# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 20:30:17 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  31  18  .  2021-08-06  2021-08-06  
;
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  NR15  0  -0.609  -2.3640  -0.7841   1.2175
 7E5  C4   C  CR15  0  -0.194  -2.4943   0.3822   0.3606
 7E5  C5   C  C     0   0.530  -3.9037   0.9114   0.3287
 7E5  C6   C  CR6   0   0.410   1.4753  -0.6179  -0.2224
 7E5  C7   C  CR16  0  -0.378   1.7817  -1.9767  -0.3153
 7E5  C8   C  CR16  0  -0.231   3.0838  -2.4150  -0.1345
 7E5  C10  C  CR16  0  -0.243   3.8089  -0.1683   0.2218
 7E5  O1   O  OH1   0  -0.589  -3.9646   2.0819  -0.2885
 7E5  O2   O  O     0  -0.436  -4.8653   0.3399   0.7786
 7E5  C1   C  CH2   0  -0.464  -2.0200  -0.0784  -1.0273
 7E5  C3   C  CH2   0  -0.289  -1.3286  -1.6500   0.6402
 7E5  C2   C  CR15  0  -0.077  -0.8569  -0.9804  -0.6614
 7E5  O3   O  O2    0  -0.456   0.2550  -0.1194  -0.4352
 7E5  C9   C  CR16  0  -0.272   4.1064  -1.5170   0.1330
 7E5  C11  C  CR6   0  -0.187   2.5048   0.3003   0.0621
 7E5  C12  C  C     0   0.515   2.2149   1.7446   0.2405
 7E5  O5   O  OH1   0  -0.597   3.2697   2.5022  -0.0527
 7E5  O4   O  O     0  -0.427   1.1697   2.2077   0.6250
 7E5  H1   H  HNR5  0   0.356  -3.2447  -1.2809   1.2422
 7E5  H3   H  HCR5  0   0.281  -1.8383   1.1876   0.7104
 7E5  H4   H  HCR6  0   0.287   1.0129  -2.7062  -0.5287
 7E5  H5   H  HCR6  0   0.270   3.2937  -3.4742  -0.2070
 7E5  H6   H  HCR6  0   0.270   4.6046   0.5308   0.4389
 7E5  H7   H  HOH1  0   0.486  -4.8825   2.3892  -0.3346
 7E5  H8   H  HCH2  0   0.262  -2.7932  -0.6821  -1.5092
 7E5  H9   H  HCH2  0   0.270  -1.7433   0.7301  -1.7026
 7E5  H10  H  HCH2  0   0.240  -0.4961  -1.7920   1.3343
 7E5  H11  H  HCH2  0   0.248  -1.7316  -2.6406   0.4218
 7E5  H12  H  HCR5  0   0.278  -0.6283  -1.7004  -1.4522
 7E5  H13  H  HCR6  0   0.261   5.1216  -1.8608   0.2745
 7E5  H14  H  HOH1  0   0.484   3.0637   3.4298   0.1351

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  1.384  0.020  1.384
 7E5  C9   C8   aromatic  1.387  0.020  1.387
 7E5  C10  C11  aromatic  1.395  0.020  1.395
 7E5  C8   C7   aromatic  1.386  0.020  1.386
 7E5  C11  C12  single    1.484  0.020  1.484
 7E5  C11  C6   aromatic  1.408  0.020  1.408
 7E5  C7   C6   aromatic  1.396  0.020  1.396
 7E5  C12  O4   double    1.206  0.020  1.206
 7E5  C12  O5   single    1.331  0.020  1.331
 7E5  C6   O3   single    1.335  0.020  1.335
 7E5  C2   C1   single    1.517  0.020  1.517
 7E5  C2   O3   single    1.424  0.020  1.424
 7E5  C2   C3   single    1.538  0.020  1.538
 7E5  C1   C4   single    1.537  0.020  1.537
 7E5  C3   N1   single    1.468  0.020  1.468
 7E5  O2   C5   double    1.206  0.020  1.206
 7E5  C4   C5   single    1.506  0.020  1.506
 7E5  C4   N1   single    1.453  0.020  1.453
 7E5  C5   O1   single    1.325  0.020  1.325
 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  O1   H7   single    0.850  0.020  0.980
 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
 7E5  O5   H14  single    0.850  0.020  0.980

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   109.51  3.000
 7E5  H1   N1   C4   109.30  3.000
 7E5  C3   N1   C4   107.75  3.000
 7E5  H3   C4   C1   108.88  3.000
 7E5  H3   C4   C5   107.98  3.000
 7E5  C1   C4   C5   112.02  3.000
 7E5  H3   C4   N1   110.36  3.000
 7E5  C5   C4   N1   112.24  3.000
 7E5  C1   C4   N1   105.32  3.000
 7E5  O2   C5   O1   123.78  3.000
 7E5  O1   C5   C4   111.32  3.000
 7E5  O2   C5   C4   124.89  3.000
 7E5  C11  C6   O3   117.18  3.000
 7E5  O3   C6   C7   123.60  3.000
 7E5  C11  C6   C7   119.18  3.000
 7E5  H4   C7   C8   118.72  3.000
 7E5  H4   C7   C6   120.92  3.000
 7E5  C8   C7   C6   120.36  3.000
 7E5  H5   C8   C9   120.24  3.000
 7E5  H5   C8   C7   118.88  3.000
 7E5  C9   C8   C7   120.87  3.000
 7E5  H6   C10  C11  119.59  3.000
 7E5  H6   C10  C9   119.00  3.000
 7E5  C11  C10  C9   121.40  3.000
 7E5  H7   O1   C5   110.24  3.000
 7E5  H9   C1   H8   108.44  3.000
 7E5  H9   C1   C2   113.34  3.000
 7E5  H8   C1   C2   108.69  3.000
 7E5  H9   C1   C4   114.56  3.000
 7E5  H8   C1   C4   110.20  3.000
 7E5  C2   C1   C4   101.36  3.000
 7E5  H11  C3   H10  106.88  3.000
 7E5  H11  C3   C2   109.82  3.000
 7E5  H10  C3   C2   111.12  3.000
 7E5  H11  C3   N1   110.71  3.000
 7E5  H10  C3   N1   111.35  3.000
 7E5  C2   C3   N1   107.00  3.000
 7E5  H12  C2   O3   110.47  3.000
 7E5  H12  C2   C3   112.92  3.000
 7E5  O3   C2   C3   111.61  3.000
 7E5  H12  C2   C1   112.17  3.000
 7E5  C3   C2   C1   103.17  3.000
 7E5  O3   C2   C1   106.11  3.000
 7E5  C2   O3   C6   120.87  3.000
 7E5  H13  C9   C10  120.22  3.000
 7E5  H13  C9   C8   120.77  3.000
 7E5  C10  C9   C8   119.00  3.000
 7E5  C12  C11  C10  119.73  3.000
 7E5  C12  C11  C6   121.06  3.000
 7E5  C10  C11  C6   119.17  3.000
 7E5  O4   C12  O5   122.57  3.000
 7E5  O5   C12  C11  111.87  3.000
 7E5  O4   C12  C11  125.54  3.000
 7E5  H14  O5   C12  109.49  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  CONST_15  H7   O1   C5   C4    180.00   0.0  0
 7E5  CONST_16  H14  O5   C12  C11   180.00   0.0  0
 7E5  Var_01    C2   C3   N1   C4     -2.16  30.0  1
 7E5  Var_02    C11  C6   O3   C2   -176.76  30.0  2
 7E5  Var_03    O4   C12  C11  C6     27.42  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-2  H14  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
 7E5  plan-3  H7   0.020

