# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:14:13 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-[(2R)-2-amino-2-carboxyethyl]-1-(4-fluorophenyl)-1H-pyrazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1cc(nn1c2ccc(F)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
 5DZ  5DZ  '5-[(2R)-2-amino-2-carboxyethyl]-1-(4-fluorophenyl)-1H-pyrazole-3-carboxylic acid'  ligand  31  21  .  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_5DZ
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
 5DZ  C01  C  C      0   0.385   1.5540  -3.5740  -0.3183
 5DZ  O02  O  O      0  -0.601   2.6621  -3.5180  -0.8843
 5DZ  O03  O  OC    -1  -0.621   1.1659  -4.4594   0.4726
 5DZ  C04  C  C      0   0.364  -4.2264   0.8408   0.0143
 5DZ  O05  O  OC    -1  -0.604  -4.4516   2.0458  -0.1977
 5DZ  O06  O  O      0  -0.599  -5.0599  -0.0828   0.0993
 5DZ  C08  C  CR16   0  -0.241   0.9271   1.9169  -0.8924
 5DZ  C09  C  CR16   0  -0.418   2.1380   2.5845  -0.9606
 5DZ  C10  C  CR6    0   0.531   2.9797   2.5471   0.1361
 5DZ  C11  C  CR16   0  -0.416   2.6449   1.8800   1.2974
 5DZ  C12  C  CR16   0  -0.267   1.4199   1.2302   1.3612
 5DZ  C13  C  CR6    0   0.327   0.5675   1.2392   0.2658
 5DZ  N14  N  NH2    0  -0.775   0.9602  -1.4289  -1.5616
 5DZ  C15  C  CH1    0  -0.199   0.5355  -2.4418  -0.6148
 5DZ  C16  C  CH2    0  -0.556   0.1100  -1.7874   0.7090
 5DZ  C17  C  CR15   0  -0.567  -2.2972  -0.8654   0.4578
 5DZ  C18  C  CR5    0   0.457  -0.9305  -0.7382   0.5308
 5DZ  N19  N  NR5    0  -0.444  -0.6815   0.5822   0.3219
 5DZ  N20  N  N      0  -0.304  -1.7926   1.2926   0.1080
 5DZ  C21  C  CR5    0   0.085  -2.7871   0.4269   0.1890
 5DZ  H5   H  HCR6   0   0.286   3.3170   1.8777   2.1450
 5DZ  H6   H  HCR6   0   0.287   1.1303   0.7279   2.2748
 5DZ  H7   H  HNH2   0   0.324   1.8247  -1.0105  -1.2377
 5DZ  H8   H  HNH2   0   0.336   1.2101  -1.8850  -2.4306
 5DZ  H10  H  HCH1   0   0.226  -0.3591  -2.9187  -1.0336
 5DZ  H11  H  HCH2   0   0.261  -0.2899  -2.5620   1.3618
 5DZ  H12  H  HCH2   0   0.248   0.9910  -1.3860   1.2163
 5DZ  H13  H  HCR5   0   0.248  -2.8653  -1.7737   0.5761
 5DZ  H3   H  HCR6   0   0.276   0.2616   1.9180  -1.7442
 5DZ  F07  F  F      0  -0.313   4.1585   3.1846   0.0689
 5DZ  H4   H  HCR6   0   0.285   2.4272   3.1167  -1.8570

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
 5DZ  F07  C10  single    1.342  0.020  1.342
 5DZ  C09  C10  aromatic  1.383  0.020  1.383
 5DZ  C09  C08  aromatic  1.385  0.020  1.385
 5DZ  C10  C11  aromatic  1.380  0.020  1.380
 5DZ  C08  C13  aromatic  1.389  0.020  1.389
 5DZ  C11  C12  aromatic  1.388  0.020  1.388
 5DZ  C13  C12  aromatic  1.388  0.020  1.388
