# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 17:48:24 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: N-(4-aminobenzene-1-carbonyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(cc1)C(=O)N[C@@H](CCC(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
 8DM  8DM  'N-(4-aminobenzene-1-carbonyl)-L-glutamic acid'  ligand  31  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_8DM
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
 8DM  C4   C  CR6    0   0.317   4.6053   0.9393  -0.4050
 8DM  C2   C  CR16   0  -0.267   3.2978  -0.7142   0.7812
 8DM  C6   C  CR16   0  -0.290   2.1870   1.0115  -0.4383
 8DM  C5   C  CR16   0  -0.314   3.4065   1.5407  -0.8142
 8DM  C1   C  CR6    0  -0.076   2.1021  -0.1314   0.3591
 8DM  C3   C  CR16   0  -0.317   4.5235  -0.2023   0.4063
 8DM  N4   N  NH2    0  -0.856   5.8165   1.4240  -0.8186
 8DM  C    C  C      0   0.537   0.8161  -0.7375   0.7995
 8DM  O    O  O      0  -0.513   0.7743  -1.5067   1.7564
 8DM  N    N  NH1    0  -0.638  -0.2840  -0.3765   0.1181
 8DM  CA   C  CH1    0  -0.192  -1.5680  -1.0015   0.3413
 8DM  CT   C  C      0   0.409  -1.6354  -2.4456  -0.2193
 8DM  O1   O  O      0  -0.600  -0.7230  -2.8194  -0.9760
 8DM  O2   O  OC    -1  -0.620  -2.6364  -3.1012   0.1352
 8DM  CB   C  CH2    0  -0.442  -2.6728  -0.1309  -0.2597
 8DM  CG   C  CH2    0  -0.575  -2.7831   1.2381   0.3901
 8DM  CD   C  C      0   0.411  -3.9106   2.1417  -0.1385
 8DM  OE1  O  OC    -1  -0.634  -3.9359   3.3043   0.3198
 8DM  OE2  O  O      0  -0.609  -4.7116   1.6587  -0.9631
 8DM  H1   H  HCR6   0   0.250   3.2693  -1.5926   1.4127
 8DM  H2   H  HCR6   0   0.249   1.2929   1.5317  -0.7607
 8DM  H3   H  HCR6   0   0.260   3.4363   2.4344  -1.4261
 8DM  H4   H  HCR6   0   0.258   5.4333  -0.6873   0.7395
 8DM  H5   H  HNH2   0   0.385   5.8377   2.3746  -1.1490
 8DM  H6   H  HNH2   0   0.385   6.6180   1.1865  -0.2572
 8DM  H7   H  HNH1   0   0.386  -0.1568   0.0579  -0.7818
 8DM  H8   H  HCH1   0   0.225  -1.7303  -1.0590   1.4214
 8DM  H10  H  HCH2   0   0.208  -2.5066  -0.0267  -1.3379
 8DM  H11  H  HCH2   0   0.225  -3.6145  -0.6679  -0.1508
 8DM  H12  H  HCH2   0   0.219  -2.9340   1.1120   1.4694
 8DM  H13  H  HCH2   0   0.219  -1.8389   1.7842   0.3005

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
 8DM  N4   C4   single    1.369  0.020  1.369
 8DM  C3   C4   aromatic  1.403  0.020  1.403
 8DM  C3   C2   aromatic  1.380  0.020  1.380
 8DM  C4   C5   aromatic  1.402  0.020  1.402
 8DM  C2   C1   aromatic  1.396  0.020  1.396
 8DM  C5   C6   aromatic  1.381  0.020  1.381
 8DM  C1   C6   aromatic  1.396  0.020  1.396
 8DM  C1   C    single    1.488  0.020  1.488
 8DM  O    C    double    1.228  0.020  1.228
 8DM  C    N    single    1.343  0.020  1.343
 8DM  CG   CD   single    1.538  0.020  1.538
 8DM  CG   CB   single    1.519  0.020  1.519
 8DM  N    CA   single    1.445  0.020  1.445
 8DM  OE2  CD   deloc     1.247  0.020  1.247
 8DM  CD   OE1  deloc     1.250  0.020  1.250
 8DM  CB   CA   single    1.530  0.020  1.530
 8DM  CA   CT   single    1.551  0.020  1.551
 8DM  CT   O1   deloc     1.243  0.020  1.243
 8DM  CT   O2   deloc     1.248  0.020  1.248
 8DM  C2   H1   single    0.930  0.020  1.080
 8DM  C6   H2   single    0.930  0.020  1.080
 8DM  C5   H3   single    0.930  0.020  1.080
 8DM  C3   H4   single    0.930  0.020  1.080
 8DM  N4   H5   single    0.890  0.020  1.040
 8DM  N4   H6   single    0.890  0.020  1.040
 8DM  N    H7   single    0.890  0.020  1.040
 8DM  CA   H8   single    0.970  0.020  1.090
 8DM  CB   H10  single    0.970  0.020  1.090
 8DM  CB   H11  single    0.970  0.020  1.090
 8DM  CG   H12  single    0.970  0.020  1.090
 8DM  CG   H13  single    0.970  0.020  1.090

