# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:27:07 2020
#   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  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_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   0.387   1.2725  -4.0538   0.2811
 5DX  O02  O   OC    -1  -0.619   2.0471  -4.6264  -0.5137
 5DX  O03  O   O      0  -0.602   0.2890  -4.5603   0.8536
 5DX  C04  C   C      0   0.365   4.3748   2.5405   0.0132
 5DX  O05  O   O      0  -0.598   5.5377   2.1100  -0.1154
 5DX  O06  O   OC    -1  -0.603   4.0217   3.7066   0.2648
 5DX  C08  C   CR16   0  -0.286  -0.8295   0.2386  -1.2802
 5DX  C09  C   CR16   0  -0.230  -2.2153   0.2536  -1.2028
 5DX  C10  C   CR6    0  -0.112  -2.8242   0.7608  -0.0662
 5DX  C11  C   CR16   0  -0.234  -2.0697   1.2541   0.9901
 5DX  C12  C   CR16   0  -0.256  -0.6881   1.2175   0.9112
 5DX  C13  C   CR6    0   0.349  -0.0660   0.7044  -0.2197
 5DX  N14  N   NH2    0  -0.776   0.6718  -1.8863   1.4782
 5DX  C15  C   CH1    0  -0.201   1.5967  -2.5678   0.5916
 5DX  C16  C   CH2    0  -0.555   1.7398  -1.7844  -0.7211
 5DX  C17  C   CR15   0  -0.565   3.4404   0.1435  -0.4528
 5DX  C18  C   CR5    0   0.453   2.1684  -0.3710  -0.5213
 5DX  N19  N   NR5    0  -0.448   1.3421   0.6854  -0.2843
 5DX  N20  N   N      0  -0.302   2.0072   1.8223  -0.0562
 5DX  C21  C   CR5    0   0.089   3.2859   1.5119  -0.1588
 5DX  H5   H   HCR6   0   0.284  -2.5430   1.6527   1.8769
 5DX  H6   H   HCR6   0   0.276  -0.0956   1.5836   1.7382
 5DX  H7   H   HNH2   0   0.325  -0.2445  -1.8631   1.0451
 5DX  H8   H   HNH2   0   0.336   0.5440  -2.4552   2.3062
 5DX  H10  H   HCH1   0   0.226   2.5803  -2.5585   1.0792
 5DX  H11  H   HCH2   0   0.262   2.4892  -2.2778  -1.3379
 5DX  H12  H   HCH2   0   0.248   0.8026  -1.8427  -1.2809
 5DX  H13  H   HCR5   0   0.250   4.3591  -0.4025  -0.5920
 5DX  H3   H   HCR6   0   0.289  -0.3549  -0.1276  -2.1805
 5DX  BR7  BR  BR     0  -0.042  -4.7079   0.7893   0.0456
 5DX  H4   H   HCR6   0   0.285  -2.7984  -0.1167  -2.0348

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  deloc     1.247  0.020  1.247
 5DX  O06  C04  deloc     1.244  0.020  1.244
 5DX  C04  C21  single    1.508  0.020  1.508
 5DX  O03  C01  deloc     1.246  0.020  1.246
 5DX  C21  C17  aromatic  1.408  0.020  1.408
 5DX  C21  N20  aromatic  1.320  0.020  1.320
 5DX  C17  C18  aromatic  1.374  0.020  1.374
 5DX  C01  O02  deloc     1.249  0.020  1.249
 5DX  C01  C15  single    1.552  0.020  1.552
 5DX  N20  N19  aromatic  1.337  0.020  1.337
 5DX  C15  C16  single    1.535  0.020  1.535
 5DX  C15  N14  single    1.451  0.020  1.451
 5DX  C18  N19  aromatic  1.362  0.020  1.362
 5DX  C18  C16  single    1.490  0.020  1.490
 5DX  N19  C13  single    1.410  0.020  1.410
 5DX  C12  C13  aromatic  1.389  0.020  1.389
 5DX  C12  C11  aromatic  1.384  0.020  1.384
 5DX  C13  C08  aromatic  1.387  0.020  1.387
 5DX  C11  C10  aromatic  1.389  0.020  1.389
 5DX  C08  C09  aromatic  1.388  0.020  1.388
 5DX  C10  C09  aromatic  1.386  0.020  1.386
 5DX  C10  BR7  single    1.887  0.020  1.887
 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  117.53  3.000
 5DX  C15  C01  O02  115.90  3.000
 5DX  O03  C01  O02  126.57  3.000
 5DX  C21  C04  O06  117.23  3.000
 5DX  C21  C04  O05  115.23  3.000
 5DX  O06  C04  O05  127.54  3.000
 5DX  H3   C08  C13  120.57  3.000
 5DX  H3   C08  C09  119.22  3.000
 5DX  C13  C08  C09  120.21  3.000
 5DX  H4   C09  C10  121.30  3.000
 5DX  H4   C09  C08  119.46  3.000
 5DX  C10  C09  C08  119.24  3.000
 5DX  C11  C10  C09  121.02  3.000
 5DX  C09  C10  BR7  119.52  3.000
 5DX  C11  C10  BR7  119.46  3.000
 5DX  H5   C11  C12  119.56  3.000
 5DX  H5   C11  C10  121.13  3.000
 5DX  C12  C11  C10  119.31  3.000
 5DX  H6   C12  C13  120.16  3.000
 5DX  H6   C12  C11  119.63  3.000
 5DX  C13  C12  C11  120.21  3.000
 5DX  N19  C13  C12  119.32  3.000
 5DX  C12  C13  C08  120.00  3.000
 5DX  N19  C13  C08  120.68  3.000
 5DX  H8   N14  H7   104.37  3.000
 5DX  H8   N14  C15  108.43  3.000
 5DX  H7   N14  C15  109.01  3.000
 5DX  H10  C15  C16  106.97  3.000
 5DX  H10  C15  N14  107.20  3.000
 5DX  C16  C15  N14  110.01  3.000
 5DX  H10  C15  C01  106.50  3.000
 5DX  N14  C15  C01  116.02  3.000
 5DX  C16  C15  C01  109.68  3.000
 5DX  H12  C16  H11  106.01  3.000
 5DX  H12  C16  C18  111.45  3.000
 5DX  H11  C16  C18  107.92  3.000
 5DX  H12  C16  C15  109.31  3.000
 5DX  H11  C16  C15  108.50  3.000
 5DX  C18  C16  C15  113.33  3.000
 5DX  H13  C17  C21  127.79  3.000
 5DX  H13  C17  C18  126.38  3.000
 5DX  C21  C17  C18  105.83  3.000
 5DX  N19  C18  C17  105.22  3.000
 5DX  N19  C18  C16  125.76  3.000
 5DX  C17  C18  C16  128.91  3.000
 5DX  N20  N19  C18  112.80  3.000
 5DX  C18  N19  C13  128.64  3.000
 5DX  N20  N19  C13  118.53  3.000
 5DX  C21  N20  N19  105.59  3.000
 5DX  N20  C21  C17  110.55  3.000
 5DX  N20  C21  C04  122.03  3.000
 5DX  C17  C21  C04  127.41  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  Var_01    C17  C21  C04  O05   -0.46  30.0  2
 5DX  Var_02    C17  C18  C16  C15   88.87  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
 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  H5   0.020
 5DX  plan-2  H6   0.020
 5DX  plan-2  H3   0.020
 5DX  plan-2  BR7  0.020
 5DX  plan-2  H4   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-4  C04  0.020
 5DX  plan-4  O05  0.020
 5DX  plan-4  O06  0.020
 5DX  plan-4  C21  0.020

