# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 05:40:37 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  23  10  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.775   1.8555   0.1580  -1.4387
 DDO  CA   C  CH1   0  -0.207   0.4399   0.4383  -1.4314
 DDO  CB   C  CH2   0  -0.428  -0.2322  -0.1900  -0.2023
 DDO  CG   C  CH2   0  -0.420   0.2983   0.3649   1.1122
 DDO  CD   C  CH2   0  -0.457  -0.3855  -0.2663   2.3185
 DDO  CE   C  CH2   0  -0.137   0.1308   0.3052   3.6237
 DDO  OZ   O  OH1   0  -0.676  -0.5329  -0.3216   4.7013
 DDO  C    C  C     0   0.520  -0.2803  -0.0348  -2.6871
 DDO  O    O  O     0  -0.442   0.1634  -0.8350  -3.4728
 DDO  OXT  O  OH1   0  -0.594  -1.4790   0.5237  -2.8175
 DDO  HN1  H  HNH2  0   0.342   2.0135  -0.8321  -1.5821
 DDO  HN2  H  HNH2  0   0.354   2.3063   0.6317  -2.2108
 DDO  HA1  H  HCH1  0   0.265   0.3055   1.5233  -1.3683
 DDO  HB1  H  HCH2  0   0.240  -1.3109  -0.0244  -0.2508
 DDO  HB2  H  HCH2  0   0.229  -0.0858  -1.2756  -0.2325
 DDO  HG1  H  HCH2  0   0.226   1.3772   0.2048   1.1699
 DDO  HG2  H  HCH2  0   0.215   0.1467   1.4496   1.1304
 DDO  HD1  H  HCH2  0   0.219  -1.4668  -0.1076   2.2540
 DDO  HD2  H  HCH2  0   0.220  -0.2243  -1.3490   2.3056
 DDO  HE1  H  HCH2  0   0.187   1.2172   0.1523   3.6800
 DDO  HE2  H  HCH2  0   0.187  -0.0328   1.3915   3.6315
 DDO  HOZ  H  HOH1  0   0.452  -0.1991   0.0562   5.5198
 DDO  HXT  H  HOH1  0   0.480  -1.9269   0.1710  -3.6011

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  1.443  0.020  1.443
 DDO  N    HN1  single  0.890  0.020  1.040
 DDO  N    HN2  single  0.890  0.020  1.040
 DDO  CA   CB   single  1.535  0.020  1.535
 DDO  CA   C    single  1.523  0.020  1.523
 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  1.412  0.020  1.412
 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    double  1.206  0.020  1.206
 DDO  C    OXT  single  1.329  0.020  1.329
 DDO  OXT  HXT  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
 DDO  HN2  N    HN1  106.27  3.000
 DDO  HN2  N    CA   110.48  3.000
 DDO  HN1  N    CA   110.10  3.000
 DDO  HA1  CA   C    107.29  3.000
 DDO  HA1  CA   CB   107.80  3.000
 DDO  C    CA   CB   109.03  3.000
 DDO  HA1  CA   N    108.25  3.000
 DDO  C    CA   N    113.54  3.000
 DDO  CB   CA   N    110.72  3.000
 DDO  HB2  CB   HB1  106.31  3.000
 DDO  HB2  CB   CG   109.78  3.000
 DDO  HB1  CB   CG   109.10  3.000
 DDO  HB2  CB   CA   108.96  3.000
 DDO  HB1  CB   CA   109.55  3.000
 DDO  CG   CB   CA   112.93  3.000
 DDO  HG2  CG   HG1  106.32  3.000
 DDO  HG2  CG   CD   109.57  3.000
 DDO  HG1  CG   CD   109.92  3.000
 DDO  HG2  CG   CB   109.09  3.000
 DDO  HG1  CG   CB   109.66  3.000
 DDO  CD   CG   CB   112.11  3.000
 DDO  HD2  CD   HD1  106.74  3.000
 DDO  HD2  CD   CE   109.45  3.000
 DDO  HD1  CD   CE   109.42  3.000
 DDO  HD2  CD   CG   109.53  3.000
 DDO  HD1  CD   CG   109.67  3.000
 DDO  CE   CD   CG   111.89  3.000
 DDO  HE2  CE   HE1  106.53  3.000
 DDO  HE2  CE   OZ   111.31  3.000
 DDO  HE1  CE   OZ   111.34  3.000
 DDO  HE2  CE   CD   109.16  3.000
 DDO  HE1  CE   CD   109.18  3.000
 DDO  OZ   CE   CD   109.25  3.000
 DDO  HOZ  OZ   CE   108.18  3.000
 DDO  OXT  C    O    123.15  3.000
 DDO  OXT  C    CA   112.14  3.000
 DDO  O    C    CA   124.70  3.000
 DDO  HXT  OXT  C    110.08  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  CONST_01  HXT  OXT  C   CA   180.00   0.0  0
 DDO  Var_01    CD   CG   CB  CA   179.73  30.0  3
 DDO  Var_02    CE   CD   CG  CB  -179.11  30.0  3
 DDO  Var_03    OZ   CE   CD  CG  -179.69  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
 DDO  plan-1  HXT  0.020

