# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:23:07 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 5,5-dihydroxy-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(O)(O)CC[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
 8WY  8WY  5,5-dihydroxy-L-norleucine  L-peptide  23  11  .  2017-07-04  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_8WY
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
 8WY  O    O  O      0  -0.600  -25.9877  -25.3008   -6.9186
 8WY  C    C  C      0   0.383  -25.1126  -26.1875   -6.8731
 8WY  OXT  O  OC    -1  -0.615  -24.1193  -26.2215   -6.1169
 8WY  CA   C  CH1    0  -0.204  -25.2418  -27.3660   -7.8748
 8WY  N    N  NH2    0  -0.785  -26.5464  -27.5073   -8.5035
 8WY  CB   C  CH2    0  -0.467  -24.1569  -27.2320   -8.9500
 8WY  CAG  C  CH2    0  -0.443  -24.0430  -28.4714   -9.8337
 8WY  CAH  C  CT     0   0.433  -23.0856  -28.3566  -11.0280
 8WY  OAK  O  OH1    0  -0.675  -21.7832  -28.0211  -10.6119
 8WY  CAI  C  CH3    0  -0.673  -22.9705  -29.6897  -11.7502
 8WY  O1   O  OH1    0  -0.672  -23.5640  -27.4344  -11.9788
 8WY  H2   H  HCH1   0   0.206  -25.0397  -28.2915   -7.3227
 8WY  H3   H  HNH2   0   0.334  -27.2219  -27.7690   -7.7954
 8WY  H4   H  HNH2   0   0.322  -26.8416  -26.5842   -8.8027
 8WY  H6   H  HCH2   0   0.223  -23.2080  -27.0361   -8.4443
 8WY  H7   H  HCH2   0   0.208  -24.3813  -26.3367   -9.5450
 8WY  H8   H  HCH2   0   0.228  -25.0324  -28.7345  -10.2126
 8WY  H9   H  HCH2   0   0.219  -23.7163  -29.3110   -9.2124
 8WY  H10  H  HOH1   0   0.446  -21.8177  -27.2565  -10.0264
 8WY  H11  H  HCH3   0   0.228  -23.9490  -30.0257  -12.0921
 8WY  H12  H  HCH3   0   0.235  -22.3143  -29.6120  -12.6189
 8WY  H13  H  HCH3   0   0.228  -22.5655  -30.4520  -11.0853
 8WY  H14  H  HOH1   0   0.443  -23.8328  -26.6210  -11.5378

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
 8WY  CAI  CAH  single  1.521  0.020  1.521
 8WY  CAH  OAK  single  1.408  0.020  1.408
 8WY  CAH  CAG  single  1.535  0.020  1.535
 8WY  CAG  CB   single  1.526  0.020  1.526
 8WY  CB   CA   single  1.530  0.020  1.530
 8WY  N    CA   single  1.458  0.019  1.458
 8WY  O    C    deloc   1.231  0.020  1.231
 8WY  CA   C    single  1.525  0.021  1.525
 8WY  C    OXT  deloc   1.249  0.020  1.249
 8WY  CAH  O1   single  1.408  0.020  1.408
 8WY  CA   H2   single  0.970  0.020  1.090
 8WY  N    H3   single  0.890  0.020  1.040
 8WY  N    H4   single  0.890  0.020  1.040
 8WY  CB   H6   single  0.970  0.020  1.090
 8WY  CB   H7   single  0.970  0.020  1.090
 8WY  CAG  H8   single  0.970  0.020  1.090
 8WY  CAG  H9   single  0.970  0.020  1.090
 8WY  OAK  H10  single  0.850  0.020  0.980
 8WY  CAI  H11  single  0.970  0.020  1.090
 8WY  CAI  H12  single  0.970  0.020  1.090
 8WY  CAI  H13  single  0.970  0.020  1.090
 8WY  O1   H14  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
 8WY  CA   C    OXT  115.87  3.000
 8WY  OXT  C    O    126.86  3.000
 8WY  CA   C    O    120.80  1.700
 8WY  H2   CA   CB   107.25  3.000
 8WY  H2   CA   N    107.51  3.000
 8WY  CB   CA   N    110.50  1.700
 8WY  H2   CA   C    107.49  3.000
 8WY  N    CA   C    111.00  2.800
 8WY  CB   CA   C    110.10  1.900
 8WY  H4   N    H3   104.32  3.000
 8WY  H4   N    CA   107.46  3.000
 8WY  H3   N    CA   108.71  3.000
 8WY  H7   CB   H6   106.38  3.000
 8WY  H7   CB   CAG  111.32  3.000
 8WY  H6   CB   CAG  110.40  3.000
 8WY  H7   CB   CA   107.86  3.000
 8WY  H6   CB   CA   107.79  3.000
 8WY  CAG  CB   CA   112.82  3.000
 8WY  H9   CAG  H8   106.42  3.000
 8WY  H9   CAG  CAH  108.24  3.000
 8WY  H8   CAG  CAH  108.26  3.000
 8WY  H9   CAG  CB   108.46  3.000
 8WY  H8   CAG  CB   109.20  3.000
 8WY  CAH  CAG  CB   115.86  3.000
 8WY  O1   CAH  CAI  106.21  3.000
 8WY  O1   CAH  OAK  110.96  3.000
 8WY  CAI  CAH  OAK  106.22  3.000
 8WY  O1   CAH  CAG  111.25  3.000
 8WY  OAK  CAH  CAG  111.40  3.000
 8WY  CAI  CAH  CAG  110.56  3.000
 8WY  H10  OAK  CAH  109.60  3.000
 8WY  H13  CAI  H12  108.18  3.000
 8WY  H13  CAI  H11  108.03  3.000
 8WY  H12  CAI  H11  108.19  3.000
 8WY  H13  CAI  CAH  110.59  3.000
 8WY  H12  CAI  CAH  111.17  3.000
 8WY  H11  CAI  CAH  110.58  3.000
 8WY  H14  O1   CAH  109.79  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
 8WY  Var_01  CAH  CAG  CB   CA   173.62  30.0  1
 8WY  Var_02  CAI  CAH  CAG  CB   174.99  30.0  1
 8WY  Var_03  H11  CAI  CAH  CAG   58.16  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
 8WY  chir_01  CA  CB  N  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
 8WY  plan-1  O    0.020
 8WY  plan-1  C    0.020
 8WY  plan-1  OXT  0.020
 8WY  plan-1  CA   0.020

