# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Sep 21 10:07:59 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  "(S)-2-AMINO-3-(3-CARBOXY-5-METHYLISOXAZOL-4-YL)PROPIONIC ACID"  ligand  25  15  .  2022-09-16  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OH1   0  -0.581   2.9634  -2.1658   0.4825
 AM1  C1   C  C     0   0.519   1.7699  -1.7227   0.1393
 AM1  O2   O  O     0  -0.415   0.8063  -2.4182  -0.0576
 AM1  C2   C  CR5   0   0.112   1.7265  -0.2482   0.0166
 AM1  N1   N  N     0  -0.137   2.7714   0.4724   0.3143
 AM1  O3   O  O     0  -0.324   2.4086   1.7503   0.1032
 AM1  C3   C  CR5   0   0.404   1.1412   1.8121  -0.3270
 AM1  C4   C  CR5   0  -0.117   0.6342   0.5531  -0.4122
 AM1  C5   C  CH2   0  -0.559  -0.7446   0.1599  -0.8112
 AM1  C6   C  CH1   0  -0.204  -1.6531  -0.0549   0.4282
 AM1  N2   N  NH2   0  -0.785  -1.7531   1.0683   1.3267
 AM1  C7   C  C     0   0.539  -3.0381  -0.4338  -0.0544
 AM1  O4   O  O     0  -0.435  -3.9936   0.2990  -0.0287
 AM1  O5   O  OH1   0  -0.590  -3.0695  -1.6640  -0.5491
 AM1  C8   C  CH3   0  -0.756   0.5666   3.1489  -0.5926
 AM1  H1   H  HOH1  0   0.494   2.9538  -3.1329   0.5515
 AM1  H2   H  HCH2  0   0.265  -1.1760   0.9480  -1.4345
 AM1  H3   H  HCH2  0   0.274  -0.7179  -0.7439  -1.4184
 AM1  H4   H  HCH1  0   0.284  -1.2497  -0.9025   0.9874
 AM1  H5   H  HNH2  0   0.360  -0.8452   1.2817   1.7173
 AM1  H6   H  HNH2  0   0.347  -2.0781   1.8976   0.8456
 AM1  H7   H  HOH1  0   0.483  -3.9539  -1.8631  -0.8917
 AM1  H8   H  HCH3  0   0.267  -0.2993   3.0629  -1.2455
 AM1  H9   H  HCH3  0   0.275   0.2426   3.6301   0.3317
 AM1  H10  H  HCH3  0   0.278   1.2921   3.8031  -1.0743

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   single    1.319  0.020  1.319
 AM1  O1  H1   single    0.850  0.020  0.980
 AM1  C1  O2   double    1.205  0.020  1.205
 AM1  C1  C2   single    1.480  0.020  1.480
 AM1  C2  N1   aromatic  1.304  0.020  1.304
 AM1  C2  C4   aromatic  1.421  0.020  1.421
 AM1  N1  O3   aromatic  1.345  0.020  1.345
 AM1  O3  C3   aromatic  1.340  0.020  1.340
 AM1  C3  C4   aromatic  1.360  0.020  1.360
 AM1  C3  C8   single    1.479  0.020  1.479
 AM1  C4  C5   single    1.488  0.020  1.488
 AM1  C5  C6   single    1.552  0.020  1.552
 AM1  C5  H2   single    0.970  0.020  1.090
 AM1  C5  H3   single    0.970  0.020  1.090
 AM1  C6  N2   single    1.442  0.020  1.442
 AM1  C6  C7   single    1.515  0.020  1.515
 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   double    1.204  0.020  1.204
 AM1  C7  O5   single    1.326  0.020  1.326
 AM1  O5  H7   single    0.850  0.020  0.980
 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  H1   O1  C1  110.17  3.000
 AM1  C2   C1  O2  122.56  3.000
 AM1  C2   C1  O1  112.51  3.000
 AM1  O2   C1  O1  124.93  3.000
 AM1  C4   C2  N1  111.92  3.000
 AM1  C4   C2  C1  127.54  3.000
 AM1  N1   C2  C1  120.54  3.000
 AM1  O3   N1  C2  105.85  3.000
 AM1  C3   O3  N1  110.45  3.000
 AM1  C8   C3  C4  132.89  3.000
 AM1  C8   C3  O3  117.83  3.000
 AM1  C4   C3  O3  109.28  3.000
 AM1  C5   C4  C3  127.36  3.000
 AM1  C5   C4  C2  130.10  3.000
 AM1  C3   C4  C2  102.50  3.000
 AM1  H3   C5  H2  106.85  3.000
 AM1  H3   C5  C6  110.17  3.000
 AM1  H2   C5  C6  108.91  3.000
 AM1  H3   C5  C4  110.24  3.000
 AM1  H2   C5  C4  109.14  3.000
 AM1  C6   C5  C4  111.40  3.000
 AM1  H4   C6  C7  107.86  3.000
 AM1  H4   C6  N2  108.12  3.000
 AM1  C7   C6  N2  109.26  3.000
 AM1  H4   C6  C5  107.46  3.000
 AM1  C7   C6  C5  108.39  3.000
 AM1  N2   C6  C5  115.50  3.000
 AM1  H6   N2  H5  107.39  3.000
 AM1  H6   N2  C6  111.36  3.000
 AM1  H5   N2  C6  110.05  3.000
 AM1  O5   C7  O4  123.61  3.000
 AM1  O5   C7  C6  111.87  3.000
 AM1  O4   C7  C6  124.50  3.000
 AM1  H7   O5  C7  110.12  3.000
 AM1  H10  C8  H9  107.91  3.000
 AM1  H10  C8  H8  108.19  3.000
 AM1  H9   C8  H8  107.87  3.000
 AM1  H10  C8  C3  111.31  3.000
 AM1  H9   C8  C3  111.21  3.000
 AM1  H8   C8  C3  110.21  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  CONST_12  H1   O1  C1  C2   180.00   0.0  0
 AM1  CONST_13  H1   O1  C1  O2     0.00   0.0  0
 AM1  CONST_14  H7   O5  C7  C6   180.00   0.0  0
 AM1  CONST_15  H7   O5  C7  O4     0.00   0.0  0
 AM1  Var_01    N1   C2  C1  O1    -3.99  30.0  2
 AM1  Var_02    C4   C2  C1  O1   175.83  30.0  2
 AM1  Var_03    N1   C2  C1  O2   175.98  30.0  2
 AM1  Var_04    C4   C2  C1  O2    -4.20  30.0  2
 AM1  Var_05    C6   C5  C4  C2    81.60  30.0  2
 AM1  Var_06    C6   C5  C4  C3   -95.82  30.0  2
 AM1  Var_07    H2   C5  C4  C2  -158.10  30.0  2
 AM1  Var_08    H3   C5  C4  C2   -41.03  30.0  2
 AM1  Var_09    H8   C8  C3  O3   160.17  30.0  2
 AM1  Var_10    H9   C8  C3  O3   -80.24  30.0  2
 AM1  Var_11    H10  C8  C3  O3    40.12  30.0  2
 AM1  Var_12    H2   C5  C4  C3    24.48  30.0  2
 AM1  Var_13    H3   C5  C4  C3   141.55  30.0  2
 AM1  Var_14    H8   C8  C3  C4   -20.80  30.0  2
 AM1  Var_15    H9   C8  C3  C4    98.79  30.0  2
 AM1  Var_16    H10  C8  C3  C4  -140.85  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-2  H1  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
 AM1  plan-3  H7  0.020

