# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 22:22:07 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (9E,12Z)-10-nitrooctadeca-9,12-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/CC(=C/CCCCCCCC(O)=O)\[N+]([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
 LNA  LNA  '(9E,12Z)-10-nitrooctadeca-9,12-dienoic acid'  ligand  54  23  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LNA
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
 LNA  O20   O  OH1    0  -0.599   9.7267   1.5124  -0.3849
 LNA  C1    C  C      0   0.549   8.7729   0.9040   0.3161
 LNA  O19   O  O      0  -0.446   8.9301   0.5398   1.4550
 LNA  C2    C  CH2    0  -0.580   7.5106   0.7402  -0.4828
 LNA  C3    C  CH2    0  -0.419   6.3987   0.0137   0.2557
 LNA  C4    C  CH2    0  -0.415   5.1529  -0.1287  -0.6094
 LNA  C5    C  CH2    0  -0.415   4.0077  -0.8369   0.1026
 LNA  C6    C  CH2    0  -0.416   2.7715  -0.9778  -0.7755
 LNA  C7    C  CH2    0  -0.419   1.5962  -1.6316  -0.0613
 LNA  C8    C  CH2    0  -0.507   0.3748  -1.7562  -0.9789
 LNA  C9    C  C1     0  -0.230  -0.7753  -2.3880  -0.2783
 LNA  C10   C  C      0   0.260  -1.8933  -1.7631   0.0950
 LNA  N21   N  N      1   0.369  -2.9277  -2.5626   0.7468
 LNA  O22   O  O      0  -0.402  -2.7298  -3.7381   0.9621
 LNA  O23   O  O     -1  -0.382  -3.9573  -1.9996   1.0420
 LNA  C11   C  CH2    0  -0.602  -2.2351  -0.3212  -0.1334
 LNA  C12   C  C1     0  -0.211  -3.0809  -0.1430  -1.3627
 LNA  C13   C  C1     0  -0.195  -4.3104   0.3601  -1.4355
 LNA  C14   C  CH2    0  -0.483  -5.1674   0.8829  -0.3281
 LNA  C15   C  CH2    0  -0.417  -5.6509   2.3078  -0.6010
 LNA  C16   C  CH2    0  -0.407  -6.6247   2.8149   0.4549
 LNA  C17   C  CH2    0  -0.418  -7.1486   4.2158   0.1637
 LNA  C18   C  CH3    0  -0.662  -8.1266   4.7128   1.2194
 LNA  H2    H  HCH2   0   0.276   7.1755   1.7351  -0.7943
 LNA  H2A   H  HCH2   0   0.274   7.7607   0.2166  -1.4112
 LNA  H3    H  HCH2   0   0.225   6.7427  -0.9769   0.5647
 LNA  H3A   H  HCH2   0   0.225   6.1445   0.5537   1.1717
 LNA  H4    H  HCH2   0   0.214   4.8177   0.8629  -0.9322
 LNA  H4A   H  HCH2   0   0.214   5.4063  -0.6750  -1.5247
 LNA  H5    H  HCH2   0   0.213   4.3385  -1.8277   0.4318
 LNA  H5A   H  HCH2   0   0.212   3.7477  -0.2845   1.0120
 LNA  H6    H  HCH2   0   0.215   2.4661   0.0117  -1.1323
 LNA  H6A   H  HCH2   0   0.216   3.0255  -1.5580  -1.6690
 LNA  H7    H  HCH2   0   0.230   1.8839  -2.6215   0.3050
 LNA  H7A   H  HCH2   0   0.229   1.3254  -1.0408   0.8190
 LNA  H8    H  HCH2   0   0.248   0.1176  -0.7763  -1.3822
 LNA  H8A   H  HCH2   0   0.263   0.6386  -2.3866  -1.8332
 LNA  H9    H  H      0   0.294  -0.6638  -3.4417  -0.0521
 LNA  H11   H  HCH2   0   0.286  -2.7051   0.1055   0.7511
 LNA  H11A  H  HCH2   0   0.274  -1.2978   0.2227  -0.2643
