# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:36:20 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-[(2R)-2-amino-2-carboxyethyl]-1-(4-bromophenyl)-1H-pyrazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1cc(nn1c2ccc(Br)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
 5DX  5DX  '5-[(2R)-2-amino-2-carboxyethyl]-1-(4-bromophenyl)-1H-pyrazole-3-carboxylic acid'  ligand  33  21  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5DX
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
 5DX  C01  C   C     0   0.565  19.4431  103.3022  377.2046
 5DX  O02  O   OH1   0  -0.586  19.4966  102.3734  376.2623
 5DX  O03  O   O     0  -0.428  18.4806  104.0019  377.3967
 5DX  C04  C   C     0   0.505  21.3388  108.3598  375.5963
 5DX  O05  O   O     0  -0.438  22.2681  108.0563  374.8874
 5DX  O06  O   OH1   0  -0.590  20.6370  109.4740  375.4656
 5DX  C08  C   CR16  0  -0.271  19.0843  106.8097  380.6900
 5DX  C09  C   CR16  0  -0.227  18.0949  106.8888  381.6585
 5DX  C10  C   CR6   0  -0.108  16.7842  107.1215  381.2702
 5DX  C11  C   CR16  0  -0.230  16.4477  107.2732  379.9318
 5DX  C12  C   CR16  0  -0.259  17.4385  107.1770  378.9687
 5DX  C13  C   CR6   0   0.327  18.7519  106.9438  379.3503
 5DX  N14  N   NH2   0  -0.782  20.9055  102.1095  378.7120
 5DX  C15  C   CH1   0  -0.210  20.7287  103.3688  378.0164
 5DX  C16  C   CH2   0  -0.554  20.7156  104.6004  378.9289
 5DX  C17  C   CR15  0  -0.535  21.4117  106.2704  377.0762
 5DX  C18  C   CR5   0   0.449  20.6590  105.8716  378.1539
 5DX  N19  N   NR5   0  -0.443  19.7577  106.8716  378.3591
 5DX  N20  N   N     0  -0.273  19.8724  107.8632  377.4879
 5DX  C21  C   CR5   0   0.151  20.8748  107.5125  376.7028
 5DX  H1   H   HOH1  0   0.481  18.6581  102.3460  375.7769
 5DX  H2   H   HOH1  0   0.488  20.9900  109.9974  374.7307
 5DX  H4   H   HCR6  0   0.290  18.3603  106.7813  382.7011
 5DX  H5   H   HCR6  0   0.289  15.4257  107.4554  379.6295
 5DX  H6   H   HCR6  0   0.285  17.1844  107.2832  377.9231
 5DX  H7   H   HNH2  0   0.363  21.8273  102.0856  379.1287
 5DX  H8   H   HNH2  0   0.353  20.2456  102.0360  379.4774
 5DX  H10  H   HCH1  0   0.281  21.5544  103.4624  377.3042
 5DX  H11  H   HCH2  0   0.272  19.8766  104.5211  379.6211
 5DX  H12  H   HCH2  0   0.287  21.6249  104.5817  379.5348
 5DX  H13  H   HCR5  0   0.282  22.2268  105.7361  376.6168
 5DX  H3   H   HCR6  0   0.296  20.1128  106.6590  380.9911
 5DX  BR7  BR  BR    0  -0.031  15.4360  107.2378  382.5827

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
 5DX  O05  C04  double    1.208  0.020  1.208
 5DX  O06  C04  single    1.323  0.020  1.323
 5DX  C04  C21  single    1.469  0.020  1.469
 5DX  O03  C01  double    1.205  0.020  1.205
 5DX  C21  C17  aromatic  1.404  0.020  1.404
 5DX  C21  N20  aromatic  1.321  0.020  1.321
 5DX  C17  C18  aromatic  1.374  0.020  1.374
