# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:56:49 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (9Z,12E)-12-nitrooctadeca-9,12-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C(/C\C=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
 LNB  LNB  '(9Z,12E)-12-nitrooctadeca-9,12-dienoic acid'  ligand  53  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LNB
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
 LNB  O20   O  OC    -1  -0.635  -10.3135   0.0902  -0.8649
 LNB  C1    C  C      0   0.409   -9.3239  -0.2991  -0.2078
 LNB  O19   O  O      0  -0.610   -9.3381  -1.1347   0.7176
 LNB  C2    C  CH2    0  -0.580   -7.9713   0.3192  -0.6022
 LNB  C3    C  CH2    0  -0.401   -6.7690  -0.0968   0.2292
 LNB  C4    C  CH2    0  -0.408   -5.4772   0.5662  -0.2359
 LNB  C5    C  CH2    0  -0.410   -4.2691   0.2043   0.6186
 LNB  C6    C  CH2    0  -0.411   -2.9817   0.8823   0.1649
 LNB  C7    C  CH2    0  -0.416   -1.7971   0.5758   1.0719
 LNB  C8    C  CH2    0  -0.484   -0.5132   1.2932   0.6523
 LNB  C9    C  C1     0  -0.195    0.5897   1.0694   1.6365
 LNB  C10   C  C1     0  -0.211    1.8032   0.5698   1.4172
 LNB  C11   C  CH2    0  -0.602    2.3830   0.1223   0.1049
 LNB  C12   C  C      0   0.256    3.6005   0.9232  -0.2472
 LNB  N21   N  N      1   0.369    3.3458   2.2344  -0.8403
 LNB  O22   O  O      0  -0.382    2.1907   2.5421  -1.0271
 LNB  O23   O  O     -1  -0.402    4.2774   2.9568  -1.1192
 LNB  C13   C  C1     0  -0.227    4.8720   0.5884  -0.0223
 LNB  C14   C  CH2    0  -0.504    5.3453  -0.6822   0.5893
 LNB  C15   C  CH2    0  -0.419    6.1543  -1.5147  -0.4097
 LNB  C16   C  CH2    0  -0.409    6.6904  -2.7978   0.2116
 LNB  C17   C  CH2    0  -0.421    7.5042  -3.6365  -0.7648
 LNB  C18   C  CH3    0  -0.662    8.0236  -4.9264  -0.1455
 LNB  H2    H  HCH2   0   0.216   -7.7885   0.0801  -1.6571
 LNB  H2A   H  HCH2   0   0.214   -8.0736   1.4106  -0.5777
 LNB  H3    H  HCH2   0   0.199   -6.9403   0.1515   1.2811
 LNB  H3A   H  HCH2   0   0.200   -6.6508  -1.1837   0.1938
 LNB  H4    H  HCH2   0   0.202   -5.2829   0.2934  -1.2795
 LNB  H4A   H  HCH2   0   0.201   -5.6058   1.6547  -0.2297
 LNB  H5    H  HCH2   0   0.204   -4.4693   0.4781   1.6608
 LNB  H5A   H  HCH2   0   0.205   -4.1305  -0.8825   0.6134
 LNB  H6    H  HCH2   0   0.209   -2.7503   0.5787  -0.8619
 LNB  H6A   H  HCH2   0   0.207   -3.1373   1.9665   0.1333
 LNB  H7    H  HCH2   0   0.212   -2.0482   0.8629   2.0990
 LNB  H7A   H  HCH2   0   0.216   -1.6177  -0.5038   1.0934
 LNB  H8    H  HCH2   0   0.233   -0.2227   0.9820  -0.3526
 LNB  H8A   H  HCH2   0   0.229   -0.7159   2.3686   0.5939
 LNB  H9    H  H      0   0.234    0.3474   1.3406   2.6613
 LNB  H10   H  H      0   0.242    2.4758   0.4709   2.2646