 LNA  H12   H  H      0   0.242  -2.6106  -0.4743  -2.2841
 LNA  H13   H  H      0   0.234  -4.7614   0.4113  -2.4237
 LNA  H14   H  HCH2   0   0.230  -6.0421   0.2303  -0.2294
 LNA  H14A  H  HCH2   0   0.232  -4.6492   0.8457   0.6318
 LNA  H15   H  HCH2   0   0.217  -4.7888   2.9798  -0.6592
 LNA  H15A  H  HCH2   0   0.212  -6.1329   2.3428  -1.5841
 LNA  H16   H  HCH2   0   0.208  -7.4692   2.1208   0.5277
 LNA  H16A  H  HCH2   0   0.208  -6.1387   2.8057   1.4369
 LNA  H17   H  HCH2   0   0.211  -6.3065   4.9107   0.0909
 LNA  H17A  H  HCH2   0   0.210  -7.6328   4.2220  -0.8178
 LNA  H18   H  HCH3   0   0.216  -8.9893   4.0491   1.3023
 LNA  H18A  H  HCH3   0   0.216  -7.6539   4.7608   2.2023
 LNA  H18B  H  HCH3   0   0.226  -8.4990   5.7104   0.9835
 LNA  HO20  H  HOH1   0   0.478  10.5249   1.6050   0.1559

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
 LNA  O20  C1    single  1.331  0.020  1.331
 LNA  C1   O19   double  1.206  0.020  1.206
 LNA  C1   C2    single  1.503  0.020  1.503
 LNA  C2   C3    single  1.520  0.020  1.520
 LNA  C3   C4    single  1.523  0.020  1.523
 LNA  C4   C5    single  1.523  0.020  1.523
 LNA  C5   C6    single  1.523  0.020  1.523
 LNA  C6   C7    single  1.523  0.020  1.523
 LNA  C7   C8    single  1.533  0.020  1.533
 LNA  C8   C9    single  1.488  0.020  1.488
 LNA  C9   C10   double  1.334  0.020  1.334
 LNA  C10  N21   single  1.461  0.020  1.461
 LNA  C10  C11   single  1.499  0.020  1.499
 LNA  N21  O22   double  1.211  0.020  1.211
 LNA  N21  O23   single  1.210  0.020  1.210
 LNA  C11  C12   single  1.503  0.020  1.503
 LNA  C12  C13   double  1.330  0.020  1.330
 LNA  C13  C14   single  1.495  0.020  1.495
 LNA  C14  C15   single  1.529  0.020  1.529
 LNA  C15  C16   single  1.523  0.020  1.523
 LNA  C16  C17   single  1.524  0.020  1.524
 LNA  C17  C18   single  1.522  0.020  1.522
 LNA  C2   H2    single  0.970  0.020  1.090
 LNA  C2   H2A   single  0.970  0.020  1.090
 LNA  C3   H3    single  0.970  0.020  1.090
 LNA  C3   H3A   single  0.970  0.020  1.090
 LNA  C4   H4    single  0.970  0.020  1.090
 LNA  C4   H4A   single  0.970  0.020  1.090
 LNA  C5   H5    single  0.970  0.020  1.090
 LNA  C5   H5A   single  0.970  0.020  1.090
 LNA  C6   H6    single  0.970  0.020  1.090
 LNA  C6   H6A   single  0.970  0.020  1.090
 LNA  C7   H7    single  0.970  0.020  1.090
 LNA  C7   H7A   single  0.970  0.020  1.090
 LNA  C8   H8    single  0.970  0.020  1.090
 LNA  C8   H8A   single  0.970  0.020  1.090
 LNA  C9   H9    single  0.930  0.020  1.080
 LNA  C11  H11   single  0.970  0.020  1.090
 LNA  C11  H11A  single  0.970  0.020  1.090
 LNA  C12  H12   single  0.930  0.020  1.080
 LNA  C13  H13   single  0.930  0.020  1.080
 LNA  C14  H14   single  0.970  0.020  1.090
 LNA  C14  H14A  single  0.970  0.020  1.090
 LNA  C15  H15   single  0.970  0.020  1.090