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
 8DM  N4   C4  C3   120.97  3.000
 8DM  C3   C4  C5   117.89  3.000
 8DM  N4   C4  C5   121.10  3.000
 8DM  H1   C2  C3   118.88  3.000
 8DM  H1   C2  C1   119.53  3.000
 8DM  C3   C2  C1   121.59  3.000
 8DM  H2   C6  C1   120.85  3.000
 8DM  H2   C6  C5   117.62  3.000
 8DM  C1   C6  C5   121.51  3.000
 8DM  H3   C5  C6   119.59  3.000
 8DM  H3   C5  C4   119.67  3.000
 8DM  C6   C5  C4   120.73  3.000
 8DM  C    C1  C6   123.70  3.000
 8DM  C    C1  C2   118.74  3.000
 8DM  C6   C1  C2   117.55  3.000
 8DM  H4   C3  C2   119.74  3.000
 8DM  H4   C3  C4   119.54  3.000
 8DM  C2   C3  C4   120.72  3.000
 8DM  H6   N4  H5   112.89  3.000
 8DM  H6   N4  C4   116.90  3.000
 8DM  H5   N4  C4   116.89  3.000
 8DM  N    C   O    122.38  3.000
 8DM  N    C   C1   116.62  3.000
 8DM  O    C   C1   120.99  3.000
 8DM  H7   N   CA   115.89  3.000
 8DM  H7   N   C    117.75  3.000
 8DM  CA   N   C    122.20  3.000
 8DM  H8   CA  CB   108.11  3.000
 8DM  H8   CA  CT   107.55  3.000
 8DM  CB   CA  CT   110.89  3.000
 8DM  H8   CA  N    107.88  3.000
 8DM  CT   CA  N    112.68  3.000
 8DM  CB   CA  N    109.57  3.000
 8DM  O2   CT  O1   127.14  3.000
 8DM  O2   CT  CA   114.93  3.000
 8DM  O1   CT  CA   117.92  3.000
 8DM  H11  CB  H10  106.04  3.000
 8DM  H11  CB  CG   109.79  3.000
 8DM  H10  CB  CG   110.25  3.000
 8DM  H11  CB  CA   107.73  3.000
 8DM  H10  CB  CA   109.34  3.000
 8DM  CG   CB  CA   113.40  3.000
 8DM  H13  CG  H12  104.87  3.000
 8DM  H13  CG  CD   108.12  3.000
 8DM  H12  CG  CD   107.74  3.000
 8DM  H13  CG  CB   110.60  3.000
 8DM  H12  CG  CB   109.10  3.000
 8DM  CD   CG  CB   115.82  3.000
 8DM  OE2  CD  OE1  126.14  3.000
 8DM  OE1  CD  CG   115.80  3.000
 8DM  OE2  CD  CG   118.07  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
 8DM  CONST_01  C1   C2  C3  C4     0.00   0.0  0
 8DM  CONST_02  C1   C6  C5  C4     0.00   0.0  0
 8DM  CONST_03  C5   C4  C3  C2     0.00   0.0  0
 8DM  CONST_04  C5   C6  C1  C2     0.00   0.0  0
 8DM  CONST_05  C3   C4  C5  C6     0.00   0.0  0
 8DM  CONST_06  C3   C2  C1  C6     0.00   0.0  0
 8DM  CONST_07  N4   C4  C3  C2   180.00   0.0  0
 8DM  CONST_08  N4   C4  C5  C6   180.00   0.0  0
 8DM  CONST_09  C    C1  C6  C5   180.00   0.0  0
 8DM  CONST_10  C    C1  C2  C3   180.00   0.0  0
 8DM  CONST_11  H1   C2  C3  C4   180.00   0.0  0
 8DM  CONST_12  H2   C6  C5  C4   180.00   0.0  0
 8DM  CONST_13  H4   C3  C4  C5   180.00   0.0  0
 8DM  CONST_14  H3   C5  C6  C1   180.00   0.0  0
 8DM  CONST_17  CA   N   C   C1   180.00   0.0  0
 8DM  CONST_19  CA   N   C   O      0.00   0.0  0
 8DM  Var_01    O    C   C1  C2    17.85  30.0  2
 8DM  Var_02    CD   CG  CB  CA  -177.90  30.0  2
 8DM  Var_03    OE2  CD  CG  CB     5.98  30.0  3

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
 8DM  chir_01  CA  N  CB  CT  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
 8DM  plan-1  C4   0.020
 8DM  plan-1  C2   0.020
 8DM  plan-1  C6   0.020
 8DM  plan-1  C5   0.020
 8DM  plan-1  C1   0.020
 8DM  plan-1  C3   0.020
 8DM  plan-1  N4   0.020
 8DM  plan-1  C    0.020
 8DM  plan-1  H1   0.020
 8DM  plan-1  H2   0.020
 8DM  plan-1  H3   0.020
 8DM  plan-1  H4   0.020
 8DM  plan-2  C1   0.020
 8DM  plan-2  C    0.020
 8DM  plan-2  O    0.020
 8DM  plan-2  N    0.020
 8DM  plan-2  CA   0.020
 8DM  plan-2  H7   0.020
 8DM  plan-3  C4   0.020
 8DM  plan-3  N4   0.020
 8DM  plan-3  H5   0.020
 8DM  plan-3  H6   0.020
 8DM  plan-4  CA   0.020
 8DM  plan-4  CT   0.020
 8DM  plan-4  O1   0.020
 8DM  plan-4  O2   0.020
 8DM  plan-5  CG   0.020
 8DM  plan-5  CD   0.020
 8DM  plan-5  OE1  0.020
 8DM  plan-5  OE2  0.020