 LNB  H11   H  HCH2   0   0.275    2.6881  -0.9226   0.1841
 LNB  H11A  H  HCH2   0   0.286    1.6479   0.1593  -0.6974
 LNB  H13   H  H      0   0.293    5.6528   1.2822  -0.3116
 LNB  H14   H  HCH2   0   0.262    5.9885  -0.4242   1.4367
 LNB  H14A  H  HCH2   0   0.250    4.5230  -1.2751   0.9915
 LNB  H15   H  HCH2   0   0.228    5.5242  -1.7577  -1.2704
 LNB  H15A  H  HCH2   0   0.227    6.9857  -0.9165  -0.7951
 LNB  H16   H  HCH2   0   0.213    7.3065  -2.5499   1.0827
 LNB  H16A  H  HCH2   0   0.214    5.8531  -3.3928   0.5921
 LNB  H17   H  HCH2   0   0.213    6.8896  -3.8721  -1.6391
 LNB  H17A  H  HCH2   0   0.213    8.3459  -3.0449  -1.1377
 LNB  H18   H  HCH3   0   0.227    8.5844  -5.5193  -0.8688
 LNB  H18A  H  HCH3   0   0.217    8.6855  -4.7223   0.6981
 LNB  H18B  H  HCH3   0   0.216    7.2033  -5.5451   0.2236

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
 LNB  C1   O20   deloc   1.250  0.020  1.250
 LNB  C2   C1    single  1.539  0.020  1.539
 LNB  O19  C1    deloc   1.247  0.020  1.247
 LNB  C3   C2    single  1.520  0.020  1.520
 LNB  C2   H2    single  0.970  0.020  1.090
 LNB  C2   H2A   single  0.970  0.020  1.090
 LNB  C4   C3    single  1.525  0.020  1.525
 LNB  C3   H3    single  0.970  0.020  1.090
 LNB  C3   H3A   single  0.970  0.020  1.090
 LNB  C5   C4    single  1.523  0.020  1.523
 LNB  C4   H4    single  0.970  0.020  1.090
 LNB  C4   H4A   single  0.970  0.020  1.090
 LNB  C6   C5    single  1.524  0.020  1.524
 LNB  C5   H5    single  0.970  0.020  1.090
 LNB  C5   H5A   single  0.970  0.020  1.090
 LNB  C7   C6    single  1.523  0.020  1.523
 LNB  C6   H6    single  0.970  0.020  1.090
 LNB  C6   H6A   single  0.970  0.020  1.090
 LNB  C7   C8    single  1.529  0.020  1.529
 LNB  C7   H7    single  0.970  0.020  1.090
 LNB  C7   H7A   single  0.970  0.020  1.090
 LNB  C9   C8    single  1.495  0.020  1.495
 LNB  C8   H8    single  0.970  0.020  1.090
 LNB  C8   H8A   single  0.970  0.020  1.090
 LNB  C10  C9    double  1.331  0.020  1.331
 LNB  C9   H9    single  0.930  0.020  1.080
 LNB  C11  C10   single  1.503  0.020  1.503
 LNB  C10  H10   single  0.930  0.020  1.080
 LNB  C12  C11   single  1.499  0.020  1.499
 LNB  C11  H11   single  0.970  0.020  1.090
 LNB  C11  H11A  single  0.970  0.020  1.090
 LNB  N21  C12   single  1.461  0.020  1.461
 LNB  C13  C12   double  1.334  0.020  1.334
 LNB  O22  N21   double  1.210  0.020  1.210
 LNB  N21  O23   single  1.211  0.020  1.211
 LNB  C13  C14   single  1.487  0.020  1.487
 LNB  C13  H13   single  0.930  0.020  1.080
 LNB  C14  C15   single  1.531  0.020  1.531
 LNB  C14  H14   single  0.970  0.020  1.090
 LNB  C14  H14A  single  0.970  0.020  1.090
 LNB  C16  C15   single  1.523  0.020  1.523
 LNB  C15  H15   single  0.970  0.020  1.090
