# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 23:52:47 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (E)-5-hydroxy-3-oxo-N-(3-oxopropylidene)-L-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC(=O)[C@H](N=CCC=O)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
 LBX  LBX  "(E)-5-hydroxy-3-oxo-N-(3-oxopropylidene)-L-norvaline"
  ligand  24  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LBX
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
 LBX  C10  C  C      0   0.431  -53.7921  19.2105  38.0059
 LBX  C13  C  CH2    0  -0.172  -54.8061  21.5355  37.9061
 LBX  C02  C  C1     0   0.168  -50.0093  15.1798  37.1466
 LBX  C03  C  CH2    0  -0.648  -51.2988  15.1326  37.9097
 LBX  C04  C  C1     0   0.005  -51.6969  16.4387  38.5140
 LBX  C06  C  CH1    0  -0.383  -53.1183  18.2077  38.9048
 LBX  C07  C  C      0   0.456  -54.1312  17.8610  40.0717
 LBX  C12  C  CH2    0  -0.585  -53.6969  20.6470  38.4493
 LBX  N05  N  N      0  -0.312  -52.7810  17.0035  38.2077
 LBX  O01  O  O      0  -0.368  -49.3665  16.1798  36.9522
 LBX  O08  O  OC    -1  -0.564  -53.7340  17.0100  40.8728
 LBX  O09  O  O      0  -0.576  -55.2055  18.4857  40.0555
 LBX  O11  O  O      0  -0.420  -54.3595  18.8930  36.9809
 LBX  O14  O  OH1    0  -0.672  -54.7640  21.7034  36.5082
 LBX  H1   H  HCH2   0   0.226  -54.7094  22.5286  38.3487
 LBX  H2   H  HCH2   0   0.194  -55.7732  21.1358  38.2386
 LBX  H3   H  H      0   0.208  -49.6769  14.2030  36.7536
 LBX  H4   H  HCH2   0   0.291  -52.0763  14.7591  37.2361
 LBX  H5   H  HCH2   0   0.290  -51.1848  14.3663  38.6865
 LBX  H6   H  H      0   0.217  -50.9999  16.8633  39.2446
 LBX  H8   H  HCH1   0   0.246  -52.2433  18.6817  39.3792
 LBX  H9   H  HCH2   0   0.268  -52.7176  21.0194  38.1232
 LBX  H10  H  HCH2   0   0.258  -53.6809  20.6977  39.5396
 LBX  H14  H  HOH1   0   0.441  -54.8325  20.8216  36.1257

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
 LBX  O01  C02  double  1.205  0.020  1.205
 LBX  O14  C13  single  1.409  0.020  1.409
 LBX  O11  C10  double  1.214  0.020  1.214
 LBX  C02  C03  single  1.499  0.020  1.499
 LBX  C03  C04  single  1.493  0.020  1.493
 LBX  C13  C12  single  1.522  0.020  1.522
 LBX  N05  C04  double  1.260  0.020  1.260
 LBX  N05  C06  single  1.432  0.020  1.432
 LBX  C10  C12  single  1.506  0.020  1.506
 LBX  C10  C06  single  1.506  0.020  1.506
 LBX  C06  C07  single  1.584  0.020  1.584
 LBX  C07  O09  deloc   1.243  0.020  1.243
 LBX  C07  O08  deloc   1.234  0.020  1.234
 LBX  C13  H1   single  0.970  0.020  1.090
 LBX  C13  H2   single  0.970  0.020  1.090
 LBX  C02  H3   single  0.930  0.020  1.080
 LBX  C03  H4   single  0.970  0.020  1.090
 LBX  C03  H5   single  0.970  0.020  1.090
 LBX  C04  H6   single  0.930  0.020  1.080
 LBX  C06  H8   single  0.970  0.020  1.090
 LBX  C12  H9   single  0.970  0.020  1.090
 LBX  C12  H10  single  0.970  0.020  1.090
 LBX  O14  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
 LBX  O11  C10  C12  121.84  3.000