 5DX  C01  O02  single    1.324  0.020  1.324
 5DX  C01  C15  single    1.522  0.020  1.522
 5DX  N20  N19  aromatic  1.325  0.020  1.325
 5DX  C15  C16  single    1.533  0.020  1.533
 5DX  C15  N14  single    1.450  0.020  1.450
 5DX  C18  N19  aromatic  1.362  0.020  1.362
 5DX  C18  C16  single    1.490  0.020  1.490
 5DX  N19  C13  single    1.414  0.020  1.414
 5DX  C12  C13  aromatic  1.387  0.020  1.387
 5DX  C12  C11  aromatic  1.385  0.020  1.385
 5DX  C13  C08  aromatic  1.387  0.020  1.387
 5DX  C11  C10  aromatic  1.388  0.020  1.388
 5DX  C08  C09  aromatic  1.387  0.020  1.387
 5DX  C10  C09  aromatic  1.387  0.020  1.387
 5DX  C10  BR7  single    1.885  0.020  1.885
 5DX  O02  H1   single    0.850  0.020  0.980
 5DX  O06  H2   single    0.850  0.020  0.980
 5DX  C08  H3   single    0.930  0.020  1.080
 5DX  C09  H4   single    0.930  0.020  1.080
 5DX  C11  H5   single    0.930  0.020  1.080
 5DX  C12  H6   single    0.930  0.020  1.080
 5DX  N14  H7   single    0.890  0.020  1.040
 5DX  N14  H8   single    0.890  0.020  1.040
 5DX  C15  H10  single    0.970  0.020  1.090
 5DX  C16  H11  single    0.970  0.020  1.090
 5DX  C16  H12  single    0.970  0.020  1.090
 5DX  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
 5DX  C15  C01  O03  124.34  3.000
 5DX  C15  C01  O02  112.09  3.000
 5DX  O03  C01  O02  123.56  3.000
 5DX  H1   O02  C01  109.95  3.000
 5DX  C21  C04  O06  113.12  3.000
 5DX  C21  C04  O05  122.71  3.000
 5DX  O06  C04  O05  124.18  3.000
 5DX  H2   O06  C04  109.67  3.000
 5DX  H3   C08  C13  120.67  3.000
 5DX  H3   C08  C09  119.45  3.000
 5DX  C13  C08  C09  119.88  3.000
 5DX  H4   C09  C10  121.25  3.000
 5DX  H4   C09  C08  119.52  3.000
 5DX  C10  C09  C08  119.23  3.000
 5DX  C11  C10  C09  121.16  3.000
 5DX  C09  C10  BR7  119.43  3.000
 5DX  C11  C10  BR7  119.42  3.000
 5DX  H5   C11  C12  119.56  3.000
 5DX  H5   C11  C10  121.14  3.000
 5DX  C12  C11  C10  119.30  3.000
 5DX  H6   C12  C13  120.33  3.000
 5DX  H6   C12  C11  119.83  3.000
 5DX  C13  C12  C11  119.84  3.000
 5DX  N19  C13  C12  119.29  3.000
 5DX  C12  C13  C08  120.58  3.000
 5DX  N19  C13  C08  120.12  3.000
 5DX  H8   N14  H7   106.29  3.000
 5DX  H8   N14  C15  110.24  3.000
 5DX  H7   N14  C15  109.22  3.000
 5DX  H10  C15  C16  108.97  3.000
 5DX  H10  C15  N14  107.13  3.000
 5DX  C16  C15  N14  114.42  3.000
 5DX  H10  C15  C01  107.10  3.000
 5DX  N14  C15  C01  108.72  3.000
 5DX  C16  C15  C01  110.21  3.000
 5DX  H12  C16  H11  106.68  3.000
 5DX  H12  C16  C18  109.55  3.000
 5DX  H11  C16  C18  111.28  3.000
 5DX  H12  C16  C15  108.02  3.000
 5DX  H11  C16  C15  109.02  3.000
 5DX  C18  C16  C15  112.10  3.000
 5DX  H13  C17  C21  127.94  3.000
 5DX  H13  C17  C18  127.23  3.000
 5DX  C21  C17  C18  104.83  3.000
 5DX  N19  C18  C17  105.53  3.000
 5DX  N19  C18  C16  124.98  3.000
