# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:01 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-(2-amino-2-carboxyethyl)-5-methylisoxazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C(O)=O)c1CC(N)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
 AM1  AM1  '4-(2-amino-2-carboxyethyl)-5-methylisoxazole-3-carboxylic acid'  ligand  23  15  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AM1
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
 AM1  O1   O  OC    -1  -0.591   3.0034  -2.1290   0.4870
 AM1  C1   C  C      0   0.377   1.8836  -1.6953   0.1719
 AM1  O2   O  O      0  -0.569   0.8442  -2.3418  -0.0447
 AM1  C2   C  CR5    0   0.048   1.7603  -0.1874   0.0324
 AM1  N1   N  N      0  -0.173   2.7809   0.5727   0.3174
 AM1  O3   O  O      0  -0.349   2.3835   1.8534   0.0964
 AM1  C3   C  CR5    0   0.386   1.1131   1.8657  -0.3273
 AM1  C4   C  CR5    0  -0.138   0.6460   0.5918  -0.4049
 AM1  C5   C  CH2    0  -0.523  -0.7286   0.1751  -0.8016
 AM1  C6   C  CH1    0  -0.201  -1.6688  -0.0543   0.4057
 AM1  N2   N  NH2    0  -0.795  -1.7552   1.0638   1.3262
 AM1  C7   C  C      0   0.395  -3.0593  -0.4353  -0.1431
 AM1  O4   O  O      0  -0.608  -3.9628   0.4211  -0.0636
 AM1  O5   O  OC    -1  -0.620  -3.1529  -1.5638  -0.6667
 AM1  C8   C  CH3    0  -0.754   0.4933   3.1835  -0.6072
 AM1  H2   H  HCH2   0   0.219  -1.1631   0.9557  -1.4361
 AM1  H3   H  HCH2   0   0.237  -0.6890  -0.7375  -1.3924
 AM1  H4   H  HCH1   0   0.217  -1.2618  -0.9102   0.9508
 AM1  H5   H  HNH2   0   0.333  -0.8251   1.3715   1.5836
 AM1  H6   H  HNH2   0   0.324  -2.2046   1.8444   0.8636
 AM1  H8   H  HCH3   0   0.261  -0.2575   3.0899  -1.3896
 AM1  H9   H  HCH3   0   0.261  -0.0018   3.5875   0.2775
 AM1  H10  H  HCH3   0   0.265   1.2353   3.9128  -0.9303

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
 AM1  O1  C1   deloc     1.241  0.020  1.241
 AM1  C1  O2   deloc     1.243  0.020  1.243
 AM1  C1  C2   single    1.519  0.020  1.519
 AM1  C2  N1   aromatic  1.304  0.020  1.304
 AM1  C2  C4   aromatic  1.428  0.020  1.428
 AM1  N1  O3   aromatic  1.359  0.020  1.359
 AM1  O3  C3   aromatic  1.339  0.020  1.339
 AM1  C3  C4   aromatic  1.359  0.020  1.359
 AM1  C3  C8   single    1.483  0.020  1.483
 AM1  C4  C5   single    1.490  0.020  1.490
 AM1  C5  C6   single    1.547  0.020  1.547
 AM1  C5  H2   single    0.970  0.020  1.090
 AM1  C5  H3   single    0.970  0.020  1.090
 AM1  C6  N2   single    1.451  0.020  1.451
 AM1  C6  C7   single    1.543  0.020  1.543
 AM1  C6  H4   single    0.970  0.020  1.090
 AM1  N2  H5   single    0.890  0.020  1.040
 AM1  N2  H6   single    0.890  0.020  1.040
 AM1  C7  O4   deloc     1.247  0.020  1.247
