# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 20:16:06 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: D-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCC(O)=O)C(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
 ZGL  ZGL  'D-alpha-glutamine        '  D-peptide  19  10  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_ZGL
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
 ZGL  C     C  C      0   0.518  34.0012  58.0440  45.3718
 ZGL  N     N  NH2    0  -0.809  32.5767  56.9213  47.0393
 ZGL  O     O  O      0  -0.497  34.2995  58.9769  44.6369
 ZGL  N1    N  NH2    0  -0.800  34.5334  56.8210  45.2686
 ZGL  CA    C  CH1    0  -0.222  33.0021  58.2106  46.5173
 ZGL  CB    C  CH2    0  -0.434  31.8638  59.1569  46.1155
 ZGL  CD    C  C      0   0.394  31.4282  59.7408  48.5482
 ZGL  CG    C  CH2    0  -0.540  30.8041  59.3099  47.2084
 ZGL  OE1   O  OC    -1  -0.610  31.4860  58.8792  49.4534
 ZGL  OE2   O  O      0  -0.609  31.8597  60.9100  48.6083
 ZGL  HN    H  HNH2   0   0.356  32.1841  57.0639  47.9626
 ZGL  HNA   H  HNH2   0   0.345  31.8280  56.5459  46.4676
 ZGL  HN1   H  HNH2   0   0.390  35.2351  56.6167  44.5770
 ZGL  HN1A  H  HNH2   0   0.401  34.2498  56.1080  45.9213
 ZGL  HA    H  HCH1   0   0.265  33.5788  58.6945  47.3153
 ZGL  HB    H  HCH2   0   0.219  32.2770  60.1360  45.8705
 ZGL  HBA   H  HCH2   0   0.220  31.3871  58.7833  45.2032
 ZGL  HG    H  HCH2   0   0.219  30.0806  60.0596  46.8747
 ZGL  HGA   H  HCH2   0   0.196  30.2553  58.3725  47.3230

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
 ZGL  N1   C     single  1.338  0.020  1.338
 ZGL  C    O     double  1.231  0.020  1.231
 ZGL  C    CA    single  1.525  0.021  1.525
 ZGL  N    CA    single  1.458  0.019  1.458
 ZGL  N    HN    single  0.890  0.020  1.040
 ZGL  N    HNA   single  0.890  0.020  1.040
 ZGL  N1   HN1   single  0.860  0.020  1.020
 ZGL  N1   HN1A  single  0.860  0.020  1.020
 ZGL  CB   CA    single  1.521  0.033  1.521
 ZGL  CA   HA    single  0.970  0.020  0.970
 ZGL  CB   CG    single  1.530  0.020  1.530
 ZGL  CB   HB    single  0.970  0.020  1.090
 ZGL  CB   HBA   single  0.970  0.020  1.090
 ZGL  CG   CD    single  1.539  0.020  1.539
 ZGL  OE2  CD    deloc   1.248  0.020  1.248
 ZGL  CD   OE1   deloc   1.251  0.020  1.251
 ZGL  CG   HG    single  0.970  0.020  1.090
 ZGL  CG   HGA   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
 ZGL  CA    C   N1   114.67  3.000
 ZGL  CA    C   O    120.80  1.700
 ZGL  N1    C   O    123.60  3.000
 ZGL  HNA   N   HN   106.24  3.000
 ZGL  HNA   N   CA   109.98  3.000
 ZGL  HN    N   CA   108.39  3.000
 ZGL  HN1A  N1  HN1  119.87  3.000
 ZGL  HN1A  N1  C    119.02  3.000
 ZGL  HN1   N1  C    121.07  3.000
 ZGL  HA    CA  CB   109.00  3.000
 ZGL  HA    CA  N    110.00  3.000
 ZGL  CB    CA  N    110.40  1.500
 ZGL  HA    CA  C    110.00  3.000
 ZGL  CB    CA  C    110.50  1.500
 ZGL  N     CA  C    111.00  2.800
 ZGL  HBA   CB  HB   106.50  3.000
 ZGL  HBA   CB  CG   109.13  3.000
 ZGL  HB    CB  CG   109.46  3.000
 ZGL  HBA   CB  CA   109.32  3.000
 ZGL  HB    CB  CA   109.36  3.000
 ZGL  CG    CB  CA   112.87  3.000
 ZGL  OE2   CD  OE1  126.48  3.000
 ZGL  OE1   CD  CG   117.10  3.000
 ZGL  OE2   CD  CG   116.39  3.000
 ZGL  HGA   CG  HG   106.73  3.000
 ZGL  HGA   CG  CD   110.65  3.000
 ZGL  HG    CG  CD   109.98  3.000
 ZGL  HGA   CG  CB   109.70  3.000
 ZGL  HG    CG  CB   107.98  3.000
 ZGL  CD    CG  CB   111.64  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
 ZGL  CONST_01  HN1   N1  C   O     0.00   0.0  0
 ZGL  CONST_02  HN1A  N1  C   O   180.00   0.0  0
 ZGL  Var_01    CD    CG  CB  CA   54.33  30.0  3
 ZGL  Var_02    OE2   CD  CG  CB   70.69  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
 ZGL  chir_01  CA  C  N  CB  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
 ZGL  plan-1  C     0.020
 ZGL  plan-1  O     0.020
 ZGL  plan-1  N1    0.020
 ZGL  plan-1  CA    0.020
 ZGL  plan-1  HN1   0.020
 ZGL  plan-1  HN1A  0.020
 ZGL  plan-2  CD    0.020
 ZGL  plan-2  CG    0.020
 ZGL  plan-2  OE1   0.020
 ZGL  plan-2  OE2   0.020

