# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 20:15:01 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  29  18  .  2022-09-16  2022-09-16
;
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  -0.579  120.7248  222.7842  279.6678
 8JI  C01  C  CR16   0  -0.276  124.1911  221.0727  274.2410
 8JI  C02  C  CR16   0  -0.241  123.2009  221.5199  275.1016
 8JI  C03  C  CR16   0  -0.318  123.4546  221.6474  276.4638
 8JI  C04  C  CR6    0   0.170  124.7047  221.3427  276.9922
 8JI  C05  C  CR16   0  -0.286  125.6888  220.8820  276.1153
 8JI  C06  C  CR16   0  -0.250  125.4394  220.7456  274.7591
 8JI  C07  C  CH1    0  -0.290  125.0299  221.4385  278.4641
 8JI  C08  C  C      0   0.428  126.1100  222.5236  278.8338
 8JI  C12  C  C      0   0.529  123.2186  222.6858  279.5772
 8JI  C14  C  CH2    0  -0.547  122.0037  222.5511  280.4666
 8JI  C16  C  C      0   0.414  119.4238  222.6977  280.4917
 8JI  N11  N  NH1    0  -0.633  123.8647  221.5381  279.3090
 8JI  O09  O  O      0  -0.581  126.6845  223.0959  277.8954
 8JI  O10  O  OC    -1  -0.602  126.3258  222.6398  280.0510
 8JI  O13  O  O      0  -0.504  123.5534  223.7638  279.1010
 8JI  O17  O  O      0  -0.616  118.3762  222.5283  279.8361
 8JI  O18  O  OC    -1  -0.603  119.5197  222.8263  281.7280
 8JI  H1   H  HCH2   0   0.221  120.6696  222.0736  278.8374
 8JI  H2   H  HCH2   0   0.231  120.7645  223.7754  279.2032
 8JI  H5   H  HCR6   0   0.246  122.6506  221.9736  277.1096
 8JI  H6   H  HCR6   0   0.235  126.6631  220.6111  276.5033
 8JI  H7   H  HCR6   0   0.244  126.2202  220.3804  274.1035
 8JI  H8   H  HCH1   0   0.258  125.5010  220.4886  278.7397
 8JI  H9   H  HCH2   0   0.242  122.0795  223.2909  281.2653
 8JI  H10  H  HCH2   0   0.230  121.9719  221.5704  280.9459
 8JI  H11  H  HNH1   0   0.391  123.5144  220.6903  279.7222
 8JI  H3   H  HCR6   0   0.245  123.9922  220.9672  273.1822
 8JI  H4   H  HCR6   0   0.244  122.2189  221.7668  274.7175

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  1.391  0.020  1.391
 8JI  C01  C02  aromatic  1.386  0.020  1.386
 8JI  C06  C05  aromatic  1.386  0.020  1.386
 8JI  C02  C03  aromatic  1.391  0.020  1.391
 8JI  C05  C04  aromatic  1.396  0.020  1.396
 8JI  C03  C04  aromatic  1.391  0.020  1.391
 8JI  C04  C07  single    1.510  0.020  1.510
 8JI  O09  C08  deloc     1.240  0.020  1.240
 8JI  C07  C08  single    1.575  0.020  1.575
 8JI  C07  N11  single    1.443  0.020  1.443
 8JI  C08  O10  deloc     1.242  0.020  1.242
 8JI  O13  C12  double    1.225  0.020  1.225
 8JI  N11  C12  single    1.344  0.020  1.344
 8JI  C15  C16  single    1.542  0.020  1.542
 8JI  C15  C14  single    1.526  0.020  1.526
 8JI  C12  C14  single    1.512  0.020  1.512
 8JI  O17  C16  deloc     1.247  0.020  1.247
 8JI  C16  O18  deloc     1.247  0.020  1.247
 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

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   105.52  3.000
