  C09  C18  aromatic  1.388  0.020  1.388
 5DY  C09  N08  single    1.414  0.020  1.414
 5DY  N01  C02  single    1.452  0.020  1.452
 5DY  C03  C04  single    1.489  0.020  1.489
 5DY  C03  C02  single    1.534  0.020  1.534
 5DY  N08  C04  aromatic  1.360  0.020  1.360
 5DY  N08  N07  aromatic  1.336  0.020  1.336
 5DY  C04  C05  aromatic  1.375  0.020  1.375
 5DY  C02  C22  single    1.551  0.020  1.551
 5DY  N07  C06  aromatic  1.322  0.020  1.322
 5DY  O23  C22  deloc     1.246  0.020  1.246
 5DY  C22  O24  deloc     1.249  0.020  1.249
 5DY  C05  C06  aromatic  1.407  0.020  1.407
 5DY  C06  C19  single    1.508  0.020  1.508
 5DY  C19  O21  deloc     1.247  0.020  1.247
 5DY  C19  O20  deloc     1.244  0.020  1.244
 5DY  N01  H1   single    0.890  0.020  1.040
 5DY  N01  H2   single    0.890  0.020  1.040
 5DY  C02  H4   single    0.970  0.020  1.090
 5DY  C03  H5   single    0.970  0.020  1.090
 5DY  C03  H6   single    0.970  0.020  1.090
 5DY  C05  H7   single    0.930  0.020  1.080
 5DY  C10  H8   single    0.930  0.020  1.080
 5DY  C11  H9   single    0.930  0.020  1.080
 5DY  C13  H10  single    0.970  0.020  1.090
 5DY  C13  H11  single    0.970  0.020  1.090
 5DY  C14  H12  single    0.970  0.020  1.090
 5DY  C14  H13  single    0.970  0.020  1.090
 5DY  C15  H14  single    0.970  0.020  1.090
 5DY  C15  H15  single    0.970  0.020  1.090
 5DY  C17  H16  single    0.930  0.020  1.080
 5DY  C18  H17  single    0.930  0.020  1.080

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
 5DY  H2   N01  H1   104.52  3.000
 5DY  H2   N01  C02  108.41  3.000
 5DY  H1   N01  C02  108.87  3.000
 5DY  H4   C02  C22  106.50  3.000
 5DY  H4   C02  C03  107.00  3.000
 5DY  C22  C02  C03  109.86  3.000
 5DY  H4   C02  N01  107.28  3.000
 5DY  C22  C02  N01  116.10  3.000
 5DY  C03  C02  N01  109.66  3.000
 5DY  H6   C03  H5   106.39  3.000
 5DY  H6   C03  C04  111.02  3.000
 5DY  H5   C03  C04  108.54  3.000
 5DY  H6   C03  C02  109.07  3.000
 5DY  H5   C03  C02  108.83  3.000
 5DY  C04  C03  C02  112.77  3.000
 5DY  N08  C04  C05  105.33  3.000
 5DY  C05  C04  C03  129.32  3.000
 5DY  N08  C04  C03  125.25  3.000
 5DY  H7   C05  C06  127.79  3.000
 5DY  H7   C05  C04  126.49  3.000
 5DY  C06  C05  C04  105.72  3.000
 5DY  C19  C06  N07  122.11  3.000
 5DY  C19  C06  C05  127.33  3.000
 5DY  N07  C06  C05  110.55  3.000
 5DY  N08  N07  C06  105.56  3.000
 5DY  C09  N08  N07  118.81  3.000
 5DY  N07  N08  C04  112.83  3.000
 5DY  C09  N08  C04  128.34  3.000
 5DY  C18  C09  C10  119.92  3.000
 5DY  C18  C09  N08  120.58  3.000
 5DY  C10  C09  N08  119.49  3.000
 5DY  H8   C10  C11  120.31  3.000
 5DY  H8   C10  C09  119.94  3.000
 5DY  C11  C10  C09  119.75  3.000
 5DY  H9   C11  C12  119.58  3.000
 5DY  H9   C11  C10  119.23  3.000
 5DY  C12  C11  C10  121.19  3.000
 5DY  C17  C12  C13  120.82  3.000
 5DY  C17  C12  C11  118.24  3.000
 5DY  C13  C12  C11  120.89  3.000
 5DY  H11  C13  H10  106.60  3.000
 5DY  H11  C13  C14  109.64  3.000
 5DY  H10  C13  C14  109.36  3.000
 5DY  H11  C13  C12  109.67  3.000
 5DY  H10  C13  C12  109.90  3.000
 5DY  C14  C13  C12  111.54  3.000
 5DY  H13  C14  H12  107.24  3.000
 5DY  H13  C14  C15  109.62  3.000
 5DY  H12  C14  C15  109.77  3.000
 5DY  H13  C14  C13  109.50  3.000
 5DY  H12  C14  C13  109.56  3.000
