# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 09:53:21 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2R,3S)-3-[(4E,7E)-nona-4,7-dienoyl]oxirane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C=C\C/C=C/CCC(=O)[C@H]1O[C@H]1C(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
 1X9  1X9  (2R,3S)-3-[(4E,7E)-nona-4,7-dienoyl]oxirane-2-carboxamide  ligand  33  16  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1X9
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
 1X9  O1   O  O     0  -0.477  -2.3838   2.9442   0.2284
 1X9  C1   C  C     0   0.462  -3.1804   2.0229   0.3235
 1X9  N    N  NH2   0  -0.784  -3.8190   1.6713   1.4384
 1X9  C2   C  CH1   0  -0.102  -3.5065   1.2227  -0.9106
 1X9  O2   O  O2    0  -0.450  -4.3229   0.0838  -0.8022
 1X9  C3   C  CH1   0  -0.098  -2.9714  -0.1326  -1.1256
 1X9  C1'  C  C     0   0.382  -2.1127  -0.7981  -0.0882
 1X9  O1'  O  O     0  -0.380  -2.5652  -1.1465   0.9743
 1X9  C2'  C  CH2   0  -0.578  -0.6789  -0.9731  -0.4931
 1X9  C3'  C  CH2   0  -0.486   0.2155  -1.5608   0.5923
 1X9  C4'  C  C1    0  -0.212   1.6127  -1.7572   0.0945
 1X9  C5'  C  C1    0  -0.204   2.6886  -1.1588   0.5954
 1X9  C6'  C  CH2   0  -0.555   4.0884  -1.3381   0.0847
 1X9  C7'  C  C1    0  -0.177   4.6372  -0.0510  -0.4594
 1X9  C8'  C  C1    0  -0.265   5.6674   0.6133   0.0557
 1X9  C9'  C  CH3   0  -0.706   6.2011   1.9143  -0.4761
 1X9  H1   H  HNH2  0   0.412  -4.4281   0.8717   1.4685
 1X9  H2   H  HNH2  0   0.411  -3.6258   2.1458   2.3060
 1X9  H3   H  HCH1  0   0.302  -3.6564   1.8398  -1.7943
 1X9  H4   H  HCH1  0   0.299  -2.7664  -0.4227  -2.1551
 1X9  H5   H  HCH2  0   0.285  -0.6653  -1.6015  -1.3916
 1X9  H6   H  HCH2  0   0.285  -0.2992   0.0004  -0.8251
 1X9  H7   H  HCH2  0   0.245   0.2190  -0.9084   1.4682
 1X9  H8   H  HCH2  0   0.246  -0.1969  -2.5219   0.9127
 1X9  H9   H  H     0   0.235   1.7318  -2.4414  -0.7436
 1X9  H10  H  H     0   0.236   2.5725  -0.4663   1.4264
 1X9  H11  H  HCH2  0   0.243   4.7342  -1.6960   0.8925
 1X9  H12  H  HCH2  0   0.244   4.0949  -2.1066  -0.6944
 1X9  H13  H  H     0   0.232   4.1186   0.3528  -1.3271
 1X9  H14  H  H     0   0.237   6.1690   0.1961   0.9254
 1X9  H15  H  HCH3  0   0.237   7.0528   2.2607   0.1066
 1X9  H16  H  HCH3  0   0.241   6.5314   1.8238  -1.5122
 1X9  H17  H  HCH3  0   0.241   5.4461   2.7016  -0.4484

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
 1X9  N    C1   single  1.332  0.020  1.332
 1X9  O2   C2   single  1.405  0.020  1.405
 1X9  O2   C3   single  1.406  0.020  1.406
 1X9  C1   C2   single  1.506  0.020  1.506
 1X9  C1   O1   double  1.222  0.020  1.222
 1X9  O1'  C1'  double  1.206  0.020  1.206
 1X9  C2   C3   single  1.473  0.020  1.473
 1X9  C1'  C2'  single  1.500  0.020  1.500
 1X9  C1'  C3   single  1.502  0.020  1.502
 1X9  C2'  C3'  single  1.524  0.020  1.524
 1X9  C3'  C4'  single  1.496  0.020  1.496
 1X9  C4'  C5'  double  1.329  0.020  1.329
 1X9  C5'  C6'  single  1.501  0.020  1.501
 1X9  C8'  C9'  single  1.503  0.020  1.503
 1X9  C8'  C7'  double  1.330  0.020  1.330
 1X9  C6'  C7'  single  1.501  0.020  1.501
 1X9  N    H1   single  0.860  0.020  1.020
 1X9  N    H2   single  0.860  0.020  1.020
 1X9  C2   H3   single  0.970  0.020  1.090
 1X9  C3   H4   single  0.970  0.020  1.090
 1X9  C2'  H5   single  0.970  0.020  1.090
 1X9  C2'  H6   single  0.970  0.020  1.090
 1X9  C3'  H7   single  0.970  0.020  1.090
 1X9  C3'  H8   single  0.970  0.020  1.090
 1X9  C4'  H9   single  0.930  0.020  1.080
 1X9  C5'  H10  single  0.930  0.020  1.080
 1X9  C6'  H11  single  0.970  0.020  1.090
 1X9  C6'  H12  single  0.970  0.020  1.090
 1X9  C7'  H13  single  0.930  0.020  1.080
