# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:31:27 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  33  21  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.519   1.6012  -3.5057  -0.3386
 5DZ  O02  O  O     0  -0.432   2.7399  -3.4591  -0.7289
 5DZ  O03  O  OH1   0  -0.592   1.1148  -4.5034   0.3891
 5DZ  C04  C  C     0   0.504  -4.1777   0.7291   0.0092
 5DZ  O05  O  OH1   0  -0.591  -4.3597   2.0141  -0.2512
 5DZ  O06  O  O     0  -0.439  -5.0717  -0.0780   0.0984
 5DZ  C08  C  CR16  0  -0.232   0.9539   1.8754  -0.9243
 5DZ  C09  C  CR16  0  -0.417   2.1556   2.5606  -0.9797
 5DZ  C10  C  CR6   0   0.540   2.9487   2.6030   0.1527
 5DZ  C11  C  CR16  0  -0.416   2.5775   1.9972   1.3370
 5DZ  C12  C  CR16  0  -0.256   1.3641   1.3267   1.3874
 5DZ  C13  C  CR6   0   0.307   0.5628   1.2612   0.2573
 5DZ  N14  N  NH2   0  -0.771   0.9493  -1.4484  -1.5766
 5DZ  C15  C  CH1   0  -0.192   0.5506  -2.4340  -0.6089
 5DZ  C16  C  CH2   0  -0.568   0.1649  -1.7634   0.7250
 5DZ  C17  C  CR15  0  -0.529  -2.2615  -0.9094   0.4625
 5DZ  C18  C  CR5   0   0.465  -0.9003  -0.7438   0.5305
 5DZ  N19  N  NR5   0  -0.436  -0.6795   0.5804   0.3045
 5DZ  N20  N  N     0  -0.274  -1.7927   1.2623   0.0884
 5DZ  C21  C  CR5   0   0.142  -2.7643   0.3704   0.1803
 5DZ  H1   H  HOH1  0   0.484   1.8066  -5.1585   0.5679
 5DZ  H2   H  HOH1  0   0.488  -5.3055   2.1973  -0.3547
 5DZ  H4   H  HCR6  0   0.290   2.4736   3.0465  -1.8922
 5DZ  H5   H  HCR6  0   0.291   3.2131   2.0567   2.2101
 5DZ  H6   H  HCR6  0   0.294   1.0437   0.8682   2.3139
 5DZ  H7   H  HNH2  0   0.346   1.8311  -1.0219  -1.3213
 5DZ  H8   H  HNH2  0   0.361   1.0881  -1.8769  -2.4823
 5DZ  H10  H  HCH1  0   0.289  -0.3392  -2.9445  -0.9901
 5DZ  H11  H  HCH2  0   0.293  -0.2056  -2.5155   1.4207
 5DZ  H12  H  HCH2  0   0.280   1.0530  -1.3263   1.1854
 5DZ  H13  H  HCR5  0   0.278  -2.8119  -1.8265   0.5934
 5DZ  H3   H  HCR6  0   0.283   0.3250   1.8137  -1.8013
 5DZ  F07  F  F     0  -0.309   4.1159   3.2581   0.0981

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    1.340  0.020  1.340
 5DZ  C09  C10  aromatic  1.383  0.020  1.383
 5DZ  C09  C08  aromatic  1.384  0.020  1.384
 5DZ  C10  C11  aromatic  1.381  0.020  1.381
 5DZ  C08  C13  aromatic  1.388  0.020  1.388
 5DZ  C11  C12  aromatic  1.387  0.020  1.387
 5DZ  C13  C12  aromatic  1.387  0.020  1.387
 5DZ  C13  N19  single    1.417  0.020  1.417
 5DZ  C16  C18  single    1.487  0.020  1.487
 5DZ  C16  C15  single    1.542  0.020  1.542
 5DZ  N19  C18  aromatic  1.361  0.020  1.361
 5DZ  N19  N20  aromatic  1.323  0.020  1.323
 5DZ  N14  C15  single    1.438  0.020  1.438
 5DZ  C18  C17  aromatic  1.373  0.020  1.373
 5DZ  N20  C21  aromatic  1.322  0.020  1.322
 5DZ  C15  C01  single    1.525  0.020  1.525
