# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 17:25:37 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{S},4~{R})-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@H](CN1)Oc2ccccc2C(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
 7E5  7E5  '(2~{S},4~{R})-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid'  ligand  29  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7E5
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
 7E5  N1   N  NH1    0  -0.591  -2.7504  -1.0203   1.0710
 7E5  C4   C  CH1    0  -0.206  -2.9811   0.2819   0.4656
 7E5  C5   C  C      0   0.393  -4.3962   0.4516  -0.1050
 7E5  C6   C  CR6    0   0.370   1.5838  -0.5379  -0.0784
 7E5  C7   C  CR16   0  -0.384   1.6727  -1.9291  -0.1366
 7E5  C8   C  CR16   0  -0.256   2.9150  -2.5529  -0.1650
 7E5  C10  C  CR16   0  -0.279   3.9813  -0.4150  -0.1111
 7E5  O1   O  OC    -1  -0.616  -4.7568   1.6243  -0.3229
 7E5  O2   O  O      0  -0.605  -5.0421  -0.5877  -0.3462
 7E5  C1   C  CH2    0  -0.492  -1.9100   0.4358  -0.6417
 7E5  C3   C  CH2    0  -0.339  -1.3147  -1.2115   1.0377
 7E5  C2   C  CH1    0   0.015  -0.8015  -0.5571  -0.2653
 7E5  O3   O  O2     0  -0.462   0.4210   0.1400  -0.1011
 7E5  C9   C  CR16   0  -0.271   4.0773  -1.8014  -0.1539
 7E5  C11  C  CR6    0  -0.152   2.7560   0.2351  -0.0483
 7E5  C12  C  C      0   0.365   2.7309   1.7519   0.0690
 7E5  O5   O  OC    -1  -0.608   3.4212   2.3748  -0.7613
 7E5  O4   O  O      0  -0.591   2.0642   2.2280   1.0023
 7E5  H1   H  HNH1   0   0.332  -3.2150  -1.7150   0.4971
 7E5  H3   H  HCH1   0   0.220  -2.8091   1.0530   1.2247
 7E5  H4   H  HCR6   0   0.265   0.7875  -2.5493  -0.1617
 7E5  H5   H  HCR6   0   0.250   2.9607  -3.6339  -0.2022
 7E5  H6   H  HCR6   0   0.243   4.8848   0.1827  -0.1167
 7E5  H8   H  HCH2   0   0.238  -2.3236   0.1743  -1.6177
 7E5  H9   H  HCH2   0   0.248  -1.5254   1.4531  -0.7155
 7E5  H10  H  HCH2   0   0.234  -0.8571  -0.6965   1.8873
 7E5  H11  H  HCH2   0   0.229  -1.0665  -2.2701   1.1259
 7E5  H12  H  HCH1   0   0.221  -0.6890  -1.3091  -1.0548
 7E5  H13  H  HCR6   0   0.228   5.0463  -2.2831  -0.1841

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
 7E5  C9   C10  aromatic  1.390  0.020  1.390
 7E5  C9   C8   aromatic  1.384  0.020  1.384
 7E5  C10  C11  aromatic  1.388  0.020  1.388
 7E5  C8   C7   aromatic  1.390  0.020  1.390
 7E5  C11  C12  single    1.521  0.020  1.521
 7E5  C11  C6   aromatic  1.404  0.020  1.404
 7E5  C7   C6   aromatic  1.395  0.020  1.395
 7E5  C12  O4   deloc     1.242  0.020  1.242
 7E5  C12  O5   deloc     1.247  0.020  1.247
 7E5  C6   O3   single    1.346  0.020  1.346
 7E5  C2   C1   single    1.535  0.020  1.535
 7E5  C2   O3   single    1.417  0.020  1.417
 7E5  C2   C3   single    1.546  0.020  1.546
 7E5  C1   C4   single    1.548  0.020  1.548
 7E5  C3   N1   single    1.449  0.020  1.449
 7E5  O2   C5   deloc     1.247  0.020  1.247
 7E5  C4   C5   single    1.535  0.020  1.535
 7E5  C4   N1   single    1.454  0.020  1.454
 7E5  C5   O1   deloc     1.246  0.020  1.246
 7E5  N1   H1   single    0.890  0.020  1.040
 7E5  C4   H3   single    0.970  0.020  1.090
 7E5  C7   H4   single    0.930  0.020  1.080
 7E5  C8   H5   single    0.930  0.020  1.080
 7E5  C10  H6   single    0.930  0.020  1.080
 7E5  C1   H8   single    0.970  0.020  1.090
 7E5  C1   H9   single    0.970  0.020  1.090
 7E5  C3   H10  single    0.970  0.020  1.090
 7E5  C3   H11  single    0.970  0.020  1.090
 7E5  C2   H12  single    0.970  0.020  1.090
