# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 14:10:43 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  33  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   0.341   4.5970   0.9249  -0.4097
 8DM  C2   C  CR16  0  -0.244   3.2903  -0.7828   0.6941
 8DM  C6   C  CR16  0  -0.257   2.1838   1.0517  -0.3668
 8DM  C5   C  CR16  0  -0.287   3.4029   1.5811  -0.7381
 8DM  C1   C  CR6   0  -0.074   2.0989  -0.1451   0.3456
 8DM  C3   C  CR16  0  -0.291   4.5137  -0.2695   0.3207
 8DM  N4   N  NH2   0  -0.829   5.8055   1.4089  -0.8273
 8DM  C    C  C     0   0.556   0.8161  -0.7548   0.7597
 8DM  O    O  O     0  -0.476   0.7389  -1.5629   1.6725
 8DM  N    N  NH1   0  -0.650  -0.2878  -0.3551   0.0721
 8DM  CA   C  CH1   0  -0.194  -1.5647  -0.9627   0.3220
 8DM  CT   C  C     0   0.553  -1.6082  -2.3784  -0.2376
 8DM  O1   O  O     0  -0.420  -0.8510  -2.8071  -1.0656
 8DM  O2   O  OH1   0  -0.575  -2.6091  -3.0731   0.2864
 8DM  CB   C  CH2   0  -0.444  -2.6891  -0.1138  -0.2776
 8DM  CG   C  CH2   0  -0.552  -2.7975   1.2317   0.4191
 8DM  CD   C  C     0   0.544  -3.8782   2.0995  -0.1623
 8DM  OE1  O  OH1   0  -0.594  -4.0637   3.2040   0.5674
 8DM  OE2  O  O     0  -0.398  -4.5054   1.8632  -1.1583
 8DM  H1   H  HCR6  0   0.245   3.2591  -1.7051   1.2587
 8DM  H2   H  HCR6  0   0.223   1.2941   1.6146  -0.6195
 8DM  H3   H  HCR6  0   0.234   3.4315   2.5164  -1.2829
 8DM  H4   H  HCR6  0   0.235   5.4194  -0.7990   0.5898
 8DM  H5   H  HNH2  0   0.363   5.8493   2.3768  -1.0940
 8DM  H6   H  HNH2  0   0.365   6.6215   1.1153  -0.3193
 8DM  H7   H  HNH1  0   0.377  -0.1473   0.0341  -0.8467
 8DM  H8   H  HCH1  0   0.281  -1.7150  -1.0309   1.4019
 8DM  H9   H  HOH1  0   0.460  -2.6348  -3.9556  -0.1068
 8DM  H10  H  HCH2  0   0.245  -2.5244   0.0207  -1.3498
 8DM  H11  H  HCH2  0   0.270  -3.6316  -0.6523  -0.1780
 8DM  H12  H  HCH2  0   0.268  -2.9941   1.0955   1.4859
 8DM  H13  H  HCH2  0   0.275  -1.8573   1.7878   0.3648
 8DM  H14  H  HOH1  0   0.450  -4.7450   3.7423   0.1433

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    1.367  0.020  1.367
 8DM  C3   C4   aromatic  1.403  0.020  1.403
 8DM  C3   C2   aromatic  1.378  0.020  1.378
 8DM  C4   C5   aromatic  1.402  0.020  1.402
 8DM  C2   C1   aromatic  1.396  0.020  1.396
 8DM  C5   C6   aromatic  1.380  0.020  1.380
 8DM  C1   C6   aromatic  1.395  0.020  1.395
 8DM  C1   C    single    1.479  0.020  1.479
 8DM  O    C    double    1.222  0.020  1.222
 8DM  C    N    single    1.361  0.020  1.361
 8DM  CG   CD   single    1.503  0.020  1.503
 8DM  CG   CB   single    1.519  0.020  1.519
 8DM  N    CA   single    1.436  0.020  1.436
 8DM  OE2  CD   double    1.201  0.020  1.201
 8DM  CD   OE1  single    1.337  0.020  1.337
 8DM  CB   CA   single    1.531  0.020  1.531
 8DM  CA   CT   single    1.523  0.020  1.523
 8DM  CT   O1   double    1.201  0.020  1.201
 8DM  CT   O2   single    1.326  0.020  1.326
 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  O2   H9   single    0.850  0.020  0.980
 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
 8DM  OE1  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
 8DM  N4   C4   C3   120.87  3.000
 8DM  C3   C4   C5   118.04  3.000
 8DM  N4   C4   C5   121.05  3.000
 8DM  H1   C2   C3   118.97  3.000
 8DM  H1   C2   C1   119.69  3.000
 8DM  C3   C2   C1   121.33  3.000
 8DM  H2   C6   C1   121.00  3.000
 8DM  H2   C6   C5   117.63  3.000
 8DM  C1   C6   C5   121.34  3.000
 8DM  H3   C5   C6   119.34  3.000
 8DM  H3   C5   C4   119.99  3.000
 8DM  C6   C5   C4   120.67  3.000
 8DM  C    C1   C6   123.31  3.000
 8DM  C    C1   C2   118.82  3.000
 8DM  C6   C1   C2   117.87  3.000
 8DM  H4   C3   C2   119.53  3.000
 8DM  H4   C3   C4   119.74  3.000
 8DM  C2   C3   C4   120.73  3.000
 8DM  H6   N4   H5   112.34  3.000
 8DM  H6   N4   C4   117.38  3.000
 8DM  H5   N4   C4   117.42  3.000
 8DM  N    C    O    121.38  3.000
 8DM  N    C    C1   116.16  3.000
 8DM  O    C    C1   122.46  3.000
 8DM  H7   N    CA   116.49  3.000
 8DM  H7   N    C    117.46  3.000
 8DM  CA   N    C    120.61  3.000
 8DM  H8   CA   CB   108.70  3.000
 8DM  H8   CA   CT   107.54  3.000
 8DM  CB   CA   CT   110.52  3.000
 8DM  H8   CA   N    108.71  3.000
 8DM  CT   CA   N    110.78  3.000
 8DM  CB   CA   N    110.50  3.000
 8DM  O2   CT   O1   124.13  3.000
 8DM  O2   CT   CA   111.30  3.000
 8DM  O1   CT   CA   124.55  3.000
 8DM  H9   O2   CT   109.73  3.000
 8DM  H11  CB   H10  106.30  3.000
 8DM  H11  CB   CG   109.51  3.000
 8DM  H10  CB   CG   110.59  3.000
 8DM  H11  CB   CA   108.99  3.000
 8DM  H10  CB   CA   109.98  3.000
 8DM  CG   CB   CA   111.34  3.000
 8DM  H13  CG   H12  105.45  3.000
 8DM  H13  CG   CD   107.78  3.000
 8DM  H12  CG   CD   108.66  3.000
 8DM  H13  CG   CB   111.48  3.000
 8DM  H12  CG   CB   110.49  3.000
 8DM  CD   CG   CB   112.67  3.000
 8DM  OE2  CD   OE1  122.89  3.000
 8DM  OE1  CD   CG   111.45  3.000
 8DM  OE2  CD   CG   125.65  3.000
 8DM  H14  OE1  CD   108.58  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  CONST_20  H9   O2   CT  CA  180.00   0.0  0
 8DM  CONST_21  H14  OE1  CD  CG  180.00   0.0  0
 8DM  Var_01    O    C    C1  C2   20.27  30.0  2
 8DM  Var_02    CD   CG   CB  CA  179.02  30.0  1
 8DM  Var_03    OE2  CD   CG  CB   -8.17  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-4  H9   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
 8DM  plan-5  H14  0.020

