# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 08:13:03 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (2~{S})-2-azanyl-4-methyl-pent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)C[C@H](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
 EO2  EO2  '(2~{S})-2-azanyl-4-methyl-pent-4-enoic acid'  L-peptide  19  9  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_EO2
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
 EO2  O    O  O      0  -0.614   -8.9469  6.3592  23.1255
 EO2  C    C  C      0   0.392   -9.9357  6.6207  22.4088
 EO2  N    N  NH2    0  -0.785  -11.6117  5.7533  20.6951
 EO2  CA   C  CH1    0  -0.216  -10.4744  5.4444  21.5481
 EO2  CB   C  CH2    0  -0.510   -9.3419  4.8518  20.7016
 EO2  CG   C  C      0   0.196   -9.7613  3.7064  19.8246
 EO2  CD   C  CH3    0  -0.724  -10.3809  2.5282  20.5139
 EO2  CE   C  C2     0  -0.605   -9.5663  3.7245  18.5065
 EO2  H5   H  HCH1   0   0.213  -10.7996  4.6717  22.2576
 EO2  H6   H  HCH2   0   0.234   -8.5538  4.5117  21.3779
 EO2  H7   H  HCH2   0   0.222   -8.9028  5.6405  20.0805
 EO2  H8   H  HCH3   0   0.237  -11.3472  2.7949  20.9467
 EO2  H9   H  HCH3   0   0.236  -10.5387  1.6948  19.8299
 EO2  H10  H  HCH3   0   0.230   -9.7531  2.1803  21.3380
 EO2  H11  H  H      0   0.220   -9.1207  4.5797  18.0121
 EO2  H12  H  H      0   0.220   -9.8424  2.8874  17.8764
 EO2  O1   O  OC    -1  -0.599  -10.5333  7.7115  22.3285
 EO2  H2   H  HNH2   0   0.330  -12.2584  6.3238  21.2266
 EO2  H3   H  HNH2   0   0.322  -11.2982  6.3623  19.9467

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
 EO2  CE  CG   double  1.333  0.020  1.333
 EO2  CG  CD   single  1.499  0.020  1.499
 EO2  CG  CB   single  1.502  0.020  1.502
 EO2  CB  CA   single  1.521  0.033  1.521
 EO2  N   CA   single  1.458  0.019  1.458
 EO2  CA  C    single  1.525  0.021  1.525
 EO2  C   O    deloc   1.231  0.020  1.231
 EO2  N   H2   single  0.890  0.020  1.040
 EO2  N   H3   single  0.890  0.020  1.040
 EO2  CA  H5   single  0.970  0.020  1.090
 EO2  CB  H6   single  0.970  0.020  1.090
 EO2  CB  H7   single  0.970  0.020  1.090
 EO2  CD  H8   single  0.970  0.020  1.090
 EO2  CD  H9   single  0.970  0.020  1.090
 EO2  CD  H10  single  0.970  0.020  1.090
 EO2  CE  H11  single  0.930  0.020  1.080
 EO2  CE  H12  single  0.930  0.020  1.080
 EO2  C   O1   deloc   1.246  0.020  1.246

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
 EO2  O1   C   CA   117.42  3.000
 EO2  O1   C   O    126.86  3.000
 EO2  CA   C   O    120.80  1.700
 EO2  H3   N   H2   104.26  3.000
 EO2  H3   N   CA   108.56  3.000
 EO2  H2   N   CA   108.12  3.000
 EO2  H5   CA  CB   107.67  3.000
 EO2  H5   CA  N    107.26  3.000
 EO2  CB   CA  N    110.40  1.500
 EO2  H5   CA  C    106.10  3.000
 EO2  N    CA  C    111.00  2.800
 EO2  CB   CA  C    110.50  1.500
 EO2  H7   CB  H6   106.61  3.000
 EO2  H7   CB  CG   109.26  3.000
 EO2  H6   CB  CG   108.98  3.000
 EO2  H7   CB  CA   109.32  3.000
 EO2  H6   CB  CA   108.14  3.000
 EO2  CG   CB  CA   114.25  3.000
 EO2  CE   CG  CD   121.73  3.000
 EO2  CD   CG  CB   116.51  3.000
 EO2  CE   CG  CB   121.75  3.000
 EO2  H10  CD  H9   108.25  3.000
 EO2  H10  CD  H8   106.69  3.000
 EO2  H9   CD  H8   107.91  3.000
 EO2  H10  CD  CG   111.07  3.000
 EO2  H9   CD  CG   111.87  3.000
 EO2  H8   CD  CG   110.86  3.000
 EO2  H12  CE  H11  116.70  3.000
 EO2  H12  CE  CG   121.83  3.000
 EO2  H11  CE  CG   121.47  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
 EO2  Var_01  CE   CG  CB  CA  123.94  30.0  1
 EO2  Var_02  H11  CE  CG  CB   -1.67   0.0  2
 EO2  Var_03  H8   CD  CG  CB   66.80  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
 EO2  chir_01  CA  CB  N  C  positiv

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
 EO2  plan-1  O    0.020
 EO2  plan-1  C    0.020
 EO2  plan-1  CA   0.020
 EO2  plan-1  O1   0.020
 EO2  plan-2  CB   0.020
 EO2  plan-2  CG   0.020
 EO2  plan-2  CD   0.020
 EO2  plan-2  CE   0.020
 EO2  plan-2  H11  0.020
 EO2  plan-2  H12  0.020

