# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:51:21 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: ethyl glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CN
#
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
 GEE  GEE  'ethyl glycinate          '  L-peptide  16  7  .  2019-03-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GEE
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
 GEE  C    C  C     0   0.578  11.6715  22.8763   0.0696
 GEE  N    N  NH2   0  -0.790  11.5052  22.8664   2.5058
 GEE  O    O  O     0  -0.446  12.1275  23.9904   0.0674
 GEE  C1   C  CH2   0  -0.176  11.7576  22.7595  -2.2963
 GEE  O1   O  O2    0  -0.458  11.4385  22.1681  -1.0280
 GEE  C2   C  CH3   0  -0.687  11.3936  21.7662  -3.3729
 GEE  CA   C  CH2   0  -0.411  11.3069  22.0871   1.3059
 GEE  H    H  HNH2  0   0.357  11.1372  22.3512   3.2942
 GEE  H2   H  HNH2  0   0.347  12.4941  22.9815   2.6854
 GEE  H1A  H  HCH2  0   0.232  11.1998  23.6898  -2.4213
 GEE  H1B  H  HCH2  0   0.232  12.8222  23.0006  -2.3323
 GEE  H2A  H  HCH3  0   0.238  11.6262  22.1943  -4.3477
 GEE  H2B  H  HCH3  0   0.235  11.9576  20.8389  -3.2727
 GEE  H2C  H  HCH3  0   0.235  10.3297  21.5299  -3.3578
 GEE  HA2  H  HCH2  0   0.268  10.2522  21.8102   1.2273
 GEE  HA3  H  HCH2  0   0.244  11.8643  21.1404   1.2664

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
 GEE  C   O    double  1.231  0.020  1.231
 GEE  C   O1   single  1.327  0.020  1.327
 GEE  C   CA   single  1.516  0.018  1.516
 GEE  N   CA   single  1.451  0.016  1.451
 GEE  C1  O1   single  1.435  0.020  1.435
 GEE  C1  C2   single  1.509  0.020  1.509
 GEE  N   H    single  0.860  0.020  0.860
 GEE  N   H2   single  0.890  0.020  1.040
 GEE  C1  H1A  single  0.970  0.020  1.090
 GEE  C1  H1B  single  0.970  0.020  1.090
 GEE  C2  H2A  single  0.970  0.020  1.090
 GEE  C2  H2B  single  0.970  0.020  1.090
 GEE  C2  H2C  single  0.970  0.020  1.090
 GEE  CA  HA2  single  0.970  0.020  1.090
 GEE  CA  HA3  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
 GEE  CA   C   O1   110.83  3.000
 GEE  CA   C   O    120.80  2.100
 GEE  O1   C   O    123.99  3.000
 GEE  H2   N   H    105.99  3.000
 GEE  H2   N   CA   110.06  3.000
 GEE  H    N   CA   114.00  3.000
 GEE  H1B  C1  H1A  107.82  3.000
 GEE  H1B  C1  C2   110.91  3.000
 GEE  H1A  C1  C2   110.84  3.000
 GEE  H1B  C1  O1   109.69  3.000
 GEE  H1A  C1  O1   109.79  3.000
 GEE  C2   C1  O1   107.79  3.000
 GEE  C1   O1  C    118.16  3.000
 GEE  H2C  C2  H2B  108.62  3.000
 GEE  H2C  C2  H2A  107.82  3.000
 GEE  H2B  C2  H2A  107.82  3.000
 GEE  H2C  C2  C1   111.60  3.000
 GEE  H2B  C2  C1   111.68  3.000
 GEE  H2A  C2  C1   109.15  3.000
 GEE  HA3  CA  HA2  105.58  3.000
 GEE  HA3  CA  N    115.14  3.000
 GEE  HA2  CA  N    109.19  3.000
 GEE  HA3  CA  C    107.34  3.000
 GEE  HA2  CA  C    107.83  3.000
 GEE  N    CA  C    113.30  2.900

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
 GEE  Var_01  C2   C1  O1  C   -179.60  30.0  1
 GEE  Var_02  O    C   CA  N      3.16  30.0  1
 GEE  Var_03  CA   C   O1  C1  -178.68  30.0  1
 GEE  Var_04  H    N   CA  C    172.59  30.0  3
 GEE  Var_05  H2A  C2  C1  O1   179.93  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
 GEE  plan-1  C   0.020
 GEE  plan-1  O   0.020
 GEE  plan-1  O1  0.020
 GEE  plan-1  CA  0.020