 LNB  C15  H15A  single  0.970  0.020  1.090
 LNB  C16  C17   single  1.523  0.020  1.523
 LNB  C16  H16   single  0.970  0.020  1.090
 LNB  C16  H16A  single  0.970  0.020  1.090
 LNB  C18  C17   single  1.522  0.020  1.522
 LNB  C17  H17   single  0.970  0.020  1.090
 LNB  C17  H17A  single  0.970  0.020  1.090
 LNB  C18  H18   single  0.970  0.020  1.090
 LNB  C18  H18A  single  0.970  0.020  1.090
 LNB  C18  H18B  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
 LNB  C2    C1   O19   118.00  3.000
 LNB  O19   C1   O20   126.15  3.000
 LNB  C2    C1   O20   115.85  3.000
 LNB  H2A   C2   H2    104.72  3.000
 LNB  H2A   C2   C3    109.52  3.000
 LNB  H2    C2   C3    109.55  3.000
 LNB  H2A   C2   C1    108.19  3.000
 LNB  H2    C2   C1    107.78  3.000
 LNB  C3    C2   C1    116.43  3.000
 LNB  H3A   C3   H3    105.87  3.000
 LNB  H3A   C3   C4    109.31  3.000
 LNB  H3    C3   C4    109.10  3.000
 LNB  H3A   C3   C2    109.86  3.000
 LNB  H3    C3   C2    109.87  3.000
 LNB  C4    C3   C2    112.60  3.000
 LNB  H4A   C4   H4    105.86  3.000
 LNB  H4A   C4   C5    109.02  3.000
 LNB  H4    C4   C5    109.54  3.000
 LNB  H4A   C4   C3    109.31  3.000
 LNB  H4    C4   C3    109.42  3.000
 LNB  C5    C4   C3    113.42  3.000
 LNB  H5A   C5   H5    105.99  3.000
 LNB  H5A   C5   C6    109.45  3.000
 LNB  H5    C5   C6    109.04  3.000
 LNB  H5A   C5   C4    109.47  3.000
 LNB  H5    C5   C4    109.22  3.000
 LNB  C6    C5   C4    113.40  3.000
 LNB  H6A   C6   H6    106.09  3.000
 LNB  H6A   C6   C7    109.07  3.000
 LNB  H6    C6   C7    109.77  3.000
 LNB  H6A   C6   C5    109.20  3.000
 LNB  H6    C6   C5    109.52  3.000
 LNB  C7    C6   C5    112.96  3.000
 LNB  H7A   C7   H7    106.12  3.000
 LNB  H7A   C7   C8    109.29  3.000
 LNB  H7    C7   C8    109.07  3.000
 LNB  H7A   C7   C6    109.73  3.000
 LNB  H7    C7   C6    109.10  3.000
 LNB  C8    C7   C6    113.27  3.000
 LNB  H8A   C8   H8    106.25  3.000
 LNB  H8A   C8   C9    108.56  3.000
 LNB  H8    C8   C9    111.54  3.000
 LNB  H8A   C8   C7    108.64  3.000
 LNB  H8    C8   C7    110.02  3.000
 LNB  C9    C8   C7    111.62  3.000
 LNB  H9    C9   C10   116.88  3.000
 LNB  H9    C9   C8    114.75  3.000
 LNB  C10   C9   C8    128.35  3.000
 LNB  H10   C10  C11   114.53  3.000
 LNB  H10   C10  C9    118.05  3.000
 LNB  C11   C10  C9    127.42  3.000
 LNB  H11A  C11  H11   105.95  3.000
 LNB  H11A  C11  C12   110.92  3.000
 LNB  H11   C11  C12   107.54  3.000
 LNB  H11A  C11  C10   111.89  3.000
 LNB  H11   C11  C10   109.24  3.000
 LNB  C12   C11  C10   111.06  3.000
 LNB  C13   C12  N21   117.37  3.000
 LNB  C13   C12  C11   126.90  3.000
 LNB  N21   C12  C11   115.66  3.000
 LNB  O23   N21  O22   123.16  3.000
 LNB  O23   N21  C12   119.63  3.000
