# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:34:54 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[(1E,3E,5E,7E)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-1,3,3-trimethylcyclohexene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C/C=C(C)/C=C/C=C(C)/C=C/C1=C(C)CCCC1(C)C
#
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
 AZE  AZE  2-[(1E,3E,5E,7E)-3,7-dimethylnona-1,3,5,7-tetraen-1-yl]-1,3,3-trimethylcyclohexene  ligand  50  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AZE
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
 AZE  C1    C  CT    0  -0.144  29.7231  21.4979  44.9502
 AZE  C2    C  CH2   0  -0.412  29.4001  21.3985  43.4550
 AZE  C3    C  CH2   0  -0.447  30.5634  20.8584  42.6468
 AZE  C4    C  CH2   0  -0.477  30.8841  19.4501  43.1110
 AZE  C5    C  C     0   0.019  30.9139  19.2965  44.6077
 AZE  C6    C  C     0   0.119  30.4222  20.2297  45.4446
 AZE  C7    C  C1    0  -0.319  30.5348  20.1056  46.9048
 AZE  C8    C  C1    0  -0.253  31.6757  19.8564  47.5663
 AZE  C9    C  C     0   0.114  31.8064  19.7194  49.0081
 AZE  C10   C  C1    0  -0.304  33.0328  19.4443  49.5132
 AZE  C11   C  C1    0  -0.263  33.3866  19.2424  50.8949
 AZE  C12   C  C1    0  -0.287  34.6429  18.9544  51.2901
 AZE  C13   C  C     0   0.140  35.0694  18.7212  52.6604
 AZE  C14   C  C1    0  -0.309  36.3592  18.4206  52.8948
 AZE  C15   C  CH3   0  -0.721  36.9742  18.1395  54.2306
 AZE  C16   C  CH3   0  -0.661  28.3970  21.7170  45.6903
 AZE  C17   C  CH3   0  -0.633  30.6322  22.7046  45.2181
 AZE  C18   C  CH3   0  -0.729  31.5042  17.9850  45.0413
 AZE  C19   C  CH3   0  -0.761  30.5737  19.8771  49.8460
 AZE  C20   C  CH3   0  -0.760  34.0438  18.8150  53.7513
 AZE  H21   H  HCH2  0   0.218  28.5400  20.7322  43.3214
 AZE  H22   H  HCH2  0   0.225  29.0930  22.3839  43.0928
 AZE  H31   H  HCH2  0   0.231  30.3253  20.8594  41.5808
 AZE  H32   H  HCH2  0   0.220  31.4386  21.5028  42.7664
 AZE  H41   H  HCH2  0   0.231  30.1486  18.7452  42.7028
 AZE  H42   H  HCH2  0   0.236  31.8478  19.1242  42.7049
 AZE  H7    H  H     0   0.247  29.6293  20.2660  47.4824
 AZE  H8    H  H     0   0.234  32.5927  19.7435  46.9944
 AZE  H10   H  H     0   0.236  33.8513  19.3536  48.8027
 AZE  H11   H  H     0   0.249  32.6047  19.3153  51.6419
 AZE  H12   H  H     0   0.236  35.4187  18.8818  50.5312
 AZE  H14   H  H     0   0.244  37.0248  18.3675  52.0382
 AZE  H151  H  HCH3  0   0.246  38.0561  18.0521  54.1483
 AZE  H152  H  HCH3  0   0.244  36.7637  18.9245  54.9592
 AZE  H153  H  HCH3  0   0.246  36.6058  17.2039  54.6596
 AZE  H161  H  HCH3  0   0.226  28.5368  21.9592  46.7443
 AZE  H162  H  HCH3  0   0.231  27.8576  22.5531  45.2390
 AZE  H163  H  HCH3  0   0.227  27.7560  20.8356  45.6258
 AZE  H171  H  HCH3  0   0.227  30.8608  22.7967  46.2811
 AZE  H172  H  HCH3  0   0.225  31.5811  22.6259  44.6849
 AZE  H173  H  HCH3  0   0.220  30.1458  23.6298  44.8991
 AZE  H181  H  HCH3  0   0.243  31.2994  17.7377  46.0798
 AZE  H182  H  HCH3  0   0.233  31.1100  17.1801  44.4147
 AZE  H183  H  HCH3  0   0.235  32.5890  17.9735  44.9049
 AZE  H191  H  HCH3  0   0.254  30.7732  19.8119  50.9125
 AZE  H192  H  HCH3  0   0.242  30.0980  20.8422  49.6589
 AZE  H193  H  HCH3  0   0.245  29.8351  19.1101  49.6023
 AZE  H201  H  HCH3  0   0.256  34.4688  18.6263  54.7349
 AZE  H202  H  HCH3  0   0.241  33.5798  19.8035  53.7721
