# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Sep 19 19:16:35 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-{[(S)-carboxy(phenyl)methyl]amino}-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)N[C@H](C(O)=O)c1ccccc1
#
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
 8JI  8JI  "N-succinyl-L-phenylglycine"  ligand  31  18  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8JI
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
 8JI  C15  C  CH2   0  -0.557  120.6464  223.1280  279.9242
 8JI  C01  C  CR16  0  -0.265  124.5487  220.8496  274.0913
 8JI  C02  C  CR16  0  -0.237  123.4667  221.3006  274.8330
 8JI  C03  C  CR16  0  -0.304  123.5837  221.4900  276.2050
 8JI  C04  C  CR6   0   0.155  124.7868  221.2334  276.8502
 8JI  C05  C  CR16  0  -0.284  125.8650  220.7688  276.1008
 8JI  C06  C  CR16  0  -0.244  125.7511  220.5792  274.7323
 8JI  C07  C  CH1   0  -0.277  124.9768  221.4181  278.3399
 8JI  C08  C  C     0   0.547  125.8011  222.6696  278.6495
 8JI  C12  C  C     0   0.590  122.9958  222.4510  279.3447
 8JI  C14  C  CH2   0  -0.593  121.8193  222.2170  280.2658
 8JI  C16  C  C     0   0.537  119.4415  222.9468  280.8079
 8JI  N11  N  NH1   0  -0.649  123.7684  221.3714  279.1208
 8JI  O09  O  O     0  -0.417  126.3450  223.3470  277.8202
 8JI  O10  O  OH1   0  -0.588  125.9306  222.8459  279.9565
 8JI  O13  O  O     0  -0.482  123.2513  223.5426  278.8602
 8JI  O17  O  O     0  -0.436  118.3030  222.9587  280.4130
 8JI  O18  O  OH1   0  -0.590  119.7619  222.8054  282.0902
 8JI  H1   H  HCH2  0   0.274  120.3247  222.9751  278.8943
 8JI  H2   H  HCH2  0   0.287  120.9538  224.1747  280.0044
 8JI  H4   H  HCR6  0   0.255  122.5223  221.5053  274.3453
 8JI  H5   H  HCR6  0   0.254  122.7189  221.8295  276.7580
 8JI  H6   H  HCR6  0   0.252  126.8038  220.5424  276.5935
 8JI  H7   H  HCR6  0   0.255  126.5995  220.2145  274.1678
 8JI  H8   H  HCH1  0   0.324  125.5942  220.5850  278.6953
 8JI  H9   H  HCH2  0   0.291  122.1712  222.4054  281.2836
 8JI  H10  H  HCH2  0   0.273  121.5155  221.1689  280.2330
 8JI  H11  H  HNH1  0   0.412  123.5124  220.4853  279.5259
 8JI  H12  H  HOH1  0   0.481  126.4810  223.6243  280.1310
 8JI  H13  H  HOH1  0   0.480  118.9572  222.7176  282.6236
 8JI  H3   H  HCR6  0   0.255  124.4538  220.6999  273.0236

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
 8JI  C01  C06  aromatic  1.389  0.020  1.389
 8JI  C01  C02  aromatic  1.387  0.020  1.387
 8JI  C06  C05  aromatic  1.386  0.020  1.386
 8JI  C02  C03  aromatic  1.390  0.020  1.390
 8JI  C05  C04  aromatic  1.393  0.020  1.393
 8JI  C03  C04  aromatic  1.389  0.020  1.389
 8JI  C04  C07  single    1.513  0.020  1.513
 8JI  O09  C08  double    1.201  0.020  1.201
 8JI  C07  C08  single    1.530  0.020  1.530
 8JI  C07  N11  single    1.439  0.020  1.439
 8JI  C08  O10  single    1.325  0.020  1.325
 8JI  O13  C12  double    1.221  0.020  1.221
