# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:01:18 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (4R)-4-hydroxy-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC[C@@H](O)C[C@H](N)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
 UXY  UXY  '(4R)-4-hydroxy-L-lysine  '  L-peptide  24  11  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_UXY
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
 UXY  N    N  NH2    0  -0.808  231.8555  297.8083  191.1243
 UXY  CA   C  CH1    0  -0.216  231.4259  297.9490  189.7349
 UXY  C    C  C      0   0.389  230.0930  298.7038  189.5117
 UXY  O    O  O      0  -0.615  229.8125  298.9523  188.3205
 UXY  C03  C  CH2    0  -0.472  231.3606  296.5701  189.0592
 UXY  C04  C  CH1    0   0.057  232.4782  295.6055  189.4963
 UXY  C06  C  CH2    0  -0.452  232.7282  294.5017  188.4751
 UXY  C07  C  CH2    0  -0.278  233.3246  294.9536  187.1474
 UXY  N08  N  NH2    0  -0.799  233.4945  293.8056  186.2622
 UXY  O05  O  OH1    0  -0.695  233.6919  296.2720  189.7664
 UXY  OXT  O  OC    -1  -0.600  229.4142  298.9872  190.5176
 UXY  H1   H  HNH2   0   0.347  231.9193  298.7251  191.5493
 UXY  H2   H  HNH2   0   0.338  231.1361  297.3245  191.6499
 UXY  H4   H  HCH1   0   0.220  232.2085  298.5249  189.2283
 UXY  H5   H  HCH2   0   0.226  231.3675  296.7284  187.9797
 UXY  H6   H  HCH2   0   0.215  230.4046  296.0869  189.2897
 UXY  H7   H  HCH1   0   0.185  232.1263  295.1067  190.4123
 UXY  H8   H  HCH2   0   0.216  231.7802  293.9909  188.2813
 UXY  H9   H  HCH2   0   0.218  233.3928  293.7541  188.9229
 UXY  H10  H  HCH2   0   0.193  234.2583  295.4994  187.3308
 UXY  H11  H  HCH2   0   0.211  232.6487  295.6572  186.6550
 UXY  H12  H  HNH2   0   0.342  233.8724  294.1190  185.3770
 UXY  H13  H  HNH2   0   0.334  234.1990  293.1904  186.6518
 UXY  H15  H  HOH1   0   0.444  233.4405  296.9072  190.4650

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
 UXY  N08  C07  single  1.460  0.020  1.460
 UXY  C07  C06  single  1.524  0.020  1.524
 UXY  C06  C04  single  1.524  0.020  1.524
 UXY  O05  C04  single  1.411  0.020  1.411
 UXY  C03  C04  single  1.540  0.020  1.540
 UXY  C03  CA   single  1.537  0.020  1.537
 UXY  O    C    deloc   1.231  0.020  1.231
 UXY  C    CA   single  1.525  0.021  1.525
 UXY  CA   N    single  1.458  0.019  1.458
 UXY  C    OXT  deloc   1.246  0.020  1.246
 UXY  N    H1   single  0.890  0.020  1.040
 UXY  N    H2   single  0.890  0.020  1.040
 UXY  CA   H4   single  0.970  0.020  1.090
 UXY  C03  H5   single  0.970  0.020  1.090
 UXY  C03  H6   single  0.970  0.020  1.090
 UXY  C04  H7   single  0.970  0.020  1.090
 UXY  C06  H8   single  0.970  0.020  1.090
 UXY  C06  H9   single  0.970  0.020  1.090
 UXY  C07  H10  single  0.970  0.020  1.090
 UXY  C07  H11  single  0.970  0.020  1.090
 UXY  N08  H12  single  0.890  0.020  1.040
 UXY  N08  H13  single  0.890  0.020  1.040
 UXY  O05  H15  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
 UXY  H2   N    H1   105.02  3.000
 UXY  H2   N    CA   109.29  3.000
 UXY  H1   N    CA   109.30  3.000
 UXY  H4   CA   C03  107.37  3.000
 UXY  H4   CA   C    106.98  3.000
 UXY  C03  CA   C    109.72  3.000
 UXY  H4   CA   N    106.28  3.000
 UXY  C    CA   N    111.00  2.800
 UXY  C03  CA   N    110.13  3.000
 UXY  OXT  C    O    127.04  3.000
 UXY  OXT  C    CA   120.80  1.700
 UXY  O    C    CA   120.80  1.700
 UXY  H6   C03  H5   106.12  3.000
 UXY  H6   C03  C04  107.30  3.000
 UXY  H5   C03  C04  111.54  3.000
 UXY  H6   C03  CA   109.89  3.000
 UXY  H5   C03  CA   107.73  3.000
 UXY  C04  C03  CA   113.98  3.000
 UXY  H7   C04  O05  109.26  3.000
 UXY  H7   C04  C06  106.36  3.000
 UXY  O05  C04  C06  109.22  3.000
 UXY  H7   C04  C03  106.75  3.000
 UXY  O05  C04  C03  112.51  3.000
 UXY  C06  C04  C03  112.49  3.000
 UXY  H9   C06  H8   106.22  3.000
 UXY  H9   C06  C07  108.72  3.000
 UXY  H8   C06  C07  108.86  3.000
 UXY  H9   C06  C04  108.64  3.000
 UXY  H8   C06  C04  108.33  3.000
 UXY  C07  C06  C04  115.66  3.000
 UXY  H11  C07  H10  106.34  3.000
 UXY  H11  C07  N08  107.77  3.000
 UXY  H10  C07  N08  113.18  3.000
 UXY  H11  C07  C06  109.96  3.000
 UXY  H10  C07  C06  109.57  3.000
 UXY  N08  C07  C06  109.92  3.000
 UXY  H13  N08  H12  105.34  3.000
 UXY  H13  N08  C07  108.98  3.000
 UXY  H12  N08  C07  109.29  3.000
 UXY  H15  O05  C04  102.86  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
 UXY  Var_01  N08  C07  C06  C04  -179.26  30.0  1
 UXY  Var_02  H12  N08  C07  C06   178.81  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
 UXY  chir_01  CA   C03  C    N    negativ
 UXY  chir_02  C04  O05  C06  C03  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
 UXY  plan-1  CA   0.020
 UXY  plan-1  C    0.020
 UXY  plan-1  O    0.020
 UXY  plan-1  OXT  0.020

