# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:36:22 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  29  16  .  2022-07-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  -0.610   4.4981  -0.9997   1.7358
 J9A  C02  C  C      0   0.411   4.8099  -0.6848   0.5704
 J9A  C03  C  CH2    0  -0.581   3.7495   0.0110  -0.2998
 J9A  C04  C  CH2    0  -0.402   2.3925   0.2185   0.3504
 J9A  C05  C  CH1    0  -0.225   1.3869   0.8938  -0.5909
 J9A  C06  C  C      0   0.516   0.0137   0.9026   0.0855
 J9A  N07  N  NH1    0  -0.628  -0.7360  -0.1897  -0.1378
 J9A  C08  C  CH2    0  -0.284  -2.0526  -0.4193   0.4117
 J9A  C09  C  CH1    0  -0.225  -3.1521  -0.4021  -0.6672
 J9A  N10  N  NH2    0  -0.791  -3.1692   0.7935  -1.4837
 J9A  C11  C  C      0   0.405  -4.5041  -0.6264   0.0475
 J9A  O12  O  O      0  -0.600  -5.2793   0.3449   0.1275
 J9A  O14  O  O      0  -0.501  -0.3364   1.8307   0.8041
 J9A  N15  N  NH2    0  -0.776   1.8423   2.2164  -0.9661
 J9A  O16  O  OC    -1  -0.634   5.9170  -0.8784   0.0241
 J9A  H1   H  HCH2   0   0.229   4.1483   0.9741  -0.6298
 J9A  H2   H  HCH2   0   0.216   3.6258  -0.5732  -1.2195
 J9A  H3   H  HCH2   0   0.221   1.9852  -0.7436   0.6715
 J9A  H4   H  HCH2   0   0.215   2.4906   0.8246   1.2564
 J9A  H5   H  HCH1   0   0.237   1.3256   0.2925  -1.5048
 J9A  H6   H  HNH1   0   0.394  -0.3625  -0.8985  -0.7496
 J9A  H7   H  HCH2   0   0.238  -2.0636  -1.3794   0.9306
 J9A  H8   H  HCH2   0   0.237  -2.2434   0.3587   1.1510
 J9A  H9   H  HCH1   0   0.213  -2.9760  -1.2605  -1.3273
 J9A  H10  H  HNH2   0   0.328  -3.5168   1.5685  -0.9340
 J9A  H11  H  HNH2   0   0.332  -2.2283   1.0308  -1.7741
 J9A  H14  H  HNH2   0   0.347   1.2192   2.6127  -1.6588
 J9A  H15  H  HNH2   0   0.337   1.7834   2.8276  -0.1601
 J9A  O1   O  OC    -1  -0.618  -4.6800  -1.7651   0.5256

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  1.448  0.020  1.448
 J9A  C09  C08  single  1.541  0.020  1.541
 J9A  C09  C11  single  1.546  0.020  1.546
 J9A  C08  N07  single  1.445  0.020  1.445
 J9A  C11  O12  deloc   1.245  0.020  1.245
 J9A  N07  C06  single  1.343  0.020  1.343
 J9A  O01  C02  deloc   1.247  0.020  1.247
 J9A  C03  C02  single  1.538  0.020  1.538
 J9A  C03  C04  single  1.519  0.020  1.519
 J9A  C02  O16  deloc   1.250  0.020  1.250
 J9A  C06  O14  double  1.225  0.020  1.225
 J9A  C06  C05  single  1.531  0.020  1.531
 J9A  C04  C05  single  1.534  0.020  1.534
 J9A  C05  N15  single  1.448  0.020  1.448
 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  C11  O1   deloc   1.247  0.020  1.247

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  115.69  3.000
 J9A  O16  C02  O01  126.23  3.000
 J9A  C03  C02  O01  118.08  3.000
 J9A  H2   C03  H1   104.91  3.000
 J9A  H2   C03  C04  109.33  3.000
 J9A  H1   C03  C04  109.55  3.000
 J9A  H2   C03  C02  108.14  3.000
 J9A  H1   C03  C02  108.53  3.000
 J9A  C04  C03  C02  115.82  3.000
 J9A  H4   C04  H3   106.12  3.000
 J9A  H4   C04  C05  108.84  3.000
 J9A  H3   C04  C05  108.88  3.000
 J9A  H4   C04  C03  110.48  3.000
 J9A  H3   C04  C03  109.78  3.000
 J9A  C05  C04  C03  112.53  3.000
 J9A  H5   C05  N15  107.62  3.000
 J9A  H5   C05  C06  108.76  3.000
 J9A  N15  C05  C06  113.04  3.000
 J9A  H5   C05  C04  107.87  3.000
 J9A  N15  C05  C04  110.78  3.000
 J9A  C06  C05  C04  108.63  3.000
 J9A  O14  C06  N07  123.64  3.000
 J9A  O14  C06  C05  121.33  3.000
 J9A  N07  C06  C05  114.99  3.000
 J9A  H6   N07  C08  117.17  3.000
 J9A  H6   N07  C06  117.76  3.000
 J9A  C08  N07  C06  125.06  3.000
 J9A  H8   C08  H7   107.68  3.000
 J9A  H8   C08  C09  110.00  3.000
 J9A  H7   C08  C09  109.61  3.000
 J9A  H8   C08  N07  107.70  3.000
 J9A  H7   C08  N07  109.25  3.000
 J9A  C09  C08  N07  112.47  3.000
 J9A  H9   C09  C11  107.77  3.000
 J9A  H9   C09  N10  107.98  3.000
 J9A  C11  C09  N10  111.74  3.000
 J9A  H9   C09  C08  107.34  3.000
 J9A  C11  C09  C08  107.39  3.000
 J9A  N10  C09  C08  114.36  3.000
 J9A  H11  N10  H10  107.18  3.000
 J9A  H11  N10  C09  110.14  3.000
 J9A  H10  N10  C09  109.27  3.000
 J9A  O1   C11  O12  126.84  3.000
 J9A  O1   C11  C09  115.66  3.000
 J9A  O12  C11  C09  117.45  3.000
 J9A  H15  N15  H14  105.80  3.000
 J9A  H15  N15  C05  109.06  3.000
 J9A  H14  N15  C05  109.95  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  Var_01    C04  C03  C02  O01    -1.44  30.0  2
 J9A  Var_02    C05  C04  C03  C02  -178.94  30.0  3
 J9A  Var_03    C09  C08  N07  C06   112.22  30.0  2

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-3  C09  0.020
 J9A  plan-3  C11  0.020
 J9A  plan-3  O12  0.020
 J9A  plan-3  O1   0.020