 8JI  N11  C12  single    1.346  0.020  1.346
 8JI  C15  C16  single    1.505  0.020  1.505
 8JI  C15  C14  single    1.524  0.020  1.524
 8JI  C12  C14  single    1.512  0.020  1.512
 8JI  O17  C16  double    1.205  0.020  1.205
 8JI  C16  O18  single    1.329  0.020  1.329
 8JI  C15  H1   single    0.970  0.020  1.090
 8JI  C15  H2   single    0.970  0.020  1.090
 8JI  C01  H3   single    0.930  0.020  1.080
 8JI  C02  H4   single    0.930  0.020  1.080
 8JI  C03  H5   single    0.930  0.020  1.080
 8JI  C05  H6   single    0.930  0.020  1.080
 8JI  C06  H7   single    0.930  0.020  1.080
 8JI  C07  H8   single    0.970  0.020  1.090
 8JI  C14  H9   single    0.970  0.020  1.090
 8JI  C14  H10  single    0.970  0.020  1.090
 8JI  N11  H11  single    0.860  0.020  1.020
 8JI  O10  H12  single    0.850  0.020  0.980
 8JI  O18  H13  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
 8JI  H2   C15  H1   106.65  3.000
 8JI  H2   C15  C16  107.29  3.000
 8JI  H1   C15  C16  107.56  3.000
 8JI  H2   C15  C14  109.83  3.000
 8JI  H1   C15  C14  110.80  3.000
 8JI  C16  C15  C14  114.37  3.000
 8JI  H3   C01  C06  120.28  3.000
 8JI  H3   C01  C02  120.27  3.000
 8JI  C06  C01  C02  119.45  3.000
 8JI  H4   C02  C03  119.50  3.000
 8JI  H4   C02  C01  120.07  3.000
 8JI  C03  C02  C01  120.43  3.000
 8JI  H5   C03  C04  120.88  3.000
 8JI  H5   C03  C02  118.71  3.000
 8JI  C04  C03  C02  120.41  3.000
 8JI  C07  C04  C05  118.25  3.000
 8JI  C07  C04  C03  122.92  3.000
 8JI  C05  C04  C03  118.83  3.000
 8JI  H6   C05  C06  119.42  3.000
 8JI  H6   C05  C04  119.70  3.000
 8JI  C06  C05  C04  120.87  3.000
 8JI  H7   C06  C05  119.77  3.000
 8JI  H7   C06  C01  120.22  3.000
 8JI  C05  C06  C01  120.00  3.000
 8JI  H8   C07  N11  105.80  3.000
 8JI  H8   C07  C08  104.63  3.000
 8JI  N11  C07  C08  111.65  3.000
 8JI  H8   C07  C04  107.29  3.000
 8JI  N11  C07  C04  115.13  3.000
 8JI  C08  C07  C04  111.51  3.000
 8JI  O10  C08  O09  124.18  3.000
 8JI  O10  C08  C07  111.16  3.000
 8JI  O09  C08  C07  124.44  3.000
 8JI  O13  C12  N11  122.05  3.000
 8JI  N11  C12  C14  115.06  3.000
 8JI  O13  C12  C14  122.86  3.000
 8JI  H10  C14  H9   106.43  3.000
 8JI  H10  C14  C12  110.29  3.000
 8JI  H9   C14  C12  106.85  3.000
 8JI  H10  C14  C15  110.67  3.000
 8JI  H9   C14  C15  110.70  3.000
 8JI  C12  C14  C15  111.70  3.000
 8JI  O18  C16  O17  123.02  3.000
 8JI  O18  C16  C15  112.72  3.000
 8JI  O17  C16  C15  124.24  3.000
 8JI  H11  N11  C12  119.52  3.000
 8JI  H11  N11  C07  117.39  3.000
 8JI  C12  N11  C07  123.09  3.000
 8JI  H12  O10  C08  109.87  3.000
 8JI  H13  O18  C16  109.90  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
 8JI  CONST_01  C04  C05  C06  C01     0.00   0.0  0
 8JI  CONST_02  C04  C03  C02  C01     0.00   0.0  0
