# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:33:31 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  20  11  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.532  -2.0469  -0.6278  -0.1987
 3AZ  N    N  NH2   0  -0.793   2.9703  -1.7059  -0.4510
 3AZ  O    O  O     0  -0.440  -2.0590  -1.8328  -0.2874
 3AZ  C1   C  CR6   0   0.106   1.5909   0.1926   0.2699
 3AZ  C2   C  CR16  0  -0.302   0.4003  -0.4990   0.0837
 3AZ  C3   C  CR6   0  -0.061  -0.8145   0.1761  -0.0059
 3AZ  C4   C  CR16  0  -0.279  -0.8447   1.5676   0.0856
 3AZ  C5   C  CR16  0  -0.227   0.3395   2.2633   0.2649
 3AZ  C6   C  CR16  0  -0.296   1.5455   1.5813   0.3537
 3AZ  OXT  O  OH1   0  -0.595  -3.1461   0.1117  -0.2637
 3AZ  HN   H  HNH2  0   0.345   3.0605  -1.4109  -1.4151
 3AZ  HNA  H  HNH2  0   0.355   3.8099  -2.2283  -0.2381
 3AZ  H2   H  HCR6  0   0.256   0.4267  -1.5777   0.0042
 3AZ  H4   H  HCR6  0   0.265  -1.7751   2.1132   0.0132
 3AZ  H5   H  HCR6  0   0.263   0.3248   3.3432   0.3285
 3AZ  H6   H  HCR6  0   0.258   2.4653   2.1390   0.4869
 3AZ  HA   H  HCH2  0   0.245   2.9999  -0.8784   1.4436
 3AZ  HAA  H  HCH2  0   0.218   3.7186   0.1807   0.2533
 3AZ  HXT  H  HOH1  0   0.487  -3.9194  -0.4592  -0.3832
 3AZ  CA   C  CH2   0  -0.337   2.9030  -0.5380   0.4085

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    double    1.231  0.020  1.231
 3AZ  C    C3   single    1.484  0.020  1.484
 3AZ  C    OXT  single    1.326  0.020  1.326
 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  1.389  0.020  1.389
 3AZ  C1   C6   aromatic  1.392  0.020  1.392
 3AZ  C1   CA   single    1.508  0.020  1.508
 3AZ  C2   C3   aromatic  1.393  0.020  1.393
 3AZ  C2   H2   single    0.930  0.020  1.080
 3AZ  C3   C4   aromatic  1.395  0.020  1.395
 3AZ  C4   C5   aromatic  1.385  0.020  1.385
 3AZ  C4   H4   single    0.930  0.020  1.080
 3AZ  C5   C6   aromatic  1.388  0.020  1.388
 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
 3AZ  OXT  HXT  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
 3AZ  OXT  C    C3  113.11  3.000
 3AZ  OXT  C    O   122.96  3.000
 3AZ  C3   C    O   123.92  3.000
 3AZ  HNA  N    HN  106.08  3.000
 3AZ  HNA  N    CA  109.23  3.000
 3AZ  HN   N    CA  109.48  3.000
 3AZ  CA   C1   C6  120.40  3.000
 3AZ  CA   C1   C2  121.11  3.000
 3AZ  C6   C1   C2  118.48  3.000
 3AZ  H2   C2   C3  119.99  3.000
 3AZ  H2   C2   C1  119.03  3.000
 3AZ  C3   C2   C1  120.98  3.000
 3AZ  C4   C3   C2  119.88  3.000
 3AZ  C4   C3   C   122.07  3.000
 3AZ  C2   C3   C   118.04  3.000
 3AZ  H4   C4   C5  119.41  3.000
 3AZ  H4   C4   C3  121.18  3.000
 3AZ  C5   C4   C3  119.41  3.000
 3AZ  H5   C5   C6  119.90  3.000
 3AZ  H5   C5   C4  119.82  3.000
 3AZ  C6   C5   C4  120.28  3.000
 3AZ  H6   C6   C5  119.49  3.000
 3AZ  H6   C6   C1  119.54  3.000
 3AZ  C5   C6   C1  120.97  3.000
 3AZ  HXT  OXT  C   109.82  3.000
 3AZ  HAA  CA   HA  105.76  3.000
 3AZ  HAA  CA   C1  108.43  3.000
 3AZ  HA   CA   C1  108.34  3.000
 3AZ  HAA  CA   N   114.11  3.000
 3AZ  HA   CA   N   110.00  3.000
 3AZ  C1   CA   N   112.06  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  CONST_15  HXT  OXT  C   C3  180.00   0.0  0
 3AZ  Var_01    C2   C1   CA  N    36.94  30.0  3
 3AZ  Var_02    C2   C3   C   O    -0.28  30.0  2
 3AZ  Var_03    HN   N    CA  C1   71.55  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
 3AZ  plan-2  HXT  0.020

