# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:16:07 2021
#   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  25  11  .  2022-08-11  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.800  231.7508  297.7872  191.2210
 UXY  CA   C  CH1   0  -0.211  231.4161  297.9698  189.8255
 UXY  C    C  C     0   0.527  230.1306  298.7199  189.5123
 UXY  O    O  O     0  -0.453  229.8767  299.1604  188.4172
 UXY  C03  C  CH2   0  -0.481  231.3678  296.6193  189.0881
 UXY  C04  C  CH1   0   0.050  232.4928  295.6678  189.5233
 UXY  C06  C  CH2   0  -0.454  232.7056  294.5323  188.5296
 UXY  C07  C  CH2   0  -0.280  233.2486  294.9418  187.1660
 UXY  N08  N  NH2   0  -0.802  233.4507  293.7591  186.3363
 UXY  O05  O  OH1   0  -0.687  233.7176  296.3405  189.7235
 UXY  OXT  O  OH1   0  -0.584  229.3083  298.8213  190.5460
 UXY  H1   H  HNH2  0   0.367  231.8173  298.6732  191.7042
 UXY  H2   H  HNH2  0   0.358  231.0535  297.2343  191.7039
 UXY  H4   H  HCH1  0   0.281  232.2136  298.5652  189.3724
 UXY  H5   H  HCH2  0   0.249  231.4012  296.8232  188.0165
 UXY  H6   H  HCH2  0   0.242  230.4151  296.1172  189.2823
 UXY  H7   H  HCH1  0   0.206  232.1721  295.2059  190.4671
 UXY  H8   H  HCH2  0   0.223  231.7554  294.0073  188.3948
 UXY  H9   H  HCH2  0   0.226  233.3930  293.8087  188.9809
 UXY  H10  H  HCH2  0   0.197  234.1598  295.5387  187.2966
 UXY  H11  H  HCH2  0   0.212  232.5294  295.5845  186.6530
 UXY  H12  H  HNH2  0   0.345  233.7548  294.0465  185.4147
 UXY  H13  H  HNH2  0   0.336  234.2179  293.2161  186.7140
 UXY  H15  H  HOH1  0   0.449  233.5518  296.9303  190.4756
 UXY  H16  H  HOH1  0   0.482  228.5000  299.2853  190.2792

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  1.459  0.020  1.459
 UXY  C07  C06  single  1.524  0.020  1.524
 UXY  C06  C04  single  1.524  0.020  1.524
 UXY  O05  C04  single  1.412  0.020  1.412
 UXY  C03  C04  single  1.536  0.020  1.536
 UXY  C03  CA   single  1.540  0.020  1.540
 UXY  O    C    double  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  single  1.325  0.020  1.325
 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
 UXY  OXT  H16  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   107.21  3.000
 UXY  H2   N    CA   111.69  3.000
 UXY  H1   N    CA   111.44  3.000
 UXY  H4   CA   C03  107.58  3.000
 UXY  H4   CA   C    105.23  3.000
 UXY  C03  CA   C    107.91  3.000
 UXY  H4   CA   N    107.44  3.000
 UXY  C    CA   N    111.00  2.800
 UXY  C03  CA   N    111.01  3.000
 UXY  OXT  C    O    123.32  3.000
 UXY  OXT  C    CA   120.80  1.700
 UXY  O    C    CA   120.80  1.700
 UXY  H6   C03  H5   106.66  3.000
 UXY  H6   C03  C04  107.64  3.000
 UXY  H5   C03  C04  111.81  3.000
 UXY  H6   C03  CA   110.17  3.000
 UXY  H5   C03  CA   107.79  3.000
 UXY  C04  C03  CA   112.62  3.000
 UXY  H7   C04  O05  109.38  3.000
 UXY  H7   C04  C06  106.72  3.000
 UXY  O05  C04  C06  109.05  3.000
 UXY  H7   C04  C03  106.85  3.000
 UXY  O05  C04  C03  112.36  3.000
 UXY  C06  C04  C03  112.27  3.000
 UXY  H9   C06  H8   106.19  3.000
 UXY  H9   C06  C07  108.82  3.000
 UXY  H8   C06  C07  109.16  3.000
 UXY  H9   C06  C04  108.13  3.000
 UXY  H8   C06  C04  108.47  3.000
 UXY  C07  C06  C04  115.66  3.000
 UXY  H11  C07  H10  106.42  3.000
 UXY  H11  C07  N08  107.52  3.000
 UXY  H10  C07  N08  113.19  3.000
 UXY  H11  C07  C06  110.10  3.000
 UXY  H10  C07  C06  109.61  3.000
 UXY  N08  C07  C06  109.91  3.000
 UXY  H13  N08  H12  105.32  3.000
 UXY  H13  N08  C07  109.11  3.000
 UXY  H12  N08  C07  109.23  3.000
 UXY  H15  O05  C04  104.56  3.000
 UXY  H16  OXT  C    109.85  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  CONST_01  H16  OXT  C    CA   180.00   0.0  0
 UXY  Var_01    N08  C07  C06  C04  177.88  30.0  1
 UXY  Var_02    H12  N08  C07  C06  176.42  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
 UXY  plan-1  H16  0.020