 8JI  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 8JI  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 8JI  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 8JI  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 8JI  CONST_07  C07  C04  C03  C02   180.00   0.0  0
 8JI  CONST_08  C07  C04  C05  C06   180.00   0.0  0
 8JI  CONST_09  H6   C05  C06  C01   180.00   0.0  0
 8JI  CONST_10  H5   C03  C02  C01   180.00   0.0  0
 8JI  CONST_11  H7   C06  C01  C02   180.00   0.0  0
 8JI  CONST_12  H3   C01  C02  C03   180.00   0.0  0
 8JI  CONST_13  H6   C05  C04  C03   180.00   0.0  0
 8JI  CONST_14  H7   C06  C05  C04   180.00   0.0  0
 8JI  CONST_15  H4   C02  C03  C04   180.00   0.0  0
 8JI  CONST_16  H3   C01  C06  C05   180.00   0.0  0
 8JI  CONST_17  H5   C03  C04  C05   180.00   0.0  0
 8JI  CONST_18  H4   C02  C01  C06   180.00   0.0  0
 8JI  CONST_19  O13  C12  N11  C07     0.00   0.0  0
 8JI  CONST_20  C14  C12  N11  C07   180.00   0.0  0
 8JI  CONST_21  H11  N11  C12  C14     0.00   0.0  0
 8JI  CONST_22  H11  N11  C12  O13   180.00   0.0  0
 8JI  CONST_23  H13  O18  C16  C15   180.00   0.0  0
 8JI  CONST_24  H12  O10  C08  C07   180.00   0.0  0
 8JI  CONST_25  H12  O10  C08  O09     0.00   0.0  0
 8JI  CONST_26  H13  O18  C16  O17     0.00   0.0  0
 8JI  Var_01    O13  C12  C14  C15    31.86  30.0  1
 8JI  Var_02    N11  C12  C14  C15  -149.76  30.0  1
 8JI  Var_03    C16  C15  C14  C12  -179.88  30.0  1
 8JI  Var_04    O17  C16  C15  C14  -139.70  30.0  3
 8JI  Var_05    O18  C16  C15  C14    41.98  30.0  3
 8JI  Var_06    H1   C15  C14  C12    58.37  30.0  1
 8JI  Var_07    H2   C15  C14  C12   -59.20  30.0  1
 8JI  Var_08    H9   C14  C15  C16   -60.94  30.0  3
 8JI  Var_09    H10  C14  C15  C16    56.83  30.0  3
 8JI  Var_10    H9   C14  C12  N11    89.04  30.0  3
 8JI  Var_11    H10  C14  C12  N11   -26.25  30.0  3
 8JI  Var_12    H9   C14  C12  O13   -89.33  30.0  3
 8JI  Var_13    H10  C14  C12  O13   155.38  30.0  3
 8JI  Var_14    H1   C15  C16  O17   -16.18  30.0  2
 8JI  Var_15    H2   C15  C16  O17    98.22  30.0  2
 8JI  Var_16    H1   C15  C16  O18   165.50  30.0  2
 8JI  Var_17    H2   C15  C16  O18   -80.10  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
 8JI  chir_01  C07  C04  C08  N11  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
 8JI  plan-1  C01  0.020
 8JI  plan-1  C02  0.020
 8JI  plan-1  C03  0.020
 8JI  plan-1  C04  0.020
 8JI  plan-1  C05  0.020
 8JI  plan-1  C06  0.020
 8JI  plan-1  C07  0.020
 8JI  plan-1  H4   0.020
 8JI  plan-1  H5   0.020
 8JI  plan-1  H6   0.020
 8JI  plan-1  H7   0.020
 8JI  plan-1  H3   0.020
 8JI  plan-2  C07  0.020
 8JI  plan-2  C12  0.020
 8JI  plan-2  C14  0.020
 8JI  plan-2  N11  0.020
 8JI  plan-2  O13  0.020
 8JI  plan-2  H11  0.020
 8JI  plan-3  C07  0.020
 8JI  plan-3  C08  0.020
 8JI  plan-3  O09  0.020
 8JI  plan-3  O10  0.020
 8JI  plan-3  H12  0.020
 8JI  plan-4  C15  0.020
 8JI  plan-4  C16  0.020
 8JI  plan-4  O17  0.020
 8JI  plan-4  O18  0.020
 8JI  plan-4  H13  0.020

