# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 03:37:42 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (3S,7E,10E)-3-hydroxy-4-oxododeca-7,10-dienamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C/C/C=C/CCC(=O)[C@@H](O)CC(N)=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
 CER  CER  (3S,7E,10E)-3-hydroxy-4-oxododeca-7,10-dienamide  ligand  35  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CER
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
 CER  C1    C  C     0   0.537   1.9494  -0.1259  -3.5274
 CER  N1    N  NH2   0  -0.799   2.6106   0.8306  -4.1900
 CER  O1    O  O     0  -0.396  -2.2531   0.8598  -1.9262
 CER  C2    C  CH2   0  -0.611   0.9179   0.3740  -2.5344
 CER  O2    O  O     0  -0.495   2.1628  -1.3198  -3.6808
 CER  C3    C  CH1   0  -0.047  -0.3946  -0.4018  -2.6843
 CER  O3    O  OH1   0  -0.656  -0.9226  -0.2777  -3.9720
 CER  C4    C  C     0   0.371  -1.3743   0.0856  -1.6240
 CER  C5    C  CH2   0  -0.571  -1.1802  -0.4401  -0.2315
 CER  C6    C  CH2   0  -0.484  -1.9560   0.3091   0.8471
 CER  C7    C  C1    0  -0.213  -1.7143  -0.2915   2.1958
 CER  C8    C  C1    0  -0.203  -1.0930   0.3208   3.1990
 CER  C9    C  CH2   0  -0.554  -0.8146  -0.2977   4.5375
 CER  C10   C  C1    0  -0.194   0.6599  -0.4505   4.7742
 CER  C11   C  C1    0  -0.227   1.3421   0.1550   5.7421
 CER  C12   C  CH3   0  -0.707   2.8110   0.0156   5.9744
 CER  HN11  H  HNH2  0   0.402   3.3442   0.5918  -4.8377
 CER  HN12  H  HNH2  0   0.409   2.4137   1.8064  -4.0526
 CER  H21   H  HCH2  0   0.271   0.7361   1.4455  -2.6515
 CER  H22   H  HCH2  0   0.285   1.3325   0.2304  -1.5333
 CER  H31   H  HCH1  0   0.267  -0.1924  -1.4631  -2.5101
 CER  HO3   H  HOH1  0   0.445  -1.3765   0.5720  -4.0326
 CER  H51   H  HCH2  0   0.273  -0.1123  -0.4562   0.0055
 CER  H52   H  HCH2  0   0.287  -1.4735  -1.4970  -0.2561
 CER  H61   H  HCH2  0   0.244  -3.0237   0.2742   0.6149
 CER  H62   H  HCH2  0   0.244  -1.6642   1.3618   0.8491
 CER  H71   H  H     0   0.235  -2.0665  -1.3114   2.3396
 CER  H81   H  H     0   0.235  -0.7301   1.3367   3.0573
 CER  H91   H  HCH2  0   0.243  -1.3025  -1.2759   4.5911
 CER  H92   H  HCH2  0   0.243  -1.2484   0.3183   5.3313
 CER  H101  H  H     0   0.232   1.1865  -1.0997   4.0775
 CER  H111  H  H     0   0.229   0.8066   0.8055   6.4304
 CER  H121  H  HCH3  0   0.235   3.3138   0.9827   5.9023
 CER  H122  H  HCH3  0   0.235   3.0179  -0.3664   6.9764
 CER  H123  H  HCH3  0   0.234   3.2732  -0.6589   5.2537

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
 CER  C1   N1    single  1.338  0.020  1.338
 CER  C1   C2    single  1.517  0.020  1.517
 CER  C1   O2    double  1.222  0.020  1.222
 CER  N1   HN11  single  0.860  0.020  1.020
 CER  N1   HN12  single  0.860  0.020  1.020
 CER  O1   C4    double  1.210  0.020  1.210
 CER  C2   C3    single  1.532  0.020  1.532
 CER  C2   H21   single  0.970  0.020  1.090
 CER  C2   H22   single  0.970  0.020  1.090
 CER  C3   O3    single  1.397  0.020  1.397
 CER  C3   C4    single  1.524  0.020  1.524
 CER  C3   H31   single  0.970  0.020  1.090
 CER  O3   HO3   single  0.850  0.020  0.980
 CER  C4   C5    single  1.501  0.020  1.501
 CER  C5   C6    single  1.525  0.020  1.525
 CER  C5   H51   single  0.970  0.020  1.090
 CER  C5   H52   single  0.970  0.020  1.090
 CER  C6   C7    single  1.496  0.020  1.496
 CER  C6   H61   single  0.970  0.020  1.090
 CER  C6   H62   single  0.970  0.020  1.090
 CER  C7   C8    double  1.329  0.020  1.329
 CER  C7   H71   single  0.930  0.020  1.080
 CER  C8   C9    single  1.501  0.020  1.501
 CER  C8   H81   single  0.930  0.020  1.080
 CER  C9   C10   single  1.501  0.020  1.501
 CER  C9   H91   single  0.970  0.020  1.090
 CER  C9   H92   single  0.970  0.020  1.090
 CER  C10  C11   double  1.330  0.020  1.330
