# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 00:00:05 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  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_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  OH1    0  -0.599   -9.8874  -0.7875  -1.4011
 LNB  C1    C  C      0   0.550   -8.9835  -0.7660  -0.4246
 LNB  O19   O  O      0  -0.446   -9.2163  -1.1620   0.6905
 LNB  C2    C  CH2    0  -0.579   -7.6732  -0.1926  -0.8874
 LNB  C3    C  CH2    0  -0.418   -6.5870  -0.2028   0.1755
 LNB  C4    C  CH2    0  -0.414   -5.2794   0.3834  -0.3425
 LNB  C5    C  CH2    0  -0.413   -4.1717   0.3734   0.7032
 LNB  C6    C  CH2    0  -0.413   -2.8630   0.9673   0.1974
 LNB  C7    C  CH2    0  -0.417   -1.7522   0.9335   1.2390
 LNB  C8    C  CH2    0  -0.485   -0.4495   1.5622   0.7422
 LNB  C9    C  C1     0  -0.194    0.6185   1.5244   1.7875
 LNB  C10   C  C1     0  -0.215    1.8294   0.9795   1.6995
 LNB  C11   C  CH2    0  -0.592    2.4253   0.2853   0.5066
 LNB  C12   C  C      0   0.257    3.6682   0.9777   0.0371
 LNB  N21   N  N      1   0.366    3.4543   2.2868  -0.5788
 LNB  O22   O  O      0  -0.381    2.3218   2.5657  -0.8998
 LNB  O23   O  O     -1  -0.400    4.3953   3.0302  -0.7485
 LNB  C13   C  C1     0  -0.229    4.9273   0.5461   0.1232
 LNB  C14   C  CH2    0  -0.503    5.3814  -0.7669   0.6541
 LNB  C15   C  CH2    0  -0.420    6.0395  -1.6016  -0.4502
 LNB  C16   C  CH2    0  -0.410    6.5453  -2.9442   0.0590
 LNB  C17   C  CH2    0  -0.421    7.2113  -3.7762  -1.0308
 LNB  C18   C  CH3    0  -0.662    7.7006  -5.1263  -0.5259
 LNB  HO20  H  HOH1   0   0.478  -10.7197  -1.1602  -1.0736
 LNB  H2    H  HCH2   0   0.274   -7.3501  -0.7489  -1.7731
 LNB  H2A   H  HCH2   0   0.276   -7.8591   0.8281  -1.2382
 LNB  H3    H  HCH2   0   0.225   -6.9170   0.3634   1.0505
 LNB  H3A   H  HCH2   0   0.224   -6.4153  -1.2275   0.5162
 LNB  H4    H  HCH2   0   0.212   -4.9511  -0.1777  -1.2244
 LNB  H4A   H  HCH2   0   0.212   -5.4495   1.4109  -0.6819
 LNB  H5    H  HCH2   0   0.210   -4.5019   0.9268   1.5892
 LNB  H5A   H  HCH2   0   0.209   -3.9985  -0.6560   1.0351
 LNB  H6    H  HCH2   0   0.210   -2.5385   0.4242  -0.6971
 LNB  H6A   H  HCH2   0   0.210   -3.0325   2.0021  -0.1197
 LNB  H7    H  HCH2   0   0.214   -2.0833   1.4540   2.1442
 LNB  H7A   H  HCH2   0   0.217   -1.5615  -0.1029   1.5350
 LNB  H8    H  HCH2   0   0.231   -0.1270   1.0637  -0.1735
 LNB  H8A   H  HCH2   0   0.231   -0.6436   2.6059   0.4712
 LNB  H9    H  H      0   0.234    0.3492   1.9846   2.7352
 LNB  H10   H  H      0   0.244    2.4811   1.0307   2.5667
 LNB  H11   H  HCH2   0   0.274    2.7008  -0.7314   0.7898
 LNB  H11A  H  HCH2   0   0.281    1.7063   0.1866  -0.3069
 LNB  H13   H  H      0   0.291    5.7183   1.1811  -0.2594
 LNB  H14   H  HCH2   0   0.261    6.1200  -0.5782   1.4399
 LNB  H14A  H  HCH2   0   0.251    4.5701  -1.3317   1.1137
 LNB  H15   H  HCH2   0   0.228    5.3172  -1.7629  -1.2556
 LNB  H15A  H  HCH2   0   0.227    6.8685  -1.0365  -0.8873
