# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:33:48 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 6-hydroxy-D-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCCCO)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
 DDO  DDO  '6-hydroxy-D-norleucine   '  ligand  22  10  .  2022-07-24  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_DDO
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
 DDO  N    N  NH2    0  -0.786   1.8033   0.1393  -1.4296
 DDO  CA   C  CH1    0  -0.211   0.3815   0.4510  -1.4273
 DDO  CB   C  CH2    0  -0.413  -0.2822  -0.1464  -0.1836
 DDO  CG   C  CH2    0  -0.416   0.2726   0.3877   1.1294
 DDO  CD   C  CH2    0  -0.454  -0.3926  -0.2401   2.3481
 DDO  CE   C  CH2    0  -0.137   0.1594   0.3153   3.6454
 DDO  OZ   O  OH1    0  -0.677  -0.4875  -0.3078   4.7362
 DDO  C    C  C      0   0.383  -0.3982   0.0034  -2.6887
 DDO  O    O  O      0  -0.609   0.1550  -0.8128  -3.4526
 DDO  OXT  O  OC    -1  -0.625  -1.5418   0.4877  -2.8246
 DDO  HN1  H  HNH2   0   0.321   1.9044  -0.8398  -1.6742
 DDO  HN2  H  HNH2   0   0.333   2.2415   0.6326  -2.1983
 DDO  HA1  H  HCH1   0   0.204   0.2854   1.5413  -1.3537
 DDO  HB1  H  HCH2   0   0.215  -1.3559   0.0504  -0.2302
 DDO  HB2  H  HCH2   0   0.202  -0.1711  -1.2381  -0.2089
 DDO  HG1  H  HCH2   0   0.215   1.3511   0.2155   1.1657
 DDO  HG2  H  HCH2   0   0.204   0.1377   1.4751   1.1593
 DDO  HD1  H  HCH2   0   0.215  -1.4731  -0.0677   2.3082
 DDO  HD2  H  HCH2   0   0.215  -0.2471  -1.3252   2.3254
 DDO  HE1  H  HCH2   0   0.185   1.2447   0.1472   3.6764
 DDO  HE2  H  HCH2   0   0.186   0.0114   1.4037   3.6633
 DDO  HOZ  H  HOH1   0   0.451  -0.1307   0.0641   5.5477

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
 DDO  N   CA   single  1.456  0.020  1.456
 DDO  N   HN1  single  0.890  0.020  1.040
 DDO  N   HN2  single  0.890  0.020  1.040
 DDO  CA  CB   single  1.531  0.020  1.531
 DDO  CA  C    single  1.549  0.020  1.549
 DDO  CA  HA1  single  0.970  0.020  1.090
 DDO  CB  CG   single  1.522  0.020  1.522
 DDO  CB  HB1  single  0.970  0.020  1.090
 DDO  CB  HB2  single  0.970  0.020  1.090
 DDO  CG  CD   single  1.524  0.020  1.524
 DDO  CG  HG1  single  0.970  0.020  1.090
 DDO  CG  HG2  single  0.970  0.020  1.090
 DDO  CD  CE   single  1.515  0.020  1.515
 DDO  CD  HD1  single  0.970  0.020  1.090
 DDO  CD  HD2  single  0.970  0.020  1.090
 DDO  CE  OZ   single  1.413  0.020  1.413
 DDO  CE  HE1  single  0.970  0.020  1.090
 DDO  CE  HE2  single  0.970  0.020  1.090
 DDO  OZ  HOZ  single  0.850  0.020  0.980
 DDO  C   O    deloc   1.247  0.020  1.247
 DDO  C   OXT  deloc   1.249  0.020  1.249

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
 DDO  HN2  N   HN1  104.12  3.000
 DDO  HN2  N   CA   108.62  3.000
 DDO  HN1  N   CA   107.72  3.000
 DDO  HA1  CA  C    107.32  3.000
 DDO  HA1  CA  CB   107.18  3.000
 DDO  C    CA  CB   109.30  3.000
 DDO  HA1  CA  N    107.37  3.000
 DDO  C    CA  N    115.37  3.000
 DDO  CB   CA  N    109.94  3.000
 DDO  HB2  CB  HB1  106.12  3.000
 DDO  HB2  CB  CG   109.39  3.000
 DDO  HB1  CB  CG   109.37  3.000
 DDO  HB2  CB  CA   109.00  3.000
 DDO  HB1  CB  CA   108.73  3.000
 DDO  CG   CB  CA   113.94  3.000
 DDO  HG2  CG  HG1  106.08  3.000
 DDO  HG2  CG  CD   109.46  3.000
 DDO  HG1  CG  CD   109.84  3.000
 DDO  HG2  CG  CB   109.07  3.000
 DDO  HG1  CG  CB   109.45  3.000
 DDO  CD   CG  CB   112.72  3.000
 DDO  HD2  CD  HD1  106.64  3.000
 DDO  HD2  CD  CE   109.42  3.000
 DDO  HD1  CD  CE   109.45  3.000
 DDO  HD2  CD  CG   109.49  3.000
 DDO  HD1  CD  CG   109.68  3.000
 DDO  CE   CD  CG   112.01  3.000
 DDO  HE2  CE  HE1  106.51  3.000
 DDO  HE2  CE  OZ   111.26  3.000
 DDO  HE1  CE  OZ   111.28  3.000
 DDO  HE2  CE  CD   109.15  3.000
 DDO  HE1  CE  CD   109.14  3.000
 DDO  OZ   CE  CD   109.42  3.000
 DDO  HOZ  OZ  CE   108.13  3.000
 DDO  OXT  C   O    126.37  3.000
 DDO  OXT  C   CA   115.93  3.000
 DDO  O    C   CA   117.69  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
 DDO  Var_01  CD  CG  CB  CA  -179.14  30.0  3
 DDO  Var_02  CE  CD  CG  CB  -179.29  30.0  3
 DDO  Var_03  OZ  CE  CD  CG  -179.66  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
 DDO  chir_01  CA  N  CB  C  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
 DDO  plan-1  CA   0.020
 DDO  plan-1  C    0.020
 DDO  plan-1  O    0.020
 DDO  plan-1  OXT  0.020

