# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:03:42 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  30  15  .  2021-08-05  2021-08-05  
;
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  -0.453   1.5832  -0.6276  -0.2393
 58B  N01  N  NH2   0  -0.773  -4.2235   1.2245  -0.3043
 58B  C02  C  CH1   0  -0.228  -2.7969   1.3671  -0.4883
 58B  C03  C  CH3   0  -0.653  -2.3372   2.7349   0.0157
 58B  N05  N  NH1   0  -0.629  -0.7493   0.0747  -0.3012
 58B  C06  C  CH1   0  -0.198   0.1566  -0.8993   0.2423
 58B  C07  C  C     0   0.519  -0.2669  -2.3176  -0.1557
 58B  N08  N  NH2   0  -0.800   0.1666  -3.2755   0.6737
 58B  O09  O  O     0  -0.479  -0.9148  -2.5345  -1.1655
 58B  C11  C  CH2   0  -0.577   2.0979   0.7163   0.2503
 58B  C12  C  C     0   0.554   3.5161   0.9886  -0.1692
 58B  O13  O  O     0  -0.443   4.1993   0.2465  -0.8298
 58B  O14  O  OH1   0  -0.596   3.9435   2.1648   0.2775
 58B  O15  O  O     0  -0.489  -2.3743  -0.2942   1.2136
 58B  H1   H  HCH2  0   0.265   2.2307  -1.4242   0.1293
 58B  H2   H  HCH2  0   0.256   1.6174  -0.6779  -1.3310
 58B  H4   H  HNH2  0   0.341  -4.4367   1.1994   0.6861
 58B  H6   H  HCH1  0   0.253  -2.5899   1.3119  -1.5617
 58B  H7   H  HCH3  0   0.230  -2.5136   2.8331   1.0885
 58B  H8   H  HCH3  0   0.233  -1.2746   2.8933  -0.1662
 58B  H9   H  HCH3  0   0.244  -2.8907   3.5236  -0.4924
 58B  H10  H  HNH1  0   0.401  -0.5377   0.4623  -1.2078
 58B  H11  H  HCH1  0   0.277   0.1358  -0.8217   1.3334
 58B  H12  H  HNH2  0   0.409   0.6781  -3.0636   1.5133
 58B  H13  H  HNH2  0   0.404   0.0022  -4.2475   0.4675
 58B  H14  H  HCH2  0   0.284   1.4767   1.5397  -0.1129
 58B  H15  H  HCH2  0   0.287   2.0466   0.7705   1.3422
 58B  H16  H  HOH1  0   0.480   4.8581   2.3151  -0.0051
 58B  C04  C  C     0   0.532  -1.9728   0.2875   0.2172
 58B  H3   H  HNH2  0   0.350  -4.5359   0.3372  -0.6789

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  1.445  0.020  1.445
 58B  O15  C04  double  1.222  0.020  1.222
 58B  O13  C12  double  1.206  0.020  1.206
 58B  C02  C04  single  1.530  0.020  1.530
 58B  C02  C03  single  1.528  0.020  1.528
 58B  C04  N05  single  1.346  0.020  1.346
 58B  C11  C12  single  1.504  0.020  1.504
 58B  C11  C10  single  1.520  0.020  1.520
 58B  C12  O14  single  1.329  0.020  1.329
 58B  N05  C06  single  1.437  0.020  1.437
 58B  C06  C10  single  1.530  0.020  1.530
 58B  C06  C07  single  1.533  0.020  1.533
 58B  O09  C07  double  1.219  0.020  1.219
 58B  C07  N08  single  1.339  0.020  1.339
 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
 58B  O14  H16  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
 58B  H2   C10  H1   106.58  3.000
 58B  H2   C10  C11  110.59  3.000
 58B  H1   C10  C11  109.62  3.000
 58B  H2   C10  C06  109.59  3.000
 58B  H1   C10  C06  108.51  3.000
 58B  C11  C10  C06  111.80  3.000
 58B  H4   N01  H3   105.96  3.000
 58B  H4   N01  C02  109.54  3.000
 58B  H3   N01  C02  110.11  3.000
 58B  H6   C02  C04  108.34  3.000
 58B  H6   C02  C03  108.15  3.000
 58B  C04  C02  C03  108.50  3.000
 58B  H6   C02  N01  107.85  3.000
 58B  C03  C02  N01  110.07  3.000
 58B  C04  C02  N01  113.78  3.000
 58B  H9   C03  H8   108.21  3.000
 58B  H9   C03  H7   108.12  3.000
 58B  H8   C03  H7   107.97  3.000
 58B  H9   C03  C02  109.96  3.000
 58B  H8   C03  C02  111.62  3.000
 58B  H7   C03  C02  110.85  3.000
 58B  H10  N05  C06  117.92  3.000
 58B  H10  N05  C04  118.45  3.000
 58B  C06  N05  C04  122.32  3.000
 58B  H11  C06  C07  108.62  3.000
 58B  H11  C06  N05  108.49  3.000
 58B  C07  C06  N05  110.78  3.000
 58B  H11  C06  C10  108.61  3.000
 58B  C07  C06  C10  109.89  3.000
 58B  N05  C06  C10  110.39  3.000
 58B  O09  C07  N08  123.90  3.000
 58B  N08  C07  C06  114.30  3.000
 58B  O09  C07  C06  121.77  3.000
 58B  H13  N08  H12  117.21  3.000
 58B  H13  N08  C07  120.71  3.000
 58B  H12  N08  C07  122.07  3.000
 58B  H15  C11  H14  105.52  3.000
 58B  H15  C11  C12  108.28  3.000
 58B  H14  C11  C12  107.86  3.000
 58B  H15  C11  C10  110.44  3.000
 58B  H14  C11  C10  111.49  3.000
 58B  C12  C11  C10  112.92  3.000
 58B  O14  C12  O13  123.14  3.000
 58B  O14  C12  C11  111.70  3.000
 58B  O13  C12  C11  125.15  3.000
 58B  H16  O14  C12  110.05  3.000
 58B  O15  C04  N05  122.53  3.000
 58B  N05  C04  C02  115.06  3.000
 58B  O15  C04  C02  122.33  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  CONST_06  H16  O14  C12  C11  180.00   0.0  0
 58B  Var_01    O13  C12  C11  C10    0.40  30.0  3
 58B  Var_02    C12  C11  C10  C06  178.02  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
 58B  plan-3  H16  0.020

