# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 20:29:33 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: N-(carboxycarbonyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)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
 OGA  OGA  N-(carboxycarbonyl)glycine  ligand  15  10  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OGA
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
 OGA  C1    C  C     0   0.464   0.4025  -0.0006  -2.2174
 OGA  C2    C  C     0   0.457  -0.5940   0.0025  -1.0510
 OGA  C4    C  CH2   0  -0.372  -0.7465  -0.0054   1.3595
 OGA  C5    C  C     0   0.523   0.1891  -0.0078   2.5413
 OGA  O1    O  O     0  -0.412   1.5951  -0.0180  -2.0616
 OGA  O2    O  OH1   0  -0.565  -0.2229   0.0177  -3.3695
 OGA  O2'   O  O     0  -0.455  -1.7952   0.0121  -1.2365
 OGA  O3    O  OH1   0  -0.582  -0.4854  -0.0113   3.6759
 OGA  N1    N  NH1   0  -0.632   0.0061  -0.0071   0.1367
 OGA  O4    O  O     0  -0.431   1.3903  -0.0059   2.4579
 OGA  H4C1  H  HCH2  0   0.301  -1.3995  -0.8807   1.4244
 OGA  H4C2  H  HCH2  0   0.301  -1.3943   0.8737   1.4249
 OGA  H2    H  HOH1  0   0.496   0.4137   0.0133  -4.1011
 OGA  H3    H  HOH1  0   0.492   0.1207  -0.0115   4.4323
 OGA  H1    H  HNH1  0   0.416   1.0149  -0.0134   0.1895

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
 OGA  C1  C2    single  1.534  0.020  1.534
 OGA  C1  O1    double  1.203  0.020  1.203
 OGA  C1  O2    single  1.311  0.020  1.311
 OGA  C2  O2'   double  1.215  0.020  1.215
 OGA  C2  N1    single  1.331  0.020  1.331
 OGA  C4  C5    single  1.507  0.020  1.507
 OGA  C4  N1    single  1.436  0.020  1.436
 OGA  C4  H4C1  single  0.970  0.020  1.090
 OGA  C4  H4C2  single  0.970  0.020  1.090
 OGA  C5  O3    single  1.320  0.020  1.320
 OGA  C5  O4    double  1.204  0.020  1.204
 OGA  O2  H2    single  0.850  0.020  0.980
 OGA  O3  H3    single  0.850  0.020  0.980
 OGA  N1  H1    single  0.860  0.020  1.020

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
 OGA  O2    C1  O1    125.95  3.000
 OGA  O2    C1  C2    110.99  3.000
 OGA  O1    C1  C2    123.06  3.000
 OGA  N1    C2  O2'   125.59  3.000
 OGA  N1    C2  C1    112.68  3.000
 OGA  O2'   C2  C1    121.73  3.000
 OGA  H4C2  C4  H4C1  106.62  3.000
 OGA  H4C2  C4  N1    111.23  3.000
 OGA  H4C1  C4  N1    111.25  3.000
 OGA  H4C2  C4  C5    108.78  3.000
 OGA  H4C1  C4  C5    108.83  3.000
 OGA  N1    C4  C5    110.02  3.000
 OGA  O4    C5  O3    124.71  3.000
 OGA  O4    C5  C4    124.39  3.000
 OGA  O3    C5  C4    110.90  3.000
 OGA  H2    O2  C1    110.47  3.000
 OGA  H3    O3  C5    110.56  3.000
 OGA  H1    N1  C4    118.61  3.000
 OGA  H1    N1  C2    119.81  3.000
 OGA  C4    N1  C2    121.58  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
 OGA  CONST_01  C4   N1  C2  C1   180.00   0.0  0
 OGA  CONST_02  O2'  C2  N1  C4     0.00   0.0  0
 OGA  CONST_03  H1   N1  C2  C1     0.00   0.0  0
 OGA  CONST_04  H2   O2  C1  C2   180.00   0.0  0
 OGA  CONST_05  H3   O3  C5  C4   180.00   0.0  0
 OGA  Var_01    C5   C4  N1  C2  -179.59  30.0  1
 OGA  Var_02    O2'  C2  C1  O1  -179.54  30.0  2
 OGA  Var_03    N1   C4  C5  O3  -179.77  30.0  2

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
 OGA  plan-1  C1   0.020
 OGA  plan-1  C2   0.020
 OGA  plan-1  C4   0.020
 OGA  plan-1  O2'  0.020
 OGA  plan-1  N1   0.020
 OGA  plan-1  H1   0.020
 OGA  plan-2  C1   0.020
 OGA  plan-2  C2   0.020
 OGA  plan-2  O1   0.020
 OGA  plan-2  O2   0.020
 OGA  plan-2  H2   0.020
 OGA  plan-3  C4   0.020
 OGA  plan-3  C5   0.020
 OGA  plan-3  O3   0.020
 OGA  plan-3  O4   0.020
 OGA  plan-3  H3   0.020

