# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:38:43 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2S,4E)-2-aminohex-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=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
 F7V  F7V  '(2S,4E)-2-aminohex-4-enoic acid'  L-peptide  19  9  .  2022-07-25  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_F7V
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
 F7V  N    N  NH2    0  -0.788  -0.2949  -1.4601   0.7454
 F7V  CA   C  CH1    0  -0.211  -0.6989  -0.0827   0.5097
 F7V  C    C  C      0   0.394  -2.1272   0.1065  -0.0648
 F7V  O    O  O      0  -0.606  -2.8309  -0.9126  -0.2113
 F7V  CB   C  CH2    0  -0.500   0.3314   0.6187  -0.3810
 F7V  CG   C  C1     0  -0.167   1.7250   0.5267   0.1495
 F7V  CD   C  C1     0  -0.242   2.7627   0.0128  -0.5050
 F7V  CE   C  CH3    0  -0.706   4.1594  -0.0650   0.0219
 F7V  O1   O  OC    -1  -0.620  -2.4659   1.2825  -0.3141
 F7V  H1   H  HNH2   0   0.330  -1.1090  -1.9718   1.0651
 F7V  H2   H  HNH2   0   0.323  -0.0649  -1.8879  -0.1455
 F7V  H4   H  HCH1   0   0.210  -0.6920   0.4356   1.4795
 F7V  H5   H  HCH2   0   0.220   0.2934   0.1959  -1.3916
 F7V  H6   H  HCH2   0   0.234   0.0376   1.6665  -0.4726
 F7V  H7   H  H      0   0.217   1.8832   0.9224   1.1520
 F7V  H8   H  H      0   0.220   2.6024  -0.3883  -1.5037
 F7V  H9   H  HCH3   0   0.231   4.2365   0.3572   1.0242
 F7V  H10  H  HCH3   0   0.231   4.5097  -1.0989   0.0659
 F7V  H11  H  HCH3   0   0.231   4.8591   0.4709  -0.6237

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
 F7V  O   C    deloc   1.231  0.020  1.231
 F7V  C   CA   single  1.525  0.021  1.525
 F7V  CB  CA   single  1.521  0.033  1.521
 F7V  CB  CG   single  1.494  0.020  1.494
 F7V  CA  N    single  1.458  0.019  1.458
 F7V  CG  CD   double  1.330  0.020  1.330
 F7V  CD  CE   single  1.495  0.020  1.495
 F7V  C   O1   deloc   1.249  0.020  1.249
 F7V  N   H1   single  0.890  0.020  1.040
 F7V  N   H2   single  0.890  0.020  1.040
 F7V  CA  H4   single  0.970  0.020  1.090
 F7V  CB  H5   single  0.970  0.020  1.090
 F7V  CB  H6   single  0.970  0.020  1.090
 F7V  CG  H7   single  0.930  0.020  1.080
 F7V  CD  H8   single  0.930  0.020  1.080
 F7V  CE  H9   single  0.970  0.020  1.090
 F7V  CE  H10  single  0.970  0.020  1.090
 F7V  CE  H11  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
 F7V  H2   N   H1   104.25  3.000
 F7V  H2   N   CA   108.65  3.000
 F7V  H1   N   CA   107.83  3.000
 F7V  H4   CA  CB   107.02  3.000
 F7V  H4   CA  C    105.96  3.000
 F7V  CB   CA  C    110.50  1.500
 F7V  H4   CA  N    107.55  3.000
 F7V  CB   CA  N    110.40  1.500
 F7V  C    CA  N    111.00  2.800
 F7V  O1   C   O    126.37  3.000
 F7V  O1   C   CA   116.01  3.000
 F7V  O    C   CA   120.80  1.700
 F7V  H6   CB  H5   106.46  3.000
 F7V  H6   CB  CG   109.87  3.000
 F7V  H5   CB  CG   109.63  3.000
 F7V  H6   CB  CA   107.88  3.000
 F7V  H5   CB  CA   109.64  3.000
 F7V  CG   CB  CA   113.12  3.000
 F7V  H7   CG  CD   118.68  3.000
 F7V  H7   CG  CB   116.10  3.000
 F7V  CD   CG  CB   125.22  3.000
 F7V  H8   CD  CE   116.23  3.000
 F7V  H8   CD  CG   118.63  3.000
 F7V  CE   CD  CG   125.14  3.000
 F7V  H11  CE  H10  106.42  3.000
 F7V  H11  CE  H9   107.94  3.000
 F7V  H10  CE  H9   107.86  3.000
 F7V  H11  CE  CD   111.38  3.000
 F7V  H10  CE  CD   111.29  3.000
 F7V  H9   CE  CD   111.71  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
 F7V  Var_01  CE  CD  CG  CB  179.30   0.0  2
 F7V  Var_02  CD  CG  CB  CA  122.84  30.0  3
 F7V  Var_03  H9  CE  CD  CG   -0.11  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
 F7V  chir_01  CA  C  CB  N  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
 F7V  plan-1  CA  0.020
 F7V  plan-1  C   0.020
 F7V  plan-1  O   0.020
 F7V  plan-1  O1  0.020
 F7V  plan-2  CB  0.020
 F7V  plan-2  CG  0.020
 F7V  plan-2  CD  0.020
 F7V  plan-2  CE  0.020
 F7V  plan-2  H7  0.020
 F7V  plan-2  H8  0.020

