# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:03:35 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 3-(aminomethyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1cccc(c1)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
 3AZ  3AZ  '3-(aminomethyl)benzoic acid'  peptide  19  11  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3AZ
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
 3AZ  C    C  C      0   0.394  -2.1503  -0.6115  -0.2342
 3AZ  N    N  NH2    0  -0.791   3.0020  -1.6271  -0.5203
 3AZ  O    O  O      0  -0.594  -2.0613  -1.8546  -0.2505
 3AZ  C1   C  CR6    0   0.111   1.5572   0.1922   0.2668
 3AZ  C2   C  CR16   0  -0.333   0.3606  -0.4988   0.0897
 3AZ  C3   C  CR6    0  -0.081  -0.8534   0.1668  -0.0473
 3AZ  C4   C  CR16   0  -0.308  -0.8604   1.5607  -0.0112
 3AZ  C5   C  CR16   0  -0.231   0.3218   2.2638   0.1602
 3AZ  C6   C  CR16   0  -0.322   1.5256   1.5827   0.2964
 3AZ  OXT  O  OC    -1  -0.596  -3.1931   0.0607  -0.3548
 3AZ  HN   H  HNH2   0   0.341   3.1053  -1.2368  -1.4486
 3AZ  HNA  H  HNH2   0   0.350   3.8606  -2.1289  -0.3329
 3AZ  H2   H  HCR6   0   0.232   0.3769  -1.5804   0.0534
 3AZ  H4   H  HCR6   0   0.239  -1.7954   2.0936  -0.1228
 3AZ  H5   H  HCR6   0   0.244   0.3110   3.3465   0.1819
 3AZ  H6   H  HCR6   0   0.243   2.4476   2.1387   0.4242
 3AZ  HA   H  HCH2   0   0.234   2.8827  -0.9896   1.4435
 3AZ  HAA  H  HCH2   0   0.211   3.6818   0.1815   0.4180
 3AZ  CA   C  CH2    0  -0.343   2.8599  -0.5468   0.4430

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
 3AZ  C   O    deloc     1.231  0.020  1.231
 3AZ  C   C3   single    1.524  0.020  1.524
 3AZ  C   OXT  deloc     1.247  0.020  1.247
 3AZ  N   CA   single    1.458  0.019  1.458
 3AZ  N   HN   single    0.890  0.020  1.040
 3AZ  N   HNA  single    0.890  0.020  1.040
 3AZ  C1  C2   aromatic  1.393  0.020  1.393
 3AZ  C1  C6   aromatic  1.391  0.020  1.391
 3AZ  C1  CA   single    1.508  0.020  1.508
 3AZ  C2  C3   aromatic  1.391  0.020  1.391
 3AZ  C2  H2   single    0.930  0.020  1.080
 3AZ  C3  C4   aromatic  1.394  0.020  1.394
 3AZ  C4  C5   aromatic  1.386  0.020  1.386
 3AZ  C4  H4   single    0.930  0.020  1.080
 3AZ  C5  C6   aromatic  1.390  0.020  1.390
 3AZ  C5  H5   single    0.930  0.020  1.080
 3AZ  C6  H6   single    0.930  0.020  1.080
 3AZ  CA  HA   single    0.970  0.020  0.970
 3AZ  CA  HAA  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
 3AZ  OXT  C   C3  116.63  3.000
 3AZ  OXT  C   O   126.61  3.000
 3AZ  C3   C   O   116.76  3.000
 3AZ  HNA  N   HN  105.93  3.000
 3AZ  HNA  N   CA  109.18  3.000
 3AZ  HN   N   CA  109.32  3.000
 3AZ  CA   C1  C6  120.46  3.000
 3AZ  CA   C1  C2  120.92  3.000
 3AZ  C6   C1  C2  118.62  3.000
 3AZ  H2   C2  C3  119.21  3.000
 3AZ  H2   C2  C1  119.15  3.000
 3AZ  C3   C2  C1  121.65  3.000
 3AZ  C4   C3  C2  118.69  3.000
 3AZ  C4   C3  C   120.62  3.000
 3AZ  C2   C3  C   120.68  3.000
 3AZ  H4   C4  C5  120.00  3.000
 3AZ  H4   C4  C3  119.61  3.000
 3AZ  C5   C4  C3  120.39  3.000
 3AZ  H5   C5  C6  119.78  3.000
 3AZ  H5   C5  C4  120.07  3.000
 3AZ  C6   C5  C4  120.15  3.000
 3AZ  H6   C6  C5  119.79  3.000
 3AZ  H6   C6  C1  119.72  3.000
 3AZ  C5   C6  C1  120.49  3.000
 3AZ  HAA  CA  HA  105.88  3.000
 3AZ  HAA  CA  C1  108.59  3.000
 3AZ  HA   CA  C1  108.85  3.000
 3AZ  HAA  CA  N   113.84  3.000
 3AZ  HA   CA  N   110.00  3.000
 3AZ  C1   CA  N   111.78  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
 3AZ  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 3AZ  CONST_02  C4  C5  C6  C1    0.00   0.0  0
 3AZ  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 3AZ  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 3AZ  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 3AZ  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 3AZ  CONST_07  C1  C2  C3  C   180.00   0.0  0
 3AZ  CONST_08  C5  C4  C3  C   180.00   0.0  0
 3AZ  CONST_09  CA  C1  C2  C3  180.00   0.0  0
 3AZ  CONST_10  CA  C1  C6  C5  180.00   0.0  0
 3AZ  CONST_11  H5  C5  C6  C1  180.00   0.0  0
 3AZ  CONST_12  H6  C6  C1  C2  180.00   0.0  0
 3AZ  CONST_13  H4  C4  C3  C2  180.00   0.0  0
 3AZ  CONST_14  H2  C2  C3  C4  180.00   0.0  0
 3AZ  Var_01    C2  C1  CA  N    45.40  30.0  3
 3AZ  Var_02    C2  C3  C   O     0.31  30.0  2
 3AZ  Var_03    HN  N   CA  C1   67.83  30.0  3

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
 3AZ  plan-1  C    0.020
 3AZ  plan-1  C1   0.020
 3AZ  plan-1  C2   0.020
 3AZ  plan-1  C3   0.020
 3AZ  plan-1  C4   0.020
 3AZ  plan-1  C5   0.020
 3AZ  plan-1  C6   0.020
 3AZ  plan-1  H2   0.020
 3AZ  plan-1  H4   0.020
 3AZ  plan-1  H5   0.020
 3AZ  plan-1  H6   0.020
 3AZ  plan-1  CA   0.020
 3AZ  plan-2  C    0.020
 3AZ  plan-2  O    0.020
 3AZ  plan-2  C3   0.020
 3AZ  plan-2  OXT  0.020