 LNA  C15  H15A  single  0.970  0.020  1.090
 LNA  C16  H16   single  0.970  0.020  1.090
 LNA  C16  H16A  single  0.970  0.020  1.090
 LNA  C17  H17   single  0.970  0.020  1.090
 LNA  C17  H17A  single  0.970  0.020  1.090
 LNA  C18  H18   single  0.970  0.020  1.090
 LNA  C18  H18A  single  0.970  0.020  1.090
 LNA  C18  H18B  single  0.970  0.020  1.090
 LNA  O20  HO20  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
 LNA  HO20  O20  C1    109.89  3.000
 LNA  C2    C1   O19   125.35  3.000
 LNA  C2    C1   O20   111.82  3.000
 LNA  O19   C1   O20   122.82  3.000
 LNA  H2A   C2   H2    105.26  3.000
 LNA  H2A   C2   C3    110.53  3.000
 LNA  H2    C2   C3    110.41  3.000
 LNA  H2A   C2   C1    108.12  3.000
 LNA  H2    C2   C1    108.01  3.000
 LNA  C3    C2   C1    114.10  3.000
 LNA  H3A   C3   H3    106.49  3.000
 LNA  H3A   C3   C4    109.38  3.000
 LNA  H3    C3   C4    109.46  3.000
 LNA  H3A   C3   C2    109.95  3.000
 LNA  H3    C3   C2    109.89  3.000
 LNA  C4    C3   C2    111.54  3.000
 LNA  H4A   C4   H4    106.02  3.000
 LNA  H4A   C4   C5    109.42  3.000
 LNA  H4    C4   C5    109.18  3.000
 LNA  H4A   C4   C3    109.39  3.000
 LNA  H4    C4   C3    109.45  3.000
 LNA  C5    C4   C3    113.13  3.000
 LNA  H5A   C5   H5    106.17  3.000
 LNA  H5A   C5   C6    109.43  3.000
 LNA  H5    C5   C6    109.56  3.000
 LNA  H5A   C5   C4    109.40  3.000
 LNA  H5    C5   C4    109.52  3.000
 LNA  C6    C5   C4    112.57  3.000
 LNA  H6A   C6   H6    106.11  3.000
 LNA  H6A   C6   C7    109.52  3.000
 LNA  H6    C6   C7    109.00  3.000
 LNA  H6A   C6   C5    109.33  3.000
 LNA  H6    C6   C5    109.30  3.000
 LNA  C7    C6   C5    113.32  3.000
 LNA  H7A   C7   H7    106.52  3.000
 LNA  H7A   C7   C8    109.16  3.000
 LNA  H7    C7   C8    109.66  3.000
 LNA  H7A   C7   C6    109.67  3.000
 LNA  H7    C7   C6    110.03  3.000
 LNA  C8    C7   C6    111.66  3.000
 LNA  H8A   C8   H8    106.61  3.000
 LNA  H8A   C8   C9    108.02  3.000
 LNA  H8    C8   C9    111.93  3.000
 LNA  H8A   C8   C7    108.80  3.000
 LNA  H8    C8   C7    109.66  3.000
 LNA  C9    C8   C7    111.64  3.000
 LNA  H9    C9   C10   118.91  3.000
 LNA  H9    C9   C8    115.58  3.000
 LNA  C10   C9   C8    125.50  3.000
 LNA  C11   C10  N21   115.65  3.000
 LNA  C11   C10  C9    126.79  3.000
 LNA  N21   C10  C9    117.51  3.000
 LNA  O23   N21  O22   123.18  3.000
 LNA  O23   N21  C10   117.18  3.000
 LNA  O22   N21  C10   119.65  3.000
 LNA  H11A  C11  H11   105.83  3.000
 LNA  H11A  C11  C12   109.03  3.000
 LNA  H11   C11  C12   112.03  3.000
 LNA  H11A  C11  C10   107.56  3.000
 LNA  H11   C11  C10   110.59  3.000
 LNA  C12   C11  C10   111.53  3.000
 LNA  H12   C12  C13   117.97  3.000
 LNA  H12   C12  C11   114.46  3.000
 LNA  C13   C12  C11   127.57  3.000
 LNA  H13   C13  C14   114.77  3.000