 8JI  H2   C15  C16  107.92  3.000
 8JI  H1   C15  C16  109.05  3.000
 8JI  H2   C15  C14  109.26  3.000
 8JI  H1   C15  C14  109.90  3.000
 8JI  C16  C15  C14  114.76  3.000
 8JI  H3   C01  C06  120.43  3.000
 8JI  H3   C01  C02  120.50  3.000
 8JI  C06  C01  C02  119.07  3.000
 8JI  H4   C02  C03  119.45  3.000
 8JI  H4   C02  C01  120.08  3.000
 8JI  C03  C02  C01  120.47  3.000
 8JI  H5   C03  C04  120.48  3.000
 8JI  H5   C03  C02  118.47  3.000
 8JI  C04  C03  C02  121.04  3.000
 8JI  C07  C04  C05  118.76  3.000
 8JI  C07  C04  C03  123.35  3.000
 8JI  C05  C04  C03  117.85  3.000
 8JI  H6   C05  C06  119.20  3.000
 8JI  H6   C05  C04  119.45  3.000
 8JI  C06  C05  C04  121.35  3.000
 8JI  H7   C06  C05  119.73  3.000
 8JI  H7   C06  C01  120.06  3.000
 8JI  C05  C06  C01  120.20  3.000
 8JI  H8   C07  N11  105.06  3.000
 8JI  H8   C07  C08  104.08  3.000
 8JI  N11  C07  C08  111.64  3.000
 8JI  H8   C07  C04  106.43  3.000
 8JI  N11  C07  C04  113.65  3.000
 8JI  C08  C07  C04  114.84  3.000
 8JI  O10  C08  O09  128.17  3.000
 8JI  O10  C08  C07  114.44  3.000
 8JI  O09  C08  C07  117.26  3.000
 8JI  O13  C12  N11  122.85  3.000
 8JI  N11  C12  C14  115.32  3.000
 8JI  O13  C12  C14  121.78  3.000
 8JI  H10  C14  H9   106.83  3.000
 8JI  H10  C14  C12  111.20  3.000
 8JI  H9   C14  C12  108.32  3.000
 8JI  H10  C14  C15  110.03  3.000
 8JI  H9   C14  C15  109.75  3.000
 8JI  C12  C14  C15  110.61  3.000
 8JI  O18  C16  O17  126.86  3.000
 8JI  O18  C16  C15  117.32  3.000
 8JI  O17  C16  C15  115.80  3.000
 8JI  H11  N11  C12  118.05  3.000
 8JI  H11  N11  C07  117.61  3.000
 8JI  C12  N11  C07  124.33  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  Var_01    O13  C12  C14  C15    68.30  30.0  1
 8JI  Var_02    N11  C12  C14  C15  -109.20  30.0  1
 8JI  Var_03    C16  C15  C14  C12  -178.80  30.0  1
 8JI  Var_04    O17  C16  C15  C14  -161.67  30.0  3
 8JI  Var_05    O18  C16  C15  C14    19.56  30.0  3
 8JI  Var_06    H1   C15  C14  C12    57.88  30.0  1
 8JI  Var_07    H2   C15  C14  C12   -57.45  30.0  1
 8JI  Var_08    H9   C14  C15  C16   -59.34  30.0  3
 8JI  Var_09    H10  C14  C15  C16    57.95  30.0  3
 8JI  Var_10    H9   C14  C12  N11   130.48  30.0  3
 8JI  Var_11    H10  C14  C12  N11    13.37  30.0  3
 8JI  Var_12    H9   C14  C12  O13   -52.02  30.0  3
 8JI  Var_13    H10  C14  C12  O13  -169.13  30.0  3
 8JI  Var_14    H1   C15  C16  O17   -37.90  30.0  2
 8JI  Var_15    H2   C15  C16  O17    76.25  30.0  2
 8JI  Var_16    H1   C15  C16  O18   143.33  30.0  2
 8JI  Var_17    H2   C15  C16  O18  -102.52  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  H5   0.020
 8JI  plan-1  H6   0.020
 8JI  plan-1  H7   0.020
 8JI  plan-1  H3   0.020
 8JI  plan-1  H4   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-4  C15  0.020
 8JI  plan-4  C16  0.020
 8JI  plan-4  O17  0.020
 8JI  plan-4  O18  0.020