 CER  C10  H101  single  0.930  0.020  1.080
 CER  C11  C12   single  1.494  0.020  1.494
 CER  C11  H111  single  0.930  0.020  1.080
 CER  C12  H121  single  0.970  0.020  1.090
 CER  C12  H122  single  0.970  0.020  1.090
 CER  C12  H123  single  0.970  0.020  1.090

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
 CER  O2    C1   C2    121.52  3.000
 CER  O2    C1   N1    123.34  3.000
 CER  C2    C1   N1    115.13  3.000
 CER  HN12  N1   HN11  117.44  3.000
 CER  HN12  N1   C1    121.97  3.000
 CER  HN11  N1   C1    120.58  3.000
 CER  H22   C2   H21   106.86  3.000
 CER  H22   C2   C3    110.37  3.000
 CER  H21   C2   C3    110.09  3.000
 CER  H22   C2   C1    107.36  3.000
 CER  H21   C2   C1    111.47  3.000
 CER  C3    C2   C1    110.60  3.000
 CER  H31   C3   C4    108.56  3.000
 CER  H31   C3   O3    107.61  3.000
 CER  C4    C3   O3    111.71  3.000
 CER  H31   C3   C2    108.50  3.000
 CER  C4    C3   C2    108.71  3.000
 CER  O3    C3   C2    111.65  3.000
 CER  HO3   O3   C3    108.28  3.000
 CER  C5    C4   C3    116.77  3.000
 CER  C5    C4   O1    123.36  3.000
 CER  C3    C4   O1    119.87  3.000
 CER  H52   C5   H51   104.57  3.000
 CER  H52   C5   C6    110.67  3.000
 CER  H51   C5   C6    110.52  3.000
 CER  H52   C5   C4    106.38  3.000
 CER  H51   C5   C4    109.41  3.000
 CER  C6    C5   C4    114.72  3.000
 CER  H62   C6   H61   106.98  3.000
 CER  H62   C6   C7    110.00  3.000
 CER  H61   C6   C7    109.66  3.000
 CER  H62   C6   C5    109.80  3.000
 CER  H61   C6   C5    109.32  3.000
 CER  C7    C6   C5    110.99  3.000
 CER  H71   C7   C8    118.88  3.000
 CER  H71   C7   C6    116.29  3.000
 CER  C8    C7   C6    124.82  3.000
 CER  H81   C8   C9    116.05  3.000
 CER  H81   C8   C7    119.18  3.000
 CER  C9    C8   C7    124.75  3.000
 CER  H92   C9   H91   106.91  3.000
 CER  H92   C9   C10   109.41  3.000
 CER  H91   C9   C10   109.82  3.000
 CER  H92   C9   C8    109.97  3.000
 CER  H91   C9   C8    109.23  3.000
 CER  C10   C9   C8    111.40  3.000
 CER  H101  C10  C11   119.30  3.000
 CER  H101  C10  C9    115.79  3.000
 CER  C11   C10  C9    124.90  3.000
 CER  H111  C11  C12   116.19  3.000
 CER  H111  C11  C10   118.70  3.000
 CER  C12   C11  C10   125.11  3.000
 CER  H123  C12  H122  108.05  3.000
 CER  H123  C12  H121  108.01  3.000
 CER  H122  C12  H121  106.44  3.000
 CER  H123  C12  C11   111.83  3.000
 CER  H122  C12  C11   111.19  3.000
 CER  H121  C12  C11   111.09  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
 CER  CONST_01  HN11  N1   C1   C2    180.00   0.0  0
 CER  CONST_02  HN12  N1   C1   C2      0.00   0.0  0
 CER  Var_01    C9    C8   C7   C6   -178.06   0.0  2
 CER  Var_02    C12   C11  C10  C9   -179.43   0.0  2
 CER  Var_03    C3    C2   C1   N1    133.87  30.0  3
 CER  Var_04    C6    C5   C4   O1    -13.65  30.0  3
 CER  Var_05    C7    C6   C5   C4    179.38  30.0  3
 CER  Var_06    C8    C7   C6   C5    114.48  30.0  3
 CER  Var_07    C10   C9   C8   C7    114.99  30.0  3
 CER  Var_08    C11   C10  C9   C8    117.11  30.0  3
 CER  Var_09    H121  C12  C11  C10   120.22  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
 CER  chir_01  C3  C2  O3  C4  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
 CER  plan-1  C1    0.020
 CER  plan-1  N1    0.020
 CER  plan-1  C2    0.020
 CER  plan-1  O2    0.020
 CER  plan-1  HN11  0.020
 CER  plan-1  HN12  0.020
 CER  plan-2  O1    0.020
 CER  plan-2  C3    0.020
 CER  plan-2  C4    0.020
 CER  plan-2  C5    0.020
 CER  plan-3  C6    0.020
 CER  plan-3  C7    0.020
 CER  plan-3  C8    0.020
 CER  plan-3  C9    0.020
 CER  plan-3  H71   0.020
 CER  plan-3  H81   0.020
 CER  plan-4  C9    0.020
 CER  plan-4  C10   0.020
 CER  plan-4  C11   0.020
 CER  plan-4  C12   0.020
 CER  plan-4  H101  0.020
 CER  plan-4  H111  0.020