 7E5  C9   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
 7E5  H1   N1   C3   110.53  3.000
 7E5  H1   N1   C4   107.77  3.000
 7E5  C3   N1   C4   105.41  3.000
 7E5  H3   C4   C1   108.48  3.000
 7E5  H3   C4   C5   108.93  3.000
 7E5  C1   C4   C5   111.16  3.000
 7E5  H3   C4   N1   108.47  3.000
 7E5  C5   C4   N1   113.57  3.000
 7E5  C1   C4   N1   106.08  3.000
 7E5  O2   C5   O1   126.90  3.000
 7E5  O1   C5   C4   115.84  3.000
 7E5  O2   C5   C4   117.20  3.000
 7E5  C11  C6   O3   116.37  3.000
 7E5  O3   C6   C7   123.81  3.000
 7E5  C11  C6   C7   119.77  3.000
 7E5  H4   C7   C8   118.27  3.000
 7E5  H4   C7   C6   121.39  3.000
 7E5  C8   C7   C6   120.34  3.000
 7E5  H5   C8   C9   120.46  3.000
 7E5  H5   C8   C7   119.10  3.000
 7E5  C9   C8   C7   120.43  3.000
 7E5  H6   C10  C11  118.55  3.000
 7E5  H6   C10  C9   119.50  3.000
 7E5  C11  C10  C9   121.95  3.000
 7E5  H9   C1   H8   107.26  3.000
 7E5  H9   C1   C2   111.43  3.000
 7E5  H8   C1   C2   109.75  3.000
 7E5  H9   C1   C4   112.66  3.000
 7E5  H8   C1   C4   110.70  3.000
 7E5  C2   C1   C4   105.06  3.000
 7E5  H11  C3   H10  107.40  3.000
 7E5  H11  C3   C2   113.79  3.000
 7E5  H10  C3   C2   108.45  3.000
 7E5  H11  C3   N1   110.59  3.000
 7E5  H10  C3   N1   109.55  3.000
 7E5  C2   C3   N1   107.01  3.000
 7E5  H12  C2   O3   109.42  3.000
 7E5  H12  C2   C3   110.54  3.000
 7E5  O3   C2   C3   113.40  3.000
 7E5  H12  C2   C1   109.95  3.000
 7E5  C3   C2   C1   103.93  3.000
 7E5  O3   C2   C1   109.47  3.000
 7E5  C2   O3   C6   119.97  3.000
 7E5  H13  C9   C10  120.42  3.000
 7E5  H13  C9   C8   120.65  3.000
 7E5  C10  C9   C8   118.92  3.000
 7E5  C12  C11  C10  119.00  3.000
 7E5  C12  C11  C6   122.45  3.000
 7E5  C10  C11  C6   118.55  3.000
 7E5  O4   C12  O5   127.32  3.000
 7E5  O5   C12  C11  115.96  3.000
 7E5  O4   C12  C11  116.68  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
 7E5  CONST_01  C9   C10  C11  C6     0.00   0.0  0
 7E5  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 7E5  CONST_03  C10  C9   C8   C7     0.00   0.0  0
 7E5  CONST_04  C10  C11  C6   C7     0.00   0.0  0
 7E5  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 7E5  CONST_06  C11  C6   C7   C8     0.00   0.0  0
 7E5  CONST_07  C12  C11  C6   C7   180.00   0.0  0
 7E5  CONST_08  O3   C6   C7   C8   180.00   0.0  0
 7E5  CONST_09  O3   C6   C11  C10  180.00   0.0  0
 7E5  CONST_10  C12  C11  C10  C9   180.00   0.0  0
 7E5  CONST_11  H6   C10  C11  C6   180.00   0.0  0
 7E5  CONST_12  H5   C8   C7   C6   180.00   0.0  0
 7E5  CONST_13  H13  C9   C8   C7   180.00   0.0  0
 7E5  CONST_14  H4   C7   C8   C9   180.00   0.0  0
 7E5  Var_01    C2   C3   N1   C4   -35.02  30.0  1
 7E5  Var_02    C11  C6   O3   C2   173.77  30.0  2
 7E5  Var_03    O4   C12  C11  C6    52.23  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
 7E5  chir_01  C4  C1  C5  N1  negativ
 7E5  chir_02  C2  O3  C3  C1  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
 7E5  plan-1  C6   0.020
 7E5  plan-1  C7   0.020
 7E5  plan-1  C8   0.020
 7E5  plan-1  C10  0.020
 7E5  plan-1  O3   0.020
 7E5  plan-1  C9   0.020
 7E5  plan-1  C11  0.020
 7E5  plan-1  C12  0.020
 7E5  plan-1  H4   0.020
 7E5  plan-1  H5   0.020
 7E5  plan-1  H6   0.020
 7E5  plan-1  H13  0.020
 7E5  plan-2  C11  0.020
 7E5  plan-2  C12  0.020
 7E5  plan-2  O5   0.020
 7E5  plan-2  O4   0.020
 7E5  plan-3  C4   0.020
 7E5  plan-3  C5   0.020
 7E5  plan-3  O1   0.020
 7E5  plan-3  O2   0.020

