# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:03:04 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(2S)-2-amino-2-carboxyethyl]-L-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(O)=O)C(=O)NC[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
 J9A  J9A  N-[(2S)-2-amino-2-carboxyethyl]-L-alpha-glutamine  L-peptide  31  16  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J9A
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
 J9A  O01  O  O     0  -0.446   4.4596  -1.1336   1.6699
 J9A  C02  C  C     0   0.549   4.6593  -0.7813   0.5337
 J9A  C03  C  CH2   0  -0.576   3.6702  -0.0703  -0.3444
 J9A  C04  C  CH2   0  -0.420   2.3129   0.1295   0.3064
 J9A  C05  C  CH1   0  -0.229   1.3412   0.8433  -0.6415
 J9A  C06  C  C     0   0.518  -0.0436   0.8925   0.0145
 J9A  N07  N  NH1   0  -0.626  -0.7575  -0.2434  -0.0910
 J9A  C08  C  CH2   0  -0.296  -2.0663  -0.4357   0.4771
 J9A  C09  C  CH1   0  -0.231  -3.1710  -0.3332  -0.6027
 J9A  N10  N  NH2   0  -0.777  -3.1436   0.8709  -1.3950
 J9A  C11  C  C     0   0.548  -4.5233  -0.4761   0.0657
 J9A  O12  O  O     0  -0.433  -5.3574   0.3900   0.1217
 J9A  O14  O  O     0  -0.486  -0.4367   1.8831   0.6124
 J9A  N15  N  NH2   0  -0.775   1.8515   2.1454  -1.0047
 J9A  O16  O  OH1   0  -0.598   5.8149  -0.9843  -0.0935
 J9A  H1   H  HCH2  0   0.287   4.0954   0.8921  -0.6395
 J9A  H2   H  HCH2  0   0.275   3.5665  -0.6395  -1.2738
 J9A  H3   H  HCH2  0   0.246   1.8938  -0.8363   0.5957
 J9A  H4   H  HCH2  0   0.241   2.4129   0.7141   1.2254
 J9A  H5   H  HCH1  0   0.256   1.2663   0.2468  -1.5573
 J9A  H6   H  HNH1  0   0.403  -0.3660  -1.0061  -0.6214
 J9A  H7   H  HCH2  0   0.264  -2.0991  -1.4096   0.9663
 J9A  H8   H  HCH2  0   0.258  -2.2235   0.3249   1.2417
 J9A  H9   H  HCH1  0   0.282  -3.0507  -1.1832  -1.2829
 J9A  H10  H  HNH2  0   0.346  -3.1224   1.6906  -0.8006
 J9A  H11  H  HNH2  0   0.358  -2.2917   0.8895  -1.9398
 J9A  H14  H  HNH2  0   0.353   1.2712   2.5564  -1.7248
 J9A  H15  H  HNH2  0   0.342   1.7888   2.7673  -0.2073
 J9A  H17  H  HOH1  0   0.478   6.4328  -1.4457   0.4927
 J9A  O1   O  OH1   0  -0.595  -4.6741  -1.6758   0.6150
 J9A  H12  H  HOH1  0   0.483  -5.5276  -1.7277   1.0715

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
 J9A  N10  C09  single  1.442  0.020  1.442
 J9A  C09  C08  single  1.548  0.020  1.548
 J9A  C09  C11  single  1.515  0.020  1.515
 J9A  C08  N07  single  1.440  0.020  1.440
 J9A  C11  O12  double  1.204  0.020  1.204
 J9A  N07  C06  single  1.346  0.020  1.346
 J9A  O01  C02  double  1.206  0.020  1.206
 J9A  C03  C02  single  1.502  0.020  1.502
 J9A  C03  C04  single  1.518  0.020  1.518
 J9A  C02  O16  single  1.330  0.020  1.330
 J9A  C06  O14  double  1.222  0.020  1.222
 J9A  C06  C05  single  1.533  0.020  1.533
 J9A  C04  C05  single  1.534  0.020  1.534
 J9A  C05  N15  single  1.445  0.020  1.445
 J9A  C03  H1   single  0.970  0.020  1.090
 J9A  C03  H2   single  0.970  0.020  1.090
 J9A  C04  H3   single  0.970  0.020  1.090
 J9A  C04  H4   single  0.970  0.020  1.090
 J9A  C05  H5   single  0.970  0.020  1.090
 J9A  N07  H6   single  0.860  0.020  1.020
 J9A  C08  H7   single  0.970  0.020  1.090
 J9A  C08  H8   single  0.970  0.020  1.090
 J9A  C09  H9   single  0.970  0.020  1.090
 J9A  N10  H10  single  0.890  0.020  1.040
 J9A  N10  H11  single  0.890  0.020  1.040
 J9A  N15  H14  single  0.890  0.020  1.040
 J9A  N15  H15  single  0.890  0.020  1.040
 J9A  O16  H17  single  0.850  0.020  0.980
 J9A  C11  O1   single  1.328  0.020  1.328
 J9A  O1   H12  single  0.850  0.020  0.980

