# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 08:52:30 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (3S,4R)-3-amino-4-hydroxyheptanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(O)=O)[C@H](O)CCC(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
 Y2Y  Y2Y  '(3S,4R)-3-amino-4-hydroxyheptanedioic acid'  ligand  24  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y2Y
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
 Y2Y  N    N  NH2    0  -0.795  40.3222  17.9753  11.7387
 Y2Y  CA   C  CH2    0  -0.597  39.3606  15.8206  15.4850
 Y2Y  C    C  C      0   0.410  40.1511  16.1056  16.7803
 Y2Y  O    O  O      0  -0.605  40.4519  17.2918  17.0215
 Y2Y  CB1  C  CH2    0  -0.549  38.3649  17.0602  10.6567
 Y2Y  CG1  C  C      0   0.403  38.2625  18.1635   9.5867
 Y2Y  OD1  O  OC    -1  -0.616  37.7987  19.2624   9.9586
 Y2Y  OD2  O  O      0  -0.618  38.6097  17.8621   8.4263
 Y2Y  C01  C  CH2    0  -0.433  39.4778  16.8799  14.3962
 Y2Y  C2   C  CH1    0   0.074  38.8343  16.4628  13.0751
 Y2Y  CA1  C  CH1    0  -0.103  38.9528  17.5365  11.9803
 Y2Y  O1   O  OH1    0  -0.680  37.4525  16.1917  13.2413
 Y2Y  H1   H  HNH2   0   0.344  40.7238  18.3802  12.5742
 Y2Y  H2   H  HNH2   0   0.329  40.9014  17.1759  11.5056
 Y2Y  H4   H  HCH2   0   0.217  38.3114  15.6931  15.7807
 Y2Y  H5   H  HCH2   0   0.208  39.6728  14.8479  15.0899
 Y2Y  H7   H  HCH2   0   0.224  37.3591  16.6639  10.8255
 Y2Y  H8   H  HCH2   0   0.186  38.9631  16.2215  10.2830
 Y2Y  H10  H  HCH2   0   0.201  40.5381  17.0783  14.2226
 Y2Y  H11  H  HCH2   0   0.204  39.0359  17.8231  14.7320
 Y2Y  H12  H  HCH1   0   0.167  39.3580  15.5598  12.7145
 Y2Y  H13  H  HCH1   0   0.203  38.3858  18.4124  12.3129
 Y2Y  H14  H  HOH1   0   0.446  37.3582  15.4496  13.8454
 Y2Y  OXT  O  OC    -1  -0.620  40.3991  15.1138  17.4968

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
 Y2Y  OD2  CG1  deloc   1.248  0.020  1.248
 Y2Y  CG1  OD1  deloc   1.249  0.020  1.249
 Y2Y  CG1  CB1  single  1.540  0.020  1.540
 Y2Y  CB1  CA1  single  1.525  0.020  1.525
 Y2Y  N    CA1  single  1.458  0.020  1.458
 Y2Y  CA1  C2   single  1.538  0.020  1.538
 Y2Y  C2   O1   single  1.418  0.020  1.418
 Y2Y  C2   C01  single  1.527  0.020  1.527
 Y2Y  C01  CA   single  1.524  0.020  1.524
 Y2Y  CA   C    single  1.544  0.020  1.544
 Y2Y  C    O    deloc   1.247  0.020  1.247
 Y2Y  N    H1   single  0.890  0.020  1.040
 Y2Y  N    H2   single  0.890  0.020  1.040
 Y2Y  CA   H4   single  0.970  0.020  1.090
 Y2Y  CA   H5   single  0.970  0.020  1.090
 Y2Y  CB1  H7   single  0.970  0.020  1.090
 Y2Y  CB1  H8   single  0.970  0.020  1.090
 Y2Y  C01  H10  single  0.970  0.020  1.090
 Y2Y  C01  H11  single  0.970  0.020  1.090
 Y2Y  C2   H12  single  0.970  0.020  1.090
 Y2Y  CA1  H13  single  0.970  0.020  1.090
 Y2Y  O1   H14  single  0.850  0.020  0.980
 Y2Y  C    OXT  deloc   1.248  0.020  1.248

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
 Y2Y  H2   N    H1   106.16  3.000
 Y2Y  H2   N    CA1  109.71  3.000
 Y2Y  H1   N    CA1  110.88  3.000
 Y2Y  H5   CA   H4   105.46  3.000
 Y2Y  H5   CA   C01  109.74  3.000
 Y2Y  H4   CA   C01  110.29  3.000
 Y2Y  H5   CA   C    108.70  3.000
 Y2Y  H4   CA   C    106.55  3.000
 Y2Y  C01  CA   C    115.58  3.000
 Y2Y  OXT  C    O    126.63  3.000
 Y2Y  OXT  C    CA   115.88  3.000
 Y2Y  O    C    CA   117.47  3.000
 Y2Y  H8   CB1  H7   106.10  3.000
 Y2Y  H8   CB1  CA1  108.94  3.000
 Y2Y  H7   CB1  CA1  109.49  3.000
 Y2Y  H8   CB1  CG1  110.34  3.000
 Y2Y  H7   CB1  CG1  107.79  3.000
 Y2Y  CA1  CB1  CG1  113.89  3.000
 Y2Y  OD2  CG1  OD1  126.33  3.000
 Y2Y  OD1  CG1  CB1  116.61  3.000
 Y2Y  OD2  CG1  CB1  117.02  3.000
 Y2Y  H11  C01  H10  106.50  3.000
 Y2Y  H11  C01  C2   109.30  3.000
 Y2Y  H10  C01  C2   108.72  3.000
 Y2Y  H11  C01  CA   110.42  3.000
 Y2Y  H10  C01  CA   108.33  3.000
 Y2Y  C2   C01  CA   113.32  3.000
 Y2Y  H12  C2   O1   110.12  3.000
 Y2Y  H12  C2   CA1  107.57  3.000
 Y2Y  O1   C2   CA1  106.98  3.000
 Y2Y  H12  C2   C01  107.81  3.000
 Y2Y  O1   C2   C01  111.19  3.000
 Y2Y  CA1  C2   C01  113.12  3.000
 Y2Y  H13  CA1  C2   107.59  3.000
 Y2Y  H13  CA1  CB1  108.29  3.000
 Y2Y  C2   CA1  CB1  111.73  3.000
 Y2Y  H13  CA1  N    107.21  3.000
 Y2Y  C2   CA1  N    113.61  3.000
 Y2Y  CB1  CA1  N    108.20  3.000
 Y2Y  H14  O1   C2   108.47  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
 Y2Y  Var_01  C2   C01  CA   C    172.24  30.0  1
 Y2Y  Var_02  C01  CA   C    O     22.24  30.0  2
 Y2Y  Var_03  CA1  CB1  CG1  OD1  -45.65  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
 Y2Y  chir_01  C2   CA1  O1   C01  positiv
 Y2Y  chir_02  CA1  N    CB1  C2   negativ

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
 Y2Y  plan-1  CA   0.020
 Y2Y  plan-1  C    0.020
 Y2Y  plan-1  O    0.020
 Y2Y  plan-1  OXT  0.020
 Y2Y  plan-2  CB1  0.020
 Y2Y  plan-2  CG1  0.020
 Y2Y  plan-2  OD1  0.020
 Y2Y  plan-2  OD2  0.020