 5DZ  C13  N19  single    1.412  0.020  1.412
 5DZ  C16  C18  single    1.488  0.020  1.488
 5DZ  C16  C15  single    1.537  0.020  1.537
 5DZ  N19  C18  aromatic  1.360  0.020  1.360
 5DZ  N19  N20  aromatic  1.336  0.020  1.336
 5DZ  N14  C15  single    1.450  0.020  1.450
 5DZ  C18  C17  aromatic  1.375  0.020  1.375
 5DZ  N20  C21  aromatic  1.321  0.020  1.321
 5DZ  C15  C01  single    1.552  0.020  1.552
 5DZ  O02  C01  deloc     1.245  0.020  1.245
 5DZ  C01  O03  deloc     1.249  0.020  1.249
 5DZ  C17  C21  aromatic  1.408  0.020  1.408
 5DZ  C21  C04  single    1.508  0.020  1.508
 5DZ  C04  O06  deloc     1.247  0.020  1.247
 5DZ  C04  O05  deloc     1.244  0.020  1.244
 5DZ  C08  H3   single    0.930  0.020  1.080
 5DZ  C09  H4   single    0.930  0.020  1.080
 5DZ  C11  H5   single    0.930  0.020  1.080
 5DZ  C12  H6   single    0.930  0.020  1.080
 5DZ  N14  H7   single    0.890  0.020  1.040
 5DZ  N14  H8   single    0.890  0.020  1.040
 5DZ  C15  H10  single    0.970  0.020  1.090
 5DZ  C16  H11  single    0.970  0.020  1.090
 5DZ  C16  H12  single    0.970  0.020  1.090
 5DZ  C17  H13  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
 5DZ  C15  C01  O03  115.74  3.000
 5DZ  O03  C01  O02  126.59  3.000
 5DZ  C15  C01  O02  117.67  3.000
 5DZ  C21  C04  O06  115.27  3.000
 5DZ  O06  C04  O05  127.45  3.000
 5DZ  C21  C04  O05  117.28  3.000
 5DZ  H3   C08  C13  119.88  3.000
 5DZ  H3   C08  C09  119.94  3.000
 5DZ  C13  C08  C09  120.18  3.000
 5DZ  H4   C09  C10  120.51  3.000
 5DZ  H4   C09  C08  120.78  3.000
 5DZ  C10  C09  C08  118.70  3.000
 5DZ  C11  C10  C09  122.18  3.000
 5DZ  C11  C10  F07  119.00  3.000
 5DZ  C09  C10  F07  118.82  3.000
 5DZ  H5   C11  C12  120.75  3.000
 5DZ  H5   C11  C10  120.63  3.000
 5DZ  C12  C11  C10  118.61  3.000
 5DZ  H6   C12  C13  120.33  3.000
 5DZ  H6   C12  C11  119.49  3.000
 5DZ  C13  C12  C11  120.18  3.000
 5DZ  N19  C13  C12  120.58  3.000
 5DZ  N19  C13  C08  119.27  3.000
 5DZ  C12  C13  C08  120.14  3.000
 5DZ  H8   N14  H7   104.45  3.000
 5DZ  H8   N14  C15  108.54  3.000
 5DZ  H7   N14  C15  109.24  3.000
 5DZ  H10  C15  C16  106.75  3.000
 5DZ  H10  C15  N14  107.06  3.000
 5DZ  C16  C15  N14  110.25  3.000
 5DZ  H10  C15  C01  106.92  3.000
 5DZ  N14  C15  C01  116.25  3.000
 5DZ  C16  C15  C01  109.14  3.000
 5DZ  H12  C16  H11  106.20  3.000
 5DZ  H12  C16  C18  111.11  3.000
 5DZ  H11  C16  C18  108.45  3.000
 5DZ  H12  C16  C15  109.46  3.000
 5DZ  H11  C16  C15  108.37  3.000
 5DZ  C18  C16  C15  112.99  3.000
 5DZ  H13  C17  C21  127.67  3.000
 5DZ  H13  C17  C18  126.60  3.000
 5DZ  C21  C17  C18  105.73  3.000
 5DZ  N19  C18  C17  105.29  3.000
 5DZ  C17  C18  C16  129.51  3.000