 AZE  H203  H  HCH3  0   0.242  33.2400  18.0924  53.5932

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
 AZE  C1   C2    single  1.533  0.020  1.533
 AZE  C1   C6    single  1.530  0.020  1.530
 AZE  C1   C16   single  1.534  0.020  1.534
 AZE  C1   C17   single  1.534  0.020  1.534
 AZE  C2   C3    single  1.516  0.020  1.516
 AZE  C2   H21   single  0.970  0.020  1.090
 AZE  C2   H22   single  0.970  0.020  1.090
 AZE  C3   C4    single  1.517  0.020  1.517
 AZE  C3   H31   single  0.970  0.020  1.090
 AZE  C3   H32   single  0.970  0.020  1.090
 AZE  C4   C5    single  1.505  0.020  1.505
 AZE  C4   H41   single  0.970  0.020  1.090
 AZE  C4   H42   single  0.970  0.020  1.090
 AZE  C5   C6    double  1.346  0.020  1.346
 AZE  C5   C18   single  1.502  0.020  1.502
 AZE  C6   C7    single  1.470  0.020  1.470
 AZE  C7   C8    double  1.342  0.020  1.342
 AZE  C7   H7    single  0.930  0.020  1.080
 AZE  C8   C9    single  1.454  0.020  1.454
 AZE  C8   H8    single  0.930  0.020  1.080
 AZE  C9   C10   double  1.355  0.020  1.355
 AZE  C9   C19   single  1.499  0.020  1.499
 AZE  C10  C11   single  1.440  0.020  1.440
 AZE  C10  H10   single  0.930  0.020  1.080
 AZE  C11  C12   double  1.348  0.020  1.348
 AZE  C11  H11   single  0.930  0.020  1.080
 AZE  C12  C13   single  1.454  0.020  1.454
 AZE  C12  H12   single  0.930  0.020  1.080
 AZE  C13  C14   double  1.345  0.020  1.345
 AZE  C13  C20   single  1.500  0.020  1.500
 AZE  C14  C15   single  1.497  0.020  1.497
 AZE  C14  H14   single  0.930  0.020  1.080
 AZE  C15  H151  single  0.970  0.020  1.090
 AZE  C15  H152  single  0.970  0.020  1.090
 AZE  C15  H153  single  0.970  0.020  1.090
 AZE  C16  H161  single  0.970  0.020  1.090
 AZE  C16  H162  single  0.970  0.020  1.090
 AZE  C16  H163  single  0.970  0.020  1.090
 AZE  C17  H171  single  0.970  0.020  1.090
 AZE  C17  H172  single  0.970  0.020  1.090
 AZE  C17  H173  single  0.970  0.020  1.090
 AZE  C18  H181  single  0.970  0.020  1.090
 AZE  C18  H182  single  0.970  0.020  1.090
 AZE  C18  H183  single  0.970  0.020  1.090
 AZE  C19  H191  single  0.970  0.020  1.090
 AZE  C19  H192  single  0.970  0.020  1.090
 AZE  C19  H193  single  0.970  0.020  1.090
 AZE  C20  H201  single  0.970  0.020  1.090
 AZE  C20  H202  single  0.970  0.020  1.090
 AZE  C20  H203  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
 AZE  C17   C1   C16   108.39  3.000
 AZE  C17   C1   C6    108.95  3.000
 AZE  C16   C1   C6    110.93  3.000
 AZE  C17   C1   C2    110.26  3.000
 AZE  C16   C1   C2    107.31  3.000
 AZE  C6    C1   C2    110.96  3.000
 AZE  H22   C2   H21   106.67  3.000
 AZE  H22   C2   C3    111.09  3.000
 AZE  H21   C2   C3    108.70  3.000
 AZE  H22   C2   C1    108.89  3.000
 AZE  H21   C2   C1    108.88  3.000
 AZE  C3    C2   C1    112.42  3.000
 AZE  H32   C3   H31   106.30  3.000
 AZE  H32   C3   C4    110.16  3.000
 AZE  H31   C3   C4    110.22  3.000
 AZE  H32   C3   C2    110.24  3.000
 AZE  H31   C3   C2    110.65  3.000
 AZE  C4    C3   C2    109.26  3.000
 AZE  H42   C4   H41   105.11  3.000
 AZE  H42   C4   C5    108.72  3.000
 AZE  H41   C4   C5    108.52  3.000
 AZE  H42   C4   C3    110.41  3.000
 AZE  H41   C4   C3    109.93  3.000
 AZE  C5    C4   C3    113.78  3.000
 AZE  C18   C5   C6    124.69  3.000
 AZE  C18   C5   C4    112.58  3.000