 5DY  C15  C14  C13  111.06  3.000
 5DY  H15  C15  H14  108.51  3.000
 5DY  H15  C15  F16  107.90  3.000
 5DY  H14  C15  F16  107.88  3.000
 5DY  H15  C15  C14  111.11  3.000
 5DY  H14  C15  C14  111.17  3.000
 5DY  F16  C15  C14  110.17  3.000
 5DY  H16  C17  C18  119.09  3.000
 5DY  H16  C17  C12  119.81  3.000
 5DY  C18  C17  C12  121.09  3.000
 5DY  H17  C18  C17  119.88  3.000
 5DY  H17  C18  C09  120.31  3.000
 5DY  C17  C18  C09  119.80  3.000
 5DY  O21  C19  O20  127.42  3.000
 5DY  O20  C19  C06  117.28  3.000
 5DY  O21  C19  C06  115.31  3.000
 5DY  O24  C22  O23  126.60  3.000
 5DY  O24  C22  C02  115.81  3.000
 5DY  O23  C22  C02  117.58  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
 5DY  CONST_03  C06  N07  N08  C04     0.00   0.0  0
 5DY  CONST_04  N07  C06  C05  C04     0.00   0.0  0
 5DY  CONST_05  C09  N08  C04  C05   180.00   0.0  0
 5DY  CONST_06  N07  N08  C04  C05     0.00   0.0  0
 5DY  CONST_07  N08  N07  C06  C05     0.00   0.0  0
 5DY  CONST_08  C09  N08  N07  C06   180.00   0.0  0
 5DY  CONST_09  N08  C04  C05  C06     0.00   0.0  0
 5DY  CONST_12  C11  C10  C09  N08   180.00   0.0  0
 5DY  CONST_13  C17  C18  C09  N08   180.00   0.0  0
 5DY  CONST_14  C12  C11  C10  C09     0.00   0.0  0
 5DY  CONST_15  C12  C17  C18  C09     0.00   0.0  0
 5DY  CONST_16  C17  C12  C11  C10     0.00   0.0  0
 5DY  CONST_17  C17  C18  C09  C10     0.00   0.0  0
 5DY  CONST_18  C18  C17  C12  C11     0.00   0.0  0
 5DY  CONST_19  C18  C09  C10  C11     0.00   0.0  0
 5DY  CONST_20  C09  N08  C04  C03     0.00   0.0  0
 5DY  CONST_21  N07  N08  C04  C03   180.00   0.0  0
 5DY  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 5DY  CONST_23  C19  C06  C05  C04   180.00   0.0  0
 5DY  CONST_24  C19  C06  N07  N08   180.00   0.0  0
 5DY  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 5DY  CONST_26  C18  C17  C12  C13   180.00   0.0  0
 5DY  CONST_27  H7   C05  C06  N07   180.00   0.0  0
 5DY  CONST_28  H8   C10  C09  N08     0.00   0.0  0
 5DY  CONST_29  H17  C18  C09  N08     0.00   0.0  0
 5DY  CONST_30  H9   C11  C10  C09   180.00   0.0  0
 5DY  CONST_31  H16  C17  C18  C09   180.00   0.0  0
 5DY  Var_01    N08  C04  C03  C02   -93.07  30.0  2
 5DY  Var_02    O21  C19  C06  C05    -1.52  30.0  2
 5DY  Var_03    C14  C13  C12  C11    95.64  30.0  2
 5DY  Var_04    C15  C14  C13  C12  -178.28  30.0  3
 5DY  Var_05    F16  C15  C14  C13  -178.78  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
 5DY  chir_01  C02  N01  C03  C22  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
 5DY  plan-1  C03  0.020
 5DY  plan-1  C04  0.020
 5DY  plan-1  C05  0.020
 5DY  plan-1  C06  0.020
 5DY  plan-1  N07  0.020
 5DY  plan-1  N08  0.020
 5DY  plan-1  C09  0.020
 5DY  plan-1  C19  0.020
 5DY  plan-1  H7   0.020
 5DY  plan-2  N08  0.020
 5DY  plan-2  C09  0.020
 5DY  plan-2  C10  0.020
 5DY  plan-2  C11  0.020
 5DY  plan-2  C12  0.020
 5DY  plan-2  C13  0.020
 5DY  plan-2  C17  0.020
 5DY  plan-2  C18  0.020
 5DY  plan-2  H8   0.020
 5DY  plan-2  H9   0.020
 5DY  plan-2  H16  0.020
 5DY  plan-2  H17  0.020
 5DY  plan-3  C06  0.020
 5DY  plan-3  C19  0.020
 5DY  plan-3  O20  0.020
 5DY  plan-3  O21  0.020
 5DY  plan-4  C02  0.020
 5DY  plan-4  C22  0.020
 5DY  plan-4  O23  0.020
 5DY  plan-4  O24  0.020

