# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 00:11:51 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: L-alanyl-D-alpha-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)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
 58B  58B  L-alanyl-D-alpha-glutamine  ligand  29  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_58B
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
 58B  C10  C  CH2    0  -0.443   1.5963  -0.5887  -0.2420
 58B  N01  N  NH2    0  -0.773  -4.2487   1.1821  -0.2969
 58B  C02  C  CH1    0  -0.228  -2.8233   1.3440  -0.4766
 58B  C03  C  CH3    0  -0.652  -2.3815   2.7120   0.0429
 58B  N05  N  NH1    0  -0.626  -0.7415   0.1112  -0.2693
 58B  C06  C  CH1    0  -0.188   0.1769  -0.8565   0.2671
 58B  C07  C  C      0   0.518  -0.2551  -2.2747  -0.1123
 58B  N08  N  NH2    0  -0.801   0.1593  -3.2248   0.7368
 58B  O09  O  O      0  -0.486  -0.8890  -2.5066  -1.1289
 58B  C11  C  CH2    0  -0.583   2.1406   0.7586   0.2049
 58B  C12  C  C      0   0.418   3.6112   1.0237  -0.1717
 58B  O13  O  O      0  -0.606   4.2271   0.1261  -0.7781
 58B  O14  O  OC    -1  -0.629   4.0656   2.1345   0.1716
 58B  O15  O  O      0  -0.494  -2.4023  -0.3775   1.1672
 58B  H1   H  HCH2   0   0.242   2.2465  -1.3827   0.1281
 58B  H2   H  HCH2   0   0.231   1.6107  -0.6676  -1.3333
 58B  H6   H  HCH1   0   0.252  -2.6142   1.3037  -1.5504
 58B  H7   H  HCH3   0   0.230  -2.5596   2.7958   1.1168
 58B  H8   H  HCH3   0   0.232  -1.3209   2.8861  -0.1353
 58B  H9   H  HCH3   0   0.243  -2.9443   3.4997  -0.4566
 58B  H10  H  HNH1   0   0.398  -0.4997   0.5612  -1.1386
 58B  H11  H  HCH1   0   0.264   0.1801  -0.7693   1.3584
 58B  H12  H  HNH2   0   0.407   0.6688  -3.0042   1.5751
 58B  H13  H  HNH2   0   0.401  -0.0026  -4.1986   0.5382
 58B  H14  H  HCH2   0   0.227   1.5381   1.5759  -0.2038
 58B  H15  H  HCH2   0   0.228   2.0429   0.8496   1.2928
 58B  H3   H  HNH2   0   0.349  -4.5481   0.2946  -0.6815
 58B  C04  C  C      0   0.529  -1.9864   0.2627   0.2122
 58B  H4   H  HNH2   0   0.340  -4.4621   1.1406   0.6929

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
 58B  N01  C02  single  1.446  0.020  1.446
 58B  O15  C04  double  1.223  0.020  1.223
 58B  O13  C12  deloc   1.246  0.020  1.246
 58B  C02  C04  single  1.531  0.020  1.531
 58B  C02  C03  single  1.529  0.020  1.529
 58B  C04  N05  single  1.343  0.020  1.343
 58B  C11  C12  single  1.541  0.020  1.541
 58B  C11  C10  single  1.520  0.020  1.520
 58B  C12  O14  deloc   1.248  0.020  1.248
 58B  N05  C06  single  1.438  0.020  1.438
 58B  C06  C10  single  1.532  0.020  1.532
 58B  C06  C07  single  1.530  0.020  1.530
 58B  O09  C07  double  1.220  0.020  1.220
 58B  C07  N08  single  1.340  0.020  1.340
 58B  C10  H1   single  0.970  0.020  1.090
 58B  C10  H2   single  0.970  0.020  1.090
 58B  N01  H3   single  0.890  0.020  1.040
 58B  N01  H4   single  0.890  0.020  1.040
 58B  C02  H6   single  0.970  0.020  1.090
 58B  C03  H7   single  0.970  0.020  1.090