 LBX  C12  C10  C06  115.53  3.000
 LBX  O11  C10  C06  122.62  3.000
 LBX  H2   C13  H1   106.64  3.000
 LBX  H2   C13  O14  111.73  3.000
 LBX  H1   C13  O14  106.93  3.000
 LBX  H2   C13  C12  108.75  3.000
 LBX  H1   C13  C12  108.78  3.000
 LBX  O14  C13  C12  113.71  3.000
 LBX  H3   C02  O01  121.09  3.000
 LBX  H3   C02  C03  114.35  3.000
 LBX  O01  C02  C03  124.56  3.000
 LBX  H5   C03  H4   105.74  3.000
 LBX  H5   C03  C04  110.62  3.000
 LBX  H4   C03  C04  110.99  3.000
 LBX  H5   C03  C02  107.04  3.000
 LBX  H4   C03  C02  107.97  3.000
 LBX  C04  C03  C02  114.07  3.000
 LBX  H6   C04  N05  122.40  3.000
 LBX  H6   C04  C03  116.06  3.000
 LBX  N05  C04  C03  121.54  3.000
 LBX  H8   C06  N05  112.60  3.000
 LBX  H8   C06  C07  106.54  3.000
 LBX  N05  C06  C07  108.98  3.000
 LBX  H8   C06  C10  109.00  3.000
 LBX  C07  C06  C10  107.42  3.000
 LBX  N05  C06  C10  112.02  3.000
 LBX  O09  C07  O08  129.28  3.000
 LBX  O08  C07  C06  115.05  3.000
 LBX  O09  C07  C06  115.67  3.000
 LBX  H10  C12  H9   105.55  3.000
 LBX  H10  C12  C13  109.88  3.000
 LBX  H9   C12  C13  110.26  3.000
 LBX  H10  C12  C10  109.83  3.000
 LBX  H9   C12  C10  107.02  3.000
 LBX  C13  C12  C10  113.93  3.000
 LBX  C06  N05  C04  117.47  3.000
 LBX  H14  O14  C13  106.42  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
 LBX  Var_01  C06  N05  C04  C03   175.93   0.0  2
 LBX  Var_02  O14  C13  C12  C10   -66.05  30.0  3
 LBX  Var_03  O11  C10  C12  C13    25.03  30.0  2
 LBX  Var_04  C06  C10  C12  C13  -155.99  30.0  2
 LBX  Var_05  N05  C04  C03  C02   119.98  30.0  3
 LBX  Var_06  O01  C02  C03  C04    -4.17  30.0  2
 LBX  Var_07  H6   C04  N05  C06    -3.16   0.0  2
 LBX  Var_08  H1   C13  C12  C10   174.91  30.0  3
 LBX  Var_09  H2   C13  C12  C10    59.13  30.0  3
 LBX  Var_10  H6   C04  C03  C02   -60.88  30.0  3
 LBX  Var_11  H3   C02  C03  C04   176.21  30.0  2
 LBX  Var_12  H9   C12  C10  C06    81.87  30.0  3
 LBX  Var_13  H10  C12  C10  C06   -32.23  30.0  3
 LBX  Var_14  H4   C03  C04  N05    -2.24  30.0  1
 LBX  Var_15  H5   C03  C04  N05  -119.29  30.0  1
 LBX  Var_16  H4   C03  C02  O01   119.69  30.0  3
 LBX  Var_17  H5   C03  C02  O01  -126.88  30.0  3
 LBX  Var_18  H9   C12  C10  O11   -97.12  30.0  3
 LBX  Var_19  H10  C12  C10  O11   148.78  30.0  3
 LBX  Var_20  H9   C12  C13  O14    54.29  30.0  3
 LBX  Var_21  H10  C12  C13  O14   170.22  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
 LBX  chir_01  C06  N05  C10  C07  negativ

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
 LBX  plan-1  C10  0.020
 LBX  plan-1  C06  0.020
 LBX  plan-1  C12  0.020
 LBX  plan-1  O11  0.020
 LBX  plan-2  C06  0.020
 LBX  plan-2  C07  0.020
 LBX  plan-2  O08  0.020
 LBX  plan-2  O09  0.020
 LBX  plan-3  C02  0.020
 LBX  plan-3  C03  0.020
 LBX  plan-3  O01  0.020
 LBX  plan-3  H3   0.020
 LBX  plan-4  C03  0.020
 LBX  plan-4  C04  0.020
 LBX  plan-4  C06  0.020
 LBX  plan-4  N05  0.020
 LBX  plan-4  H6   0.020

