# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:23:01 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N~5~-[(1Z)-2-oxoethanimidoyl]-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)C=O)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
 WT2  WT2  N~5~-[(1Z)-2-oxoethanimidoyl]-L-ornithine  ligand  25  13  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_WT2
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
 WT2  CH    C  C1     0   0.114  -4.6426   0.5547   0.3928
 WT2  CZ    C  C      0   0.335  -3.4945  -0.2924  -0.1051
 WT2  NH    N  N      0  -0.647  -3.6569  -1.4098  -0.7012
 WT2  NE    N  NH1    0  -0.647  -2.2895   0.2442   0.1507
 WT2  CD    C  CH2    0  -0.228  -1.0533  -0.3782  -0.2595
 WT2  CG    C  CH2    0  -0.463   0.1417   0.3856   0.2860
 WT2  CB    C  CH2    0  -0.417   1.4618  -0.2529  -0.1194
 WT2  CA    C  CH1    0  -0.213   2.6901   0.5292   0.3554
 WT2  C     C  C      0   0.385   3.9629  -0.3132   0.0913
 WT2  OA2   O  O      0  -0.608   4.7341   0.0733  -0.8094
 WT2  OA1   O  OC    -1  -0.624   4.1002  -1.3351   0.7965
 WT2  N     N  NH2    0  -0.786   2.6910   1.8579  -0.2384
 WT2  OH    O  O      0  -0.348  -5.7882   0.2238   0.2507
 WT2  HA    H  HCH1   0   0.208   2.5990   0.6536   1.4410
 WT2  HN1   H  HNH2   0   0.334   3.4212   2.4085   0.1975
 WT2  HN2   H  HNH2   0   0.322   2.9936   1.7626  -1.2017
 WT2  HB1C  H  HCH2   0   0.221   1.5159  -1.2677   0.2807
 WT2  HB2C  H  HCH2   0   0.208   1.5035  -0.3499  -1.2114
 WT2  HG1C  H  HCH2   0   0.230   0.1117   1.4189  -0.0681
 WT2  HG2C  H  HCH2   0   0.222   0.0765   0.4253   1.3784
 WT2  HD1C  H  HCH2   0   0.227  -1.0388  -1.4131   0.0952
 WT2  HD2C  H  HCH2   0   0.224  -1.0015  -0.4278  -1.3535
 WT2  HH1N  H  H      0   0.332  -4.6470  -1.6243  -0.7630
 WT2  HH    H  H      0   0.219  -4.3699   1.4979   0.8958
 WT2  HNE   H  HNH1   0   0.399  -2.2424   1.1597   0.5671

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
 WT2  OA1  C     deloc   1.249  0.020  1.249
 WT2  C    OA2   deloc   1.247  0.020  1.247
 WT2  C    CA    single  1.549  0.020  1.549
 WT2  CA   N     single  1.455  0.020  1.455
 WT2  CA   CB    single  1.532  0.020  1.532
 WT2  CB   CG    single  1.521  0.020  1.521
 WT2  CG   CD    single  1.520  0.020  1.520
 WT2  CD   NE    single  1.444  0.020  1.444
 WT2  NE   CZ    single  1.344  0.020  1.344
 WT2  CZ   NH    double  1.277  0.020  1.277
 WT2  CZ   CH    single  1.511  0.020  1.511
 WT2  CH   OH    double  1.201  0.020  1.201
 WT2  CA   HA    single  0.970  0.020  1.090
 WT2  N    HN1   single  0.890  0.020  1.040
 WT2  N    HN2   single  0.890  0.020  1.040
 WT2  CB   HB1C  single  0.970  0.020  1.090
 WT2  CB   HB2C  single  0.970  0.020  1.090
 WT2  CG   HG1C  single  0.970  0.020  1.090