 58B  C03  H8   single  0.970  0.020  1.090
 58B  C03  H9   single  0.970  0.020  1.090
 58B  N05  H10  single  0.860  0.020  1.020
 58B  C06  H11  single  0.970  0.020  1.090
 58B  N08  H12  single  0.860  0.020  1.020
 58B  N08  H13  single  0.860  0.020  1.020
 58B  C11  H14  single  0.970  0.020  1.090
 58B  C11  H15  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
 58B  H2   C10  H1   106.15  3.000
 58B  H2   C10  C11  110.63  3.000
 58B  H1   C10  C11  109.39  3.000
 58B  H2   C10  C06  109.33  3.000
 58B  H1   C10  C06  108.20  3.000
 58B  C11  C10  C06  112.89  3.000
 58B  H4   N01  H3   105.83  3.000
 58B  H4   N01  C02  109.49  3.000
 58B  H3   N01  C02  110.03  3.000
 58B  H6   C02  C04  108.11  3.000
 58B  H6   C02  C03  108.13  3.000
 58B  C04  C02  C03  108.73  3.000
 58B  H6   C02  N01  107.83  3.000
 58B  C03  C02  N01  110.06  3.000
 58B  C04  C02  N01  113.82  3.000
 58B  H9   C03  H8   108.20  3.000
 58B  H9   C03  H7   108.13  3.000
 58B  H8   C03  H7   107.90  3.000
 58B  H9   C03  C02  109.99  3.000
 58B  H8   C03  C02  111.65  3.000
 58B  H7   C03  C02  110.85  3.000
 58B  H10  N05  C06  117.96  3.000
 58B  H10  N05  C04  118.74  3.000
 58B  C06  N05  C04  122.28  3.000
 58B  H11  C06  C07  108.77  3.000
 58B  H11  C06  N05  108.67  3.000
 58B  C07  C06  N05  110.54  3.000
 58B  H11  C06  C10  108.34  3.000
 58B  C07  C06  C10  109.95  3.000
 58B  N05  C06  C10  110.50  3.000
 58B  O09  C07  N08  123.63  3.000
 58B  N08  C07  C06  114.38  3.000
 58B  O09  C07  C06  121.96  3.000
 58B  H13  N08  H12  117.26  3.000
 58B  H13  N08  C07  120.73  3.000
 58B  H12  N08  C07  121.97  3.000
 58B  H15  C11  H14  105.04  3.000
 58B  H15  C11  C12  108.26  3.000
 58B  H14  C11  C12  107.80  3.000
 58B  H15  C11  C10  109.47  3.000
 58B  H14  C11  C10  110.79  3.000
 58B  C12  C11  C10  114.98  3.000
 58B  O14  C12  O13  126.50  3.000
 58B  O14  C12  C11  115.68  3.000
 58B  O13  C12  C11  117.82  3.000
 58B  O15  C04  N05  122.43  3.000
 58B  N05  C04  C02  115.15  3.000
 58B  O15  C04  C02  122.36  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
 58B  CONST_01  C06  N05  C04  C02  180.00   0.0  0
 58B  CONST_02  O15  C04  N05  C06    0.00   0.0  0
 58B  CONST_03  H10  N05  C04  C02    0.00   0.0  0
 58B  CONST_04  H12  N08  C07  C06    0.00   0.0  0
 58B  CONST_05  H13  N08  C07  C06  180.00   0.0  0
 58B  Var_01    O13  C12  C11  C10   -1.11  30.0  3
 58B  Var_02    C12  C11  C10  C06  174.68  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
 58B  chir_01  C02  N01  C04  C03  positiv
 58B  chir_02  C06  N05  C10  C07  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
 58B  plan-1  C06  0.020
 58B  plan-1  C07  0.020
 58B  plan-1  N08  0.020
 58B  plan-1  O09  0.020
 58B  plan-1  H12  0.020
 58B  plan-1  H13  0.020
 58B  plan-2  C02  0.020
 58B  plan-2  N05  0.020
 58B  plan-2  C06  0.020
 58B  plan-2  O15  0.020
 58B  plan-2  H10  0.020
 58B  plan-2  C04  0.020
 58B  plan-3  C11  0.020
 58B  plan-3  C12  0.020
 58B  plan-3  O13  0.020
 58B  plan-3  O14  0.020