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
 J9A  O16  C02  C03  111.63  3.000
 J9A  O16  C02  O01  122.91  3.000
 J9A  C03  C02  O01  125.46  3.000
 J9A  H2   C03  H1   105.40  3.000
 J9A  H2   C03  C04  110.34  3.000
 J9A  H1   C03  C04  110.34  3.000
 J9A  H2   C03  C02  108.22  3.000
 J9A  H1   C03  C02  108.58  3.000
 J9A  C04  C03  C02  113.61  3.000
 J9A  H4   C04  H3   106.58  3.000
 J9A  H4   C04  C05  109.18  3.000
 J9A  H3   C04  C05  109.41  3.000
 J9A  H4   C04  C03  110.41  3.000
 J9A  H3   C04  C03  109.89  3.000
 J9A  C05  C04  C03  111.26  3.000
 J9A  H5   C05  N15  107.74  3.000
 J9A  H5   C05  C06  108.27  3.000
 J9A  N15  C05  C06  113.43  3.000
 J9A  H5   C05  C04  107.85  3.000
 J9A  N15  C05  C04  110.55  3.000
 J9A  C06  C05  C04  108.83  3.000
 J9A  O14  C06  N07  123.50  3.000
 J9A  O14  C06  C05  121.73  3.000
 J9A  N07  C06  C05  114.74  3.000
 J9A  H6   N07  C08  117.36  3.000
 J9A  H6   N07  C06  118.29  3.000
 J9A  C08  N07  C06  124.34  3.000
 J9A  H8   C08  H7   107.71  3.000
 J9A  H8   C08  C09  109.89  3.000
 J9A  H7   C08  C09  110.52  3.000
 J9A  H8   C08  N07  108.35  3.000
 J9A  H7   C08  N07  108.89  3.000
 J9A  C09  C08  N07  111.39  3.000
 J9A  H9   C09  C11  107.39  3.000
 J9A  H9   C09  N10  107.74  3.000
 J9A  C11  C09  N10  109.77  3.000
 J9A  H9   C09  C08  107.66  3.000
 J9A  C11  C09  C08  108.84  3.000
 J9A  N10  C09  C08  115.15  3.000
 J9A  H11  N10  H10  106.48  3.000
 J9A  H11  N10  C09  109.11  3.000
 J9A  H10  N10  C09  110.72  3.000
 J9A  O1   C11  O12  123.50  3.000
 J9A  O1   C11  C09  111.65  3.000
 J9A  O12  C11  C09  124.83  3.000
 J9A  H15  N15  H14  105.97  3.000
 J9A  H15  N15  C05  109.48  3.000
 J9A  H14  N15  C05  110.02  3.000
 J9A  H17  O16  C02  109.96  3.000
 J9A  H12  O1   C11  110.07  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
 J9A  CONST_01  C08  N07  C06  C05   180.00   0.0  0
 J9A  CONST_02  O14  C06  N07  C08     0.00   0.0  0
 J9A  CONST_03  H6   N07  C06  C05     0.00   0.0  0
 J9A  CONST_04  H17  O16  C02  O01     0.00   0.0  0
 J9A  CONST_05  H12  O1   C11  C09   180.00   0.0  0
 J9A  Var_01    C04  C03  C02  O01    -2.74  30.0  2
 J9A  Var_02    C05  C04  C03  C02  -179.28  30.0  3
 J9A  Var_03    C09  C08  N07  C06   102.90  30.0  1

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
 J9A  chir_01  C05  C06  C04  N15  positiv
 J9A  chir_02  C09  N10  C11  C08  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
 J9A  plan-1  C05  0.020
 J9A  plan-1  C06  0.020
 J9A  plan-1  N07  0.020
 J9A  plan-1  C08  0.020
 J9A  plan-1  O14  0.020
 J9A  plan-1  H6   0.020
 J9A  plan-2  O01  0.020
 J9A  plan-2  C02  0.020
 J9A  plan-2  C03  0.020
 J9A  plan-2  O16  0.020
 J9A  plan-2  H17  0.020
 J9A  plan-3  C09  0.020
 J9A  plan-3  C11  0.020
 J9A  plan-3  O12  0.020
 J9A  plan-3  O1   0.020
 J9A  plan-3  H12  0.020