 LNB  O22   N21  C12   117.21  3.000
 LNB  H13   C13  C14   115.30  3.000
 LNB  H13   C13  C12   118.75  3.000
 LNB  C14   C13  C12   125.95  3.000
 LNB  H14A  C14  H14   106.60  3.000
 LNB  H14A  C14  C15   110.08  3.000
 LNB  H14   C14  C15   108.82  3.000
 LNB  H14A  C14  C13   112.10  3.000
 LNB  H14   C14  C13   107.69  3.000
 LNB  C15   C14  C13   111.36  3.000
 LNB  H15A  C15  H15   106.37  3.000
 LNB  H15A  C15  C16   109.68  3.000
 LNB  H15   C15  C16   109.67  3.000
 LNB  H15A  C15  C14   109.51  3.000
 LNB  H15   C15  C14   109.25  3.000
 LNB  C16   C15  C14   112.20  3.000
 LNB  H16A  C16  H16   106.06  3.000
 LNB  H16A  C16  C17   109.39  3.000
 LNB  H16   C16  C17   109.51  3.000
 LNB  H16A  C16  C15   109.28  3.000
 LNB  H16   C16  C15   109.37  3.000
 LNB  C17   C16  C15   112.99  3.000
 LNB  H17A  C17  H17   106.03  3.000
 LNB  H17A  C17  C18   109.53  3.000
 LNB  H17   C17  C18   109.53  3.000
 LNB  H17A  C17  C16   109.38  3.000
 LNB  H17   C17  C16   109.31  3.000
 LNB  C18   C17  C16   112.84  3.000
 LNB  H18B  C18  H18A  107.48  3.000
 LNB  H18B  C18  H18   107.61  3.000
 LNB  H18A  C18  H18   107.60  3.000
 LNB  H18B  C18  C17   111.18  3.000
 LNB  H18A  C18  C17   111.28  3.000
 LNB  H18   C18  C17   111.49  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
 LNB  Var_01  C11  C10  C9   C8      1.17   0.0  2
 LNB  Var_02  C14  C13  C12  C11     2.20   0.0  2
 LNB  Var_03  C3   C2   C1   O20   177.31  30.0  2
 LNB  Var_04  C4   C3   C2   C1   -179.99  30.0  1
 LNB  Var_05  C5   C4   C3   C2    177.76  30.0  2
 LNB  Var_06  C6   C5   C4   C3   -179.21  30.0  1
 LNB  Var_07  C7   C6   C5   C4    176.76  30.0  2
 LNB  Var_08  C8   C7   C6   C5   -177.91  30.0  1
 LNB  Var_09  C9   C8   C7   C6    174.67  30.0  3
 LNB  Var_10  C10  C9   C8   C7    123.85  30.0  2
 LNB  Var_11  C12  C11  C10  C9    119.09  30.0  1
 LNB  Var_12  N21  C12  C11  C10   -80.73  30.0  1
 LNB  Var_13  O22  N21  C12  C11    -1.92  30.0  2
 LNB  Var_14  C15  C14  C13  C12   114.80  30.0  3
 LNB  Var_15  C16  C15  C14  C13   177.97  30.0  3
 LNB  Var_16  C17  C16  C15  C14  -179.71  30.0  1
 LNB  Var_17  C18  C17  C16  C15  -179.28  30.0  3
 LNB  Var_18  H18  C18  C17  C16   178.78  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
 LNB  plan-1  O20  0.020
 LNB  plan-1  C1   0.020
 LNB  plan-1  O19  0.020
 LNB  plan-1  C2   0.020
 LNB  plan-2  C8   0.020
 LNB  plan-2  C9   0.020
 LNB  plan-2  C10  0.020
 LNB  plan-2  C11  0.020
 LNB  plan-2  H9   0.020
 LNB  plan-2  H10  0.020
 LNB  plan-3  C11  0.020
 LNB  plan-3  C12  0.020
 LNB  plan-3  N21  0.020
 LNB  plan-3  C13  0.020
 LNB  plan-3  C14  0.020
 LNB  plan-3  H13  0.020
 LNB  plan-4  C12  0.020
 LNB  plan-4  N21  0.020
 LNB  plan-4  O22  0.020
 LNB  plan-4  O23  0.020