 5DZ  N19  C18  C16  125.09  3.000
 5DZ  N20  N19  C18  112.87  3.000
 5DZ  N20  N19  C13  118.80  3.000
 5DZ  C18  N19  C13  128.30  3.000
 5DZ  C21  N20  N19  105.53  3.000
 5DZ  N20  C21  C17  110.57  3.000
 5DZ  C17  C21  C04  127.32  3.000
 5DZ  N20  C21  C04  122.12  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
 5DZ  CONST_01  C11  C10  C09  C08    0.00   0.0  0
 5DZ  CONST_02  C11  C12  C13  C08    0.00   0.0  0
 5DZ  CONST_05  C12  C11  C10  C09    0.00   0.0  0
 5DZ  CONST_06  C12  C13  C08  C09    0.00   0.0  0
 5DZ  CONST_07  N19  C13  C08  C09  180.00   0.0  0
 5DZ  CONST_08  C13  C08  C09  C10    0.00   0.0  0
 5DZ  CONST_09  C13  C12  C11  C10    0.00   0.0  0
 5DZ  CONST_10  N19  C13  C12  C11  180.00   0.0  0
 5DZ  CONST_13  C17  C18  N19  C13  180.00   0.0  0
 5DZ  CONST_14  C21  N20  N19  C13  180.00   0.0  0
 5DZ  CONST_15  N20  N19  C18  C17    0.00   0.0  0
 5DZ  CONST_16  N19  N20  C21  C17    0.00   0.0  0
 5DZ  CONST_17  C21  N20  N19  C18    0.00   0.0  0
 5DZ  CONST_18  N20  C21  C17  C18    0.00   0.0  0
 5DZ  CONST_19  C21  C17  C18  N19    0.00   0.0  0
 5DZ  CONST_20  N19  N20  C21  C04  180.00   0.0  0
 5DZ  CONST_21  C18  C17  C21  C04  180.00   0.0  0
 5DZ  CONST_22  C08  C09  C10  F07  180.00   0.0  0
 5DZ  CONST_23  C12  C11  C10  F07  180.00   0.0  0
 5DZ  CONST_24  C16  C18  N19  C13    0.00   0.0  0
 5DZ  CONST_25  N20  N19  C18  C16  180.00   0.0  0
 5DZ  CONST_26  C21  C17  C18  C16  180.00   0.0  0
 5DZ  CONST_27  H6   C12  C13  C08  180.00   0.0  0
 5DZ  CONST_28  H5   C11  C10  C09  180.00   0.0  0
 5DZ  CONST_29  H3   C08  C09  C10  180.00   0.0  0
 5DZ  CONST_30  H4   C09  C10  C11  180.00   0.0  0
 5DZ  CONST_31  H13  C17  C18  N19  180.00   0.0  0
 5DZ  Var_01    N20  C21  C04  O05   -0.77  30.0  2
 5DZ  Var_02    N19  C18  C16  C15  -90.45  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
 5DZ  chir_01  C15  C16  N14  C01  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
 5DZ  plan-1  C04  0.020
 5DZ  plan-1  C13  0.020
 5DZ  plan-1  C16  0.020
 5DZ  plan-1  C17  0.020
 5DZ  plan-1  C18  0.020
 5DZ  plan-1  N19  0.020
 5DZ  plan-1  N20  0.020
 5DZ  plan-1  C21  0.020
 5DZ  plan-1  H13  0.020
 5DZ  plan-2  C08  0.020
 5DZ  plan-2  C09  0.020
 5DZ  plan-2  C10  0.020
 5DZ  plan-2  C11  0.020
 5DZ  plan-2  C12  0.020
 5DZ  plan-2  C13  0.020
 5DZ  plan-2  N19  0.020
 5DZ  plan-2  H5   0.020
 5DZ  plan-2  H6   0.020
 5DZ  plan-2  H3   0.020
 5DZ  plan-2  F07  0.020
 5DZ  plan-2  H4   0.020
 5DZ  plan-3  C01  0.020
 5DZ  plan-3  O02  0.020
 5DZ  plan-3  O03  0.020
 5DZ  plan-3  C15  0.020
 5DZ  plan-4  C04  0.020
 5DZ  plan-4  O05  0.020
 5DZ  plan-4  O06  0.020
 5DZ  plan-4  C21  0.020