 LNA  H13   C13  C12   116.80  3.000
 LNA  C14   C13  C12   128.43  3.000
 LNA  H14A  C14  H14   106.23  3.000
 LNA  H14A  C14  C15   109.80  3.000
 LNA  H14   C14  C15   108.58  3.000
 LNA  H14A  C14  C13   111.56  3.000
 LNA  H14   C14  C13   108.43  3.000
 LNA  C15   C14  C13   112.02  3.000
 LNA  H15A  C15  H15   106.21  3.000
 LNA  H15A  C15  C16   109.27  3.000
 LNA  H15   C15  C16   109.63  3.000
 LNA  H15A  C15  C14   109.21  3.000
 LNA  H15   C15  C14   109.43  3.000
 LNA  C16   C15  C14   112.87  3.000
 LNA  H16A  C16  H16   106.08  3.000
 LNA  H16A  C16  C17   109.36  3.000
 LNA  H16   C16  C17   109.27  3.000
 LNA  H16A  C16  C15   109.57  3.000
 LNA  H16   C16  C15   109.15  3.000
 LNA  C17   C16  C15   113.17  3.000
 LNA  H17A  C17  H17   106.09  3.000
 LNA  H17A  C17  C18   109.62  3.000
 LNA  H17   C17  C18   109.47  3.000
 LNA  H17A  C17  C16   109.19  3.000
 LNA  H17   C17  C16   109.39  3.000
 LNA  C18   C17  C16   112.86  3.000
 LNA  H18B  C18  H18A  107.60  3.000
 LNA  H18B  C18  H18   107.62  3.000
 LNA  H18A  C18  H18   107.49  3.000
 LNA  H18B  C18  C17   111.59  3.000
 LNA  H18A  C18  C17   111.13  3.000
 LNA  H18   C18  C17   111.21  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
 LNA  CONST_01  HO20  O20  C1   O19     0.00   0.0  0
 LNA  Var_01    N21   C10  C9   C8    178.61   0.0  2
 LNA  Var_02    C14   C13  C12  C11     0.32   0.0  2
 LNA  Var_03    C3    C2   C1   O20   178.30  30.0  3
 LNA  Var_04    C4    C3   C2   C1   -179.59  30.0  3
 LNA  Var_05    C5    C4   C3   C2   -179.26  30.0  3
 LNA  Var_06    C6    C5   C4   C3   -179.75  30.0  3
 LNA  Var_07    C7    C6   C5   C4   -177.59  30.0  3
 LNA  Var_08    C8    C7   C6   C5   -179.92  30.0  3
 LNA  Var_09    C9    C8   C7   C6   -179.68  30.0  3
 LNA  Var_10    C10   C9   C8   C7    109.14  30.0  3
 LNA  Var_11    O22   N21  C10  C9      2.16  30.0  2
 LNA  Var_12    C12   C11  C10  C9     96.05  30.0  3
 LNA  Var_13    C13   C12  C11  C10   119.13  30.0  3
 LNA  Var_14    C15   C14  C13  C12   125.45  30.0  3
 LNA  Var_15    C16   C15  C14  C13   174.93  30.0  3
 LNA  Var_16    C17   C16  C15  C14  -177.98  30.0  3
 LNA  Var_17    C18   C17  C16  C15   179.70  30.0  3
 LNA  Var_18    H18   C18  C17  C16   -59.01  30.0  3

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
 LNA  plan-1  O20   0.020
 LNA  plan-1  C1    0.020
 LNA  plan-1  O19   0.020
 LNA  plan-1  C2    0.020
 LNA  plan-1  HO20  0.020
 LNA  plan-2  C8    0.020
 LNA  plan-2  C9    0.020
 LNA  plan-2  C10   0.020
 LNA  plan-2  N21   0.020
 LNA  plan-2  C11   0.020
 LNA  plan-2  H9    0.020
 LNA  plan-3  C10   0.020
 LNA  plan-3  N21   0.020
 LNA  plan-3  O22   0.020
 LNA  plan-3  O23   0.020
 LNA  plan-4  C11   0.020
 LNA  plan-4  C12   0.020
 LNA  plan-4  C13   0.020
 LNA  plan-4  C14   0.020
 LNA  plan-4  H12   0.020
 LNA  plan-4  H13   0.020