 5DX  C17  C18  C16  129.41  3.000
 5DX  N20  N19  C18  113.16  3.000
 5DX  C18  N19  C13  127.88  3.000
 5DX  N20  N19  C13  118.96  3.000
 5DX  C21  N20  N19  104.94  3.000
 5DX  N20  C21  C17  111.54  3.000
 5DX  N20  C21  C04  122.31  3.000
 5DX  C17  C21  C04  126.15  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
 5DX  CONST_03  C11  C12  C13  C08    0.00   0.0  0
 5DX  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 5DX  CONST_05  N19  C13  C08  C09  180.00   0.0  0
 5DX  CONST_06  C12  C13  C08  C09    0.00   0.0  0
 5DX  CONST_07  C12  C11  C10  C09    0.00   0.0  0
 5DX  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 5DX  CONST_09  C13  C08  C09  C10    0.00   0.0  0
 5DX  CONST_10  N19  C13  C12  C11  180.00   0.0  0
 5DX  CONST_13  C21  N20  N19  C13  180.00   0.0  0
 5DX  CONST_14  C17  C18  N19  C13  180.00   0.0  0
 5DX  CONST_15  N19  N20  C21  C17    0.00   0.0  0
 5DX  CONST_16  N20  N19  C18  C17    0.00   0.0  0
 5DX  CONST_17  N20  C21  C17  C18    0.00   0.0  0
 5DX  CONST_18  C21  N20  N19  C18    0.00   0.0  0
 5DX  CONST_19  C21  C17  C18  N19    0.00   0.0  0
 5DX  CONST_20  C18  C17  C21  C04  180.00   0.0  0
 5DX  CONST_21  N19  N20  C21  C04  180.00   0.0  0
 5DX  CONST_22  C12  C11  C10  BR7  180.00   0.0  0
 5DX  CONST_23  C08  C09  C10  BR7  180.00   0.0  0
 5DX  CONST_24  C16  C18  N19  C13    0.00   0.0  0
 5DX  CONST_25  C21  C17  C18  C16  180.00   0.0  0
 5DX  CONST_26  N20  N19  C18  C16  180.00   0.0  0
 5DX  CONST_27  H6   C12  C13  C08  180.00   0.0  0
 5DX  CONST_28  H5   C11  C10  C09  180.00   0.0  0
 5DX  CONST_29  H3   C08  C09  C10  180.00   0.0  0
 5DX  CONST_30  H4   C09  C10  C11  180.00   0.0  0
 5DX  CONST_31  H13  C17  C18  N19  180.00   0.0  0
 5DX  CONST_32  H2   O06  C04  C21  180.00   0.0  0
 5DX  CONST_33  H1   O02  C01  O03    0.00   0.0  0
 5DX  Var_01    C17  C21  C04  O05   -0.65  30.0  2
 5DX  Var_02    C17  C18  C16  C15  -48.18  30.0  1

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
 5DX  chir_01  C15  C01  C16  N14  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
 5DX  plan-1  C04  0.020
 5DX  plan-1  C13  0.020
 5DX  plan-1  C16  0.020
 5DX  plan-1  C17  0.020
 5DX  plan-1  C18  0.020
 5DX  plan-1  N19  0.020
 5DX  plan-1  N20  0.020
 5DX  plan-1  C21  0.020
 5DX  plan-1  H13  0.020
 5DX  plan-2  C08  0.020
 5DX  plan-2  C09  0.020
 5DX  plan-2  C10  0.020
 5DX  plan-2  C11  0.020
 5DX  plan-2  C12  0.020
 5DX  plan-2  C13  0.020
 5DX  plan-2  N19  0.020
 5DX  plan-2  H4   0.020
 5DX  plan-2  H5   0.020
 5DX  plan-2  H6   0.020
 5DX  plan-2  H3   0.020
 5DX  plan-2  BR7  0.020
 5DX  plan-3  C01  0.020
 5DX  plan-3  O02  0.020
 5DX  plan-3  O03  0.020
 5DX  plan-3  C15  0.020
 5DX  plan-3  H1   0.020
 5DX  plan-4  C04  0.020
 5DX  plan-4  O05  0.020
 5DX  plan-4  O06  0.020
 5DX  plan-4  C21  0.020
 5DX  plan-4  H2   0.020