 WT2  CG   HG2C  single  0.970  0.020  1.090
 WT2  CD   HD1C  single  0.970  0.020  1.090
 WT2  CD   HD2C  single  0.970  0.020  1.090
 WT2  NH   HH1N  single  0.890  0.020  1.040
 WT2  CH   HH    single  0.930  0.020  1.080
 WT2  NE   HNE   single  0.860  0.020  1.020

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
 WT2  HH    CH  OH    121.69  3.000
 WT2  HH    CH  CZ    116.21  3.000
 WT2  OH    CH  CZ    122.10  3.000
 WT2  NE    CZ  NH    123.54  3.000
 WT2  NH    CZ  CH    123.21  3.000
 WT2  NE    CZ  CH    113.25  3.000
 WT2  HH1N  NH  CZ    109.72  3.000
 WT2  HNE   NE  CD    118.01  3.000
 WT2  HNE   NE  CZ    118.94  3.000
 WT2  CD    NE  CZ    122.80  3.000
 WT2  HD2C  CD  HD1C  106.26  3.000
 WT2  HD2C  CD  CG    110.11  3.000
 WT2  HD1C  CD  CG    110.40  3.000
 WT2  HD2C  CD  NE    110.10  3.000
 WT2  HD1C  CD  NE    109.09  3.000
 WT2  CG    CD  NE    110.78  3.000
 WT2  HG2C  CG  HG1C  106.71  3.000
 WT2  HG2C  CG  CB    109.43  3.000
 WT2  HG1C  CG  CB    109.53  3.000
 WT2  HG2C  CG  CD    109.24  3.000
 WT2  HG1C  CG  CD    109.72  3.000
 WT2  CB    CG  CD    112.07  3.000
 WT2  HB2C  CB  HB1C  106.29  3.000
 WT2  HB2C  CB  CA    108.86  3.000
 WT2  HB1C  CB  CA    108.74  3.000
 WT2  HB2C  CB  CG    109.59  3.000
 WT2  HB1C  CB  CG    109.59  3.000
 WT2  CA    CB  CG    113.51  3.000
 WT2  HA    CA  N     107.48  3.000
 WT2  HA    CA  C     107.38  3.000
 WT2  N     CA  C     115.24  3.000
 WT2  HA    CA  CB    107.35  3.000
 WT2  N     CA  CB    109.89  3.000
 WT2  C     CA  CB    109.17  3.000
 WT2  OA1   C   OA2   126.38  3.000
 WT2  OA2   C   CA    117.56  3.000
 WT2  OA1   C   CA    116.04  3.000
 WT2  HN2   N   HN1   104.17  3.000
 WT2  HN2   N   CA    107.57  3.000
 WT2  HN1   N   CA    108.73  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
 WT2  CONST_01  CD    NE  CZ  CH   180.00   0.0  0
 WT2  CONST_02  CD    NE  CZ  NH     0.00   0.0  0
 WT2  CONST_03  HNE   NE  CZ  CH     0.00   0.0  0
 WT2  CONST_04  HH1N  NH  CZ  CH     0.00   0.0  0
 WT2  Var_01    CG    CD  NE  CZ  -174.44  30.0  1
 WT2  Var_02    OH    CH  CZ  NH    -0.27  30.0  2
 WT2  Var_03    CB    CG  CD  NE   179.51  30.0  2
 WT2  Var_04    CA    CB  CG  CD   177.17  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
 WT2  chir_01  CA  C  N  CB  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
 WT2  plan-1  CH    0.020
 WT2  plan-1  CZ    0.020
 WT2  plan-1  NH    0.020
 WT2  plan-1  NE    0.020
 WT2  plan-1  CD    0.020
 WT2  plan-1  HH1N  0.020
 WT2  plan-1  HNE   0.020
 WT2  plan-2  CA    0.020
 WT2  plan-2  C     0.020
 WT2  plan-2  OA2   0.020
 WT2  plan-2  OA1   0.020
 WT2  plan-3  CH    0.020
 WT2  plan-3  CZ    0.020
 WT2  plan-3  OH    0.020
 WT2  plan-3  HH    0.020

