# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 22:12:40 2020
#   Inital geometry file: a 32 line input string
#   Ligand name: glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(N)=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
 GM1  GM1  'glycinamide              '  ligand  11  5  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GM1
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
 GM1  C1    C  C     0   0.494  -0.1116   0.0679  -0.5221
 GM1  N1    N  NH2   0  -0.801   0.5758  -0.0510  -1.6700
 GM1  O1    O  O     0  -0.492  -1.3255   0.1917  -0.4802
 GM1  C2    C  CH2   0  -0.406   0.7526   0.0582   0.7276
 GM1  N2    N  NH2   0  -0.791  -0.0492  -0.0650   1.9246
 GM1  HN11  H  HNH2  0   0.399   0.1088   0.0371  -2.5575
 GM1  HN12  H  HNH2  0   0.405   1.5800  -0.1029  -1.6819
 GM1  H21   H  HCH2  0   0.239   1.3833   0.9595   0.6892
 GM1  H22   H  HCH2  0   0.256   1.4419  -0.7879   0.6701
 GM1  HN21  H  HNH2  0   0.353   0.5688  -0.1014   2.7244
 GM1  HN22  H  HNH2  0   0.344  -0.6064   0.7705   2.0473

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
 GM1  C1  N1    single  1.343  0.020  1.343
 GM1  C1  O1    double  1.221  0.020  1.221
 GM1  C1  C2    single  1.519  0.020  1.519
 GM1  N1  HN11  single  0.860  0.020  1.020
 GM1  N1  HN12  single  0.860  0.020  1.020
 GM1  C2  N2    single  1.446  0.020  1.446
 GM1  C2  H21   single  0.970  0.020  1.090
 GM1  C2  H22   single  0.970  0.020  1.090
 GM1  N2  HN21  single  0.890  0.020  1.040
 GM1  N2  HN22  single  0.890  0.020  1.040

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
 GM1  C2    C1  O1    122.54  3.000
 GM1  C2    C1  N1    114.28  3.000
 GM1  O1    C1  N1    123.17  3.000
 GM1  HN12  N1  HN11  117.22  3.000
 GM1  HN12  N1  C1    121.72  3.000
 GM1  HN11  N1  C1    120.54  3.000
 GM1  H22   C2  H21   105.71  3.000
 GM1  H22   C2  N2    109.10  3.000
 GM1  H21   C2  N2    114.61  3.000
 GM1  H22   C2  C1    108.68  3.000
 GM1  H21   C2  C1    106.98  3.000
 GM1  N2    C2  C1    111.47  3.000
 GM1  HN22  N2  HN21  105.68  3.000
 GM1  HN22  N2  C2    109.60  3.000
 GM1  HN21  N2  C2    108.59  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
 GM1  CONST_01  HN11  N1  C1  O1     0.00   0.0  0
 GM1  CONST_02  HN12  N1  C1  O1   180.00   0.0  0
 GM1  Var_01    N2    C2  C1  N1  -169.15  30.0  3
 GM1  Var_02    HN21  N2  C2  C1   177.93  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
 GM1  plan-1  C1    0.020
 GM1  plan-1  N1    0.020
 GM1  plan-1  O1    0.020
 GM1  plan-1  C2    0.020
 GM1  plan-1  HN11  0.020
 GM1  plan-1  HN12  0.020