 1X9  C8'  H14  single  0.930  0.020  1.080
 1X9  C9'  H15  single  0.970  0.020  1.090
 1X9  C9'  H16  single  0.970  0.020  1.090
 1X9  C9'  H17  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
 1X9  C2   C1   N    116.21  3.000
 1X9  C2   C1   O1   118.55  3.000
 1X9  N    C1   O1   125.22  3.000
 1X9  H2   N    H1   117.69  3.000
 1X9  H2   N    C1   120.30  3.000
 1X9  H1   N    C1   121.69  3.000
 1X9  H3   C2   C3   116.95  3.000
 1X9  H3   C2   O2   116.24  3.000
 1X9  C3   C2   O2    58.44  3.000
 1X9  H3   C2   C1   113.20  3.000
 1X9  C3   C2   C1   121.98  3.000
 1X9  O2   C2   C1   119.54  3.000
 1X9  C3   O2   C2    63.18  3.000
 1X9  H4   C3   C1'  115.29  3.000
 1X9  H4   C3   O2   116.05  3.000
 1X9  C1'  C3   O2   117.30  3.000
 1X9  H4   C3   C2   116.84  3.000
 1X9  C1'  C3   C2   120.97  3.000
 1X9  O2   C3   C2    58.38  3.000
 1X9  C2'  C1'  O1'  124.24  3.000
 1X9  C2'  C1'  C3   114.31  3.000
 1X9  O1'  C1'  C3   121.45  3.000
 1X9  H6   C2'  H5   104.86  3.000
 1X9  H6   C2'  C3'  110.78  3.000
 1X9  H5   C2'  C3'  110.81  3.000
 1X9  H6   C2'  C1'  108.01  3.000
 1X9  H5   C2'  C1'  107.44  3.000
 1X9  C3'  C2'  C1'  114.43  3.000
 1X9  H8   C3'  H7   106.93  3.000
 1X9  H8   C3'  C4'  109.52  3.000
 1X9  H7   C3'  C4'  110.01  3.000
 1X9  H8   C3'  C2'  109.04  3.000
 1X9  H7   C3'  C2'  110.04  3.000
 1X9  C4'  C3'  C2'  111.20  3.000
 1X9  H9   C4'  C5'  118.99  3.000
 1X9  H9   C4'  C3'  116.16  3.000
 1X9  C5'  C4'  C3'  124.85  3.000
 1X9  H10  C5'  C6'  115.82  3.000
 1X9  H10  C5'  C4'  119.21  3.000
 1X9  C6'  C5'  C4'  124.96  3.000
 1X9  H12  C6'  H11  107.00  3.000
 1X9  H12  C6'  C7'  109.99  3.000
 1X9  H11  C6'  C7'  109.40  3.000
 1X9  H12  C6'  C5'  109.37  3.000
 1X9  H11  C6'  C5'  109.77  3.000
 1X9  C7'  C6'  C5'  111.21  3.000
 1X9  H13  C7'  C8'  119.51  3.000
 1X9  H13  C7'  C6'  115.64  3.000
 1X9  C8'  C7'  C6'  124.83  3.000
 1X9  H14  C8'  C9'  116.82  3.000
 1X9  H14  C8'  C7'  118.40  3.000
 1X9  C9'  C8'  C7'  124.78  3.000
 1X9  H17  C9'  H16  107.06  3.000
 1X9  H17  C9'  H15  107.35  3.000
 1X9  H16  C9'  H15  107.33  3.000
 1X9  H17  C9'  C8'  111.70  3.000
 1X9  H16  C9'  C8'  111.81  3.000
 1X9  H15  C9'  C8'  111.33  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
 1X9  CONST_01  H1   N    C1   C2      0.00   0.0  0
 1X9  CONST_02  H2   N    C1   C2    180.00   0.0  0
 1X9  Var_01    C1'  C3   O2   C2    111.24  30.0  1
 1X9  Var_02    O2   C2   C1   O1    174.16  30.0  3
 1X9  Var_03    O1'  C1'  C3   C2     68.54  30.0  1
 1X9  Var_04    C3'  C2'  C1'  C3    176.03  30.0  3
 1X9  Var_05    C6'  C5'  C4'  C3'  -179.03   0.0  2
 1X9  Var_06    C9'  C8'  C7'  C6'  -178.90   0.0  2
 1X9  Var_07    C4'  C3'  C2'  C1'   177.62  30.0  3
 1X9  Var_08    C5'  C4'  C3'  C2'   118.33  30.0  3
 1X9  Var_09    C7'  C6'  C5'  C4'   116.26  30.0  3
 1X9  Var_10    C8'  C7'  C6'  C5'   115.09  30.0  3
 1X9  Var_11    H15  C9'  C8'  C7'  -179.58  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
 1X9  chir_01  C2  O2  C1   C3  both
 1X9  chir_02  C3  O2  C1'  C2  both

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
 1X9  plan-1  O1   0.020
 1X9  plan-1  C1   0.020
 1X9  plan-1  N    0.020
 1X9  plan-1  C2   0.020
 1X9  plan-1  H1   0.020
 1X9  plan-1  H2   0.020
 1X9  plan-2  C3   0.020
 1X9  plan-2  C1'  0.020
 1X9  plan-2  O1'  0.020
 1X9  plan-2  C2'  0.020
 1X9  plan-3  C3'  0.020
 1X9  plan-3  C4'  0.020
 1X9  plan-3  C5'  0.020
 1X9  plan-3  C6'  0.020
 1X9  plan-3  H9   0.020
 1X9  plan-3  H10  0.020
 1X9  plan-4  C6'  0.020
 1X9  plan-4  C7'  0.020
 1X9  plan-4  C8'  0.020
 1X9  plan-4  C9'  0.020
 1X9  plan-4  H13  0.020
 1X9  plan-4  H14  0.020