 5DZ  O02  C01  double    1.205  0.020  1.205
 5DZ  C01  O03  single    1.327  0.020  1.327
 5DZ  C17  C21  aromatic  1.404  0.020  1.404
 5DZ  C21  C04  single    1.468  0.020  1.468
 5DZ  C04  O06  double    1.208  0.020  1.208
 5DZ  C04  O05  single    1.324  0.020  1.324
 5DZ  O03  H1   single    0.850  0.020  0.980
 5DZ  O05  H2   single    0.850  0.020  0.980
 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  111.90  3.000
 5DZ  O03  C01  O02  123.59  3.000
 5DZ  C15  C01  O02  124.51  3.000
 5DZ  H1   O03  C01  110.34  3.000
 5DZ  C21  C04  O06  122.73  3.000
 5DZ  O06  C04  O05  124.16  3.000
 5DZ  C21  C04  O05  113.11  3.000
 5DZ  H2   O05  C04  109.80  3.000
 5DZ  H3   C08  C13  120.10  3.000
 5DZ  H3   C08  C09  120.05  3.000
 5DZ  C13  C08  C09  119.85  3.000
 5DZ  H4   C09  C10  120.55  3.000
 5DZ  H4   C09  C08  120.76  3.000
 5DZ  C10  C09  C08  118.70  3.000
 5DZ  C11  C10  C09  122.31  3.000
 5DZ  C11  C10  F07  118.92  3.000
 5DZ  C09  C10  F07  118.77  3.000
 5DZ  H5   C11  C12  120.75  3.000
 5DZ  H5   C11  C10  120.68  3.000
 5DZ  C12  C11  C10  118.57  3.000
 5DZ  H6   C12  C13  120.43  3.000
 5DZ  H6   C12  C11  119.66  3.000
 5DZ  C13  C12  C11  119.90  3.000
 5DZ  N19  C13  C12  120.13  3.000
 5DZ  N19  C13  C08  119.20  3.000
 5DZ  C12  C13  C08  120.66  3.000
 5DZ  H8   N14  H7   106.54  3.000
 5DZ  H8   N14  C15  110.51  3.000
 5DZ  H7   N14  C15  111.14  3.000
 5DZ  H10  C15  C16  107.51  3.000
 5DZ  H10  C15  N14  108.11  3.000
 5DZ  C16  C15  N14  110.70  3.000
 5DZ  H10  C15  C01  107.10  3.000
 5DZ  N14  C15  C01  114.21  3.000
 5DZ  C16  C15  C01  108.94  3.000
 5DZ  H12  C16  H11  106.49  3.000
 5DZ  H12  C16  C18  111.31  3.000
 5DZ  H11  C16  C18  108.25  3.000
 5DZ  H12  C16  C15  109.60  3.000
 5DZ  H11  C16  C15  109.70  3.000
 5DZ  C18  C16  C15  111.36  3.000
 5DZ  H13  C17  C21  128.13  3.000
 5DZ  H13  C17  C18  127.09  3.000
 5DZ  C21  C17  C18  104.78  3.000
 5DZ  N19  C18  C17  105.66  3.000
 5DZ  C17  C18  C16  129.34  3.000
 5DZ  N19  C18  C16  124.91  3.000
 5DZ  N20  N19  C18  113.08  3.000
 5DZ  N20  N19  C13  118.97  3.000
 5DZ  C18  N19  C13  127.95  3.000
 5DZ  C21  N20  N19  105.02  3.000
 5DZ  N20  C21  C17  111.46  3.000
 5DZ  C17  C21  C04  126.23  3.000
 5DZ  N20  C21  C04  122.31  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  CONST_32  H2   O05  C04  C21  180.00   0.0  0
 5DZ  CONST_33  H1   O03  C01  O02    0.00   0.0  0
 5DZ  Var_01    N20  C21  C04  O05    0.48  30.0  3
 5DZ  Var_02    N19  C18  C16  C15  -92.28  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  H4   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-3  C01  0.020
 5DZ  plan-3  O02  0.020
 5DZ  plan-3  O03  0.020
 5DZ  plan-3  C15  0.020
 5DZ  plan-3  H1   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
 5DZ  plan-4  H2   0.020