 LNB  H16   H  HCH2   0   0.214    7.2552  -2.7816   0.8770
 LNB  H16A  H  HCH2   0   0.214    5.7098  -3.5083   0.4872
 LNB  H17   H  HCH2   0   0.213    6.5054  -3.9245  -1.8535
 LNB  H17A  H  HCH2   0   0.213    8.0520  -3.2148  -1.4498
 LNB  H18   H  HCH3   0   0.227    8.1622  -5.7090  -1.3237
 LNB  H18A  H  HCH3   0   0.217    8.4413  -5.0053   0.2663
 LNB  H18B  H  HCH3   0   0.216    6.8779  -5.7174  -0.1189

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   single  1.331  0.020  1.331
 LNB  O20  HO20  single  0.850  0.020  0.980
 LNB  C2   C1    single  1.503  0.020  1.503
 LNB  O19  C1    double  1.206  0.020  1.206
 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  1.524  0.020  1.524
 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  1.498  0.020  1.498
 LNB  C11  H11   single  0.970  0.020  1.090
 LNB  C11  H11A  single  0.970  0.020  1.090
 LNB  N21  C12   single  1.462  0.020  1.462
 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  1.533  0.020  1.533
 LNB  C14  H14   single  0.970  0.020  1.090
 LNB  C14  H14A  single  0.970  0.020  1.090
 LNB  C16  C15   single  1.522  0.020  1.522
 LNB  C15  H15   single  0.970  0.020  1.090
 LNB  C15  H15A  single  0.970  0.020  1.090
 LNB  C16  C17   single  1.524  0.020  1.524
 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  HO20  O20  C1    109.97  3.000
 LNB  C2    C1   O19   125.32  3.000
 LNB  O19   C1   O20   122.82  3.000
 LNB  C2    C1   O20   111.85  3.000
 LNB  H2A   C2   H2    105.34  3.000
 LNB  H2A   C2   C3    110.59  3.000
 LNB  H2    C2   C3    110.58  3.000
 LNB  H2A   C2   C1    107.83  3.000
 LNB  H2    C2   C1    108.21  3.000
 LNB  C3    C2   C1    113.90  3.000
 LNB  H3A   C3   H3    106.46  3.000
 LNB  H3A   C3   C4    109.38  3.000
 LNB  H3    C3   C4    109.38  3.000
 LNB  H3A   C3   C2    109.66  3.000
 LNB  H3    C3   C2    109.90  3.000
 LNB  C4    C3   C2    111.90  3.000
 LNB  H4A   C4   H4    106.11  3.000
 LNB  H4A   C4   C5    109.38  3.000
 LNB  H4    C4   C5    109.35  3.000
 LNB  H4A   C4   C3    109.45  3.000
 LNB  H4    C4   C3    109.49  3.000
 LNB  C5    C4   C3    112.84  3.000
 LNB  H5A   C5   H5    106.10  3.000
 LNB  H5A   C5   C6    109.34  3.000
 LNB  H5    C5   C6    109.30  3.000
 LNB  H5A   C5   C4    109.22  3.000
 LNB  H5    C5   C4    109.43  3.000
 LNB  C6    C5   C4    113.21  3.000
 LNB  H6A   C6   H6    106.12  3.000
 LNB  H6A   C6   C7    109.37  3.000
 LNB  H6    C6   C7    109.34  3.000
 LNB  H6A   C6   C5    109.36  3.000
 LNB  H6    C6   C5    109.41  3.000
 LNB  C7    C6   C5    113.00  3.000
 LNB  H7A   C7   H7    106.20  3.000
 LNB  H7A   C7   C8    109.19  3.000
 LNB  H7    C7   C8    109.31  3.000
 LNB  H7A   C7   C6    109.45  3.000
 LNB  H7    C7   C6    109.52  3.000
 LNB  C8    C7   C6    112.95  3.000
 LNB  H8A   C8   H8    106.26  3.000
 LNB  H8A   C8   C9    108.88  3.000
 LNB  H8    C8   C9    111.35  3.000
 LNB  H8A   C8   C7    108.73  3.000
 LNB  H8    C8   C7    109.67  3.000
 LNB  C9    C8   C7    111.78  3.000
 LNB  H9    C9   C10   117.14  3.000