 AM1  C7  O5   deloc     1.248  0.020  1.248
 AM1  C8  H8   single    0.970  0.020  1.090
 AM1  C8  H9   single    0.970  0.020  1.090
 AM1  C8  H10  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
 AM1  C2   C1  O2  115.61  3.000
 AM1  C2   C1  O1  116.31  3.000
 AM1  O2   C1  O1  128.08  3.000
 AM1  C4   C2  N1  111.07  3.000
 AM1  C4   C2  C1  129.26  3.000
 AM1  N1   C2  C1  119.66  3.000
 AM1  O3   N1  C2  106.55  3.000
 AM1  C3   O3  N1  109.72  3.000
 AM1  C8   C3  C4  132.73  3.000
 AM1  C8   C3  O3  117.66  3.000
 AM1  C4   C3  O3  109.61  3.000
 AM1  C5   C4  C3  126.47  3.000
 AM1  C5   C4  C2  130.44  3.000
 AM1  C3   C4  C2  103.04  3.000
 AM1  H3   C5  H2  107.31  3.000
 AM1  H3   C5  C6  108.75  3.000
 AM1  H2   C5  C6  108.45  3.000
 AM1  H3   C5  C4  110.22  3.000
 AM1  H2   C5  C4  108.71  3.000
 AM1  C6   C5  C4  113.22  3.000
 AM1  H4   C6  C7  108.63  3.000
 AM1  H4   C6  N2  108.01  3.000
 AM1  C7   C6  N2  111.25  3.000
 AM1  H4   C6  C5  106.19  3.000
 AM1  C7   C6  C5  107.86  3.000
 AM1  N2   C6  C5  114.64  3.000
 AM1  H6   N2  H5  106.83  3.000
 AM1  H6   N2  C6  109.31  3.000
 AM1  H5   N2  C6  109.91  3.000
 AM1  O5   C7  O4  126.40  3.000
 AM1  O5   C7  C6  116.13  3.000
 AM1  O4   C7  C6  117.42  3.000
 AM1  H10  C8  H9  107.55  3.000
 AM1  H10  C8  H8  108.32  3.000
 AM1  H9   C8  H8  107.56  3.000
 AM1  H10  C8  C3  111.48  3.000
 AM1  H9   C8  C3  111.44  3.000
 AM1  H8   C8  C3  110.34  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
 AM1  CONST_01  C3  O3  N1  C2    0.00   0.0  0
 AM1  CONST_02  O3  C3  C4  C2    0.00   0.0  0
 AM1  CONST_03  C3  C4  C2  N1    0.00   0.0  0
 AM1  CONST_04  C4  C3  O3  N1    0.00   0.0  0
 AM1  CONST_05  C4  C2  N1  O3    0.00   0.0  0
 AM1  CONST_06  O3  N1  C2  C1  180.00   0.0  0
 AM1  CONST_07  C3  C4  C2  C1  180.00   0.0  0
 AM1  CONST_08  C8  C3  C4  C2  180.00   0.0  0
 AM1  CONST_09  C5  C4  C2  N1  180.00   0.0  0
 AM1  CONST_10  C8  C3  O3  N1  180.00   0.0  0
 AM1  CONST_11  C5  C4  C3  O3  180.00   0.0  0
 AM1  Var_01    N1  C2  C1  O1   -3.95  30.0  2
 AM1  Var_02    C6  C5  C4  C2   81.66  30.0  2
 AM1  Var_03    H8  C8  C3  O3  150.06  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
 AM1  chir_01  C6  C5  N2  C7  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
 AM1  plan-1  C1  0.020
 AM1  plan-1  C2  0.020
 AM1  plan-1  N1  0.020
 AM1  plan-1  O3  0.020
 AM1  plan-1  C3  0.020
 AM1  plan-1  C4  0.020
 AM1  plan-1  C5  0.020
 AM1  plan-1  C8  0.020
 AM1  plan-2  O1  0.020
 AM1  plan-2  C1  0.020
 AM1  plan-2  O2  0.020
 AM1  plan-2  C2  0.020
 AM1  plan-3  C6  0.020
 AM1  plan-3  C7  0.020
 AM1  plan-3  O4  0.020
 AM1  plan-3  O5  0.020