 LNB  H9    C9   C8    114.95  3.000
 LNB  C10   C9   C8    127.90  3.000
 LNB  H10   C10  C11   114.67  3.000
 LNB  H10   C10  C9    118.30  3.000
 LNB  C11   C10  C9    127.03  3.000
 LNB  H11A  C11  H11   106.02  3.000
 LNB  H11A  C11  C12   110.80  3.000
 LNB  H11   C11  C12   107.61  3.000
 LNB  H11A  C11  C10   111.87  3.000
 LNB  H11   C11  C10   108.94  3.000
 LNB  C12   C11  C10   111.35  3.000
 LNB  C13   C12  N21   117.06  3.000
 LNB  C13   C12  C11   127.83  3.000
 LNB  N21   C12  C11   115.11  3.000
 LNB  O23   N21  O22   123.27  3.000
 LNB  O23   N21  C12   119.66  3.000
 LNB  O22   N21  C12   117.07  3.000
 LNB  H13   C13  C14   114.85  3.000
 LNB  H13   C13  C12   118.45  3.000
 LNB  C14   C13  C12   126.65  3.000
 LNB  H14A  C14  H14   106.79  3.000
 LNB  H14A  C14  C15   109.94  3.000
 LNB  H14   C14  C15   108.74  3.000
 LNB  H14A  C14  C13   112.37  3.000
 LNB  H14   C14  C13   108.07  3.000
 LNB  C15   C14  C13   110.77  3.000
 LNB  H15A  C15  H15   106.40  3.000
 LNB  H15A  C15  C16   109.71  3.000
 LNB  H15   C15  C16   109.61  3.000
 LNB  H15A  C15  C14   109.38  3.000
 LNB  H15   C15  C14   109.11  3.000
 LNB  C16   C15  C14   112.45  3.000
 LNB  H16A  C16  H16   106.19  3.000
 LNB  H16A  C16  C17   109.37  3.000
 LNB  H16   C16  C17   109.38  3.000
 LNB  H16A  C16  C15   109.36  3.000
 LNB  H16   C16  C15   109.53  3.000
 LNB  C17   C16  C15   112.79  3.000
 LNB  H17A  C17  H17   106.10  3.000
 LNB  H17A  C17  C18   109.58  3.000
 LNB  H17   C17  C18   109.67  3.000
 LNB  H17A  C17  C16   109.23  3.000
 LNB  H17   C17  C16   109.25  3.000
 LNB  C18   C17  C16   112.80  3.000
 LNB  H18B  C18  H18A  107.50  3.000
 LNB  H18B  C18  H18   107.60  3.000
 LNB  H18A  C18  H18   107.64  3.000
 LNB  H18B  C18  C17   111.21  3.000
 LNB  H18A  C18  C17   111.14  3.000
 LNB  H18   C18  C17   111.55  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  CONST_01  HO20  O20  C1   O19     0.00   0.0  0
 LNB  Var_01    C11   C10  C9   C8      1.13   0.0  2
 LNB  Var_02    C14   C13  C12  C11     3.17   0.0  2
 LNB  Var_03    C3    C2   C1   O20  -177.43  30.0  2
 LNB  Var_04    C4    C3   C2   C1    179.82  30.0  1
 LNB  Var_05    C5    C4   C3   C2   -179.55  30.0  1
 LNB  Var_06    C6    C5   C4   C3   -179.57  30.0  2
 LNB  Var_07    C7    C6   C5   C4   -179.03  30.0  1
 LNB  Var_08    C8    C7   C6   C5   -178.54  30.0  2
 LNB  Var_09    C9    C8   C7   C6    179.57  30.0  3
 LNB  Var_10    C10   C9   C8   C7    123.11  30.0  2
 LNB  Var_11    C12   C11  C10  C9    119.58  30.0  1
 LNB  Var_12    N21   C12  C11  C10   -69.77  30.0  2
 LNB  Var_13    O22   N21  C12  C11   -14.68  30.0  2
 LNB  Var_14    C15   C14  C13  C12   115.53  30.0  3
 LNB  Var_15    C16   C15  C14  C13   178.81  30.0  3
 LNB  Var_16    C17   C16  C15  C14  -179.54  30.0  1
 LNB  Var_17    C18   C17  C16  C15  -179.23  30.0  3
 LNB  Var_18    H18   C18  C17  C16   179.31  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-1  HO20  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