 AZE  C6    C5   C4    122.70  3.000
 AZE  C7    C6   C5    122.08  3.000
 AZE  C7    C6   C1    115.21  3.000
 AZE  C5    C6   C1    122.71  3.000
 AZE  H7    C7   C8    118.30  3.000
 AZE  H7    C7   C6    116.88  3.000
 AZE  C8    C7   C6    124.78  3.000
 AZE  H8    C8   C9    115.86  3.000
 AZE  H8    C8   C7    118.51  3.000
 AZE  C9    C8   C7    125.63  3.000
 AZE  C19   C9   C10   123.88  3.000
 AZE  C19   C9   C8    118.06  3.000
 AZE  C10   C9   C8    118.05  3.000
 AZE  H10   C10  C11   115.47  3.000
 AZE  H10   C10  C9    117.04  3.000
 AZE  C11   C10  C9    127.48  3.000
 AZE  H11   C11  C12   118.99  3.000
 AZE  H11   C11  C10   118.32  3.000
 AZE  C12   C11  C10   122.68  3.000
 AZE  H12   C12  C13   115.95  3.000
 AZE  H12   C12  C11   118.32  3.000
 AZE  C13   C12  C11   125.73  3.000
 AZE  C20   C13  C14   122.88  3.000
 AZE  C20   C13  C12   118.34  3.000
 AZE  C14   C13  C12   118.78  3.000
 AZE  H14   C14  C15   116.28  3.000
 AZE  H14   C14  C13   117.47  3.000
 AZE  C15   C14  C13   126.25  3.000
 AZE  H153  C15  H152  106.77  3.000
 AZE  H153  C15  H151  107.21  3.000
 AZE  H152  C15  H151  107.45  3.000
 AZE  H153  C15  C14   111.87  3.000
 AZE  H152  C15  C14   112.41  3.000
 AZE  H151  C15  C14   110.85  3.000
 AZE  H163  C16  H162  107.67  3.000
 AZE  H163  C16  H161  108.16  3.000
 AZE  H162  C16  H161  107.01  3.000
 AZE  H163  C16  C1    111.33  3.000
 AZE  H162  C16  C1    109.68  3.000
 AZE  H161  C16  C1    112.77  3.000
 AZE  H173  C17  H172  107.79  3.000
 AZE  H173  C17  H171  107.83  3.000
 AZE  H172  C17  H171  107.45  3.000
 AZE  H173  C17  C1    110.56  3.000
 AZE  H172  C17  C1    111.91  3.000
 AZE  H171  C17  C1    111.14  3.000
 AZE  H183  C18  H182  106.16  3.000
 AZE  H183  C18  H181  107.68  3.000
 AZE  H182  C18  H181  108.18  3.000
 AZE  H183  C18  C5    111.29  3.000
 AZE  H182  C18  C5    109.61  3.000
 AZE  H181  C18  C5    113.61  3.000
 AZE  H193  C19  H192  106.72  3.000
 AZE  H193  C19  H191  107.52  3.000
 AZE  H192  C19  H191  107.52  3.000
 AZE  H193  C19  C9    110.95  3.000
 AZE  H192  C19  C9    110.82  3.000
 AZE  H191  C19  C9    113.03  3.000
 AZE  H203  C20  H202  106.79  3.000
 AZE  H203  C20  H201  107.67  3.000
 AZE  H202  C20  H201  107.80  3.000
 AZE  H203  C20  C13   110.89  3.000
 AZE  H202  C20  C13   111.15  3.000
 AZE  H201  C20  C13   112.30  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
 AZE  Var_01  C4    C3   C2   C1     62.09  30.0  1
 AZE  Var_02  C4    C5   C6   C1      3.25  30.0  1
 AZE  Var_03  C5    C6   C1   C2     12.37  30.0  1
 AZE  Var_04  C5    C4   C3   C2    -44.93  30.0  1
 AZE  Var_05  C6    C1   C2   C3    -45.04  30.0  1
 AZE  Var_06  C6    C5   C4   C3     13.70  30.0  1
 AZE  Var_07  C8    C7   C6   C1   -128.10  30.0  2
 AZE  Var_08  H161  C16  C1   C2   -170.82  30.0  3
 AZE  Var_09  H171  C17  C1   C2    179.26  30.0  3
 AZE  Var_10  H181  C18  C5   C4   -164.66  30.0  3
 AZE  Var_11  C9    C8   C7   C6   -179.47   0.0  2
 AZE  Var_12  C11   C10  C9   C8   -178.69   0.0  2
 AZE  Var_13  C13   C12  C11  C10  -179.15   0.0  2
 AZE  Var_14  C15   C14  C13  C12  -179.49   0.0  2
 AZE  Var_15  C10   C9   C8   C7    178.89  30.0  2
 AZE  Var_16  C12   C11  C10  C9    179.10  30.0  2
 AZE  Var_17  C14   C13  C12  C11   178.87  30.0  2
 AZE  Var_18  H191  C19  C9   C8   -176.92  30.0  3
 AZE  Var_19  H201  C20  C13  C12  -179.83  30.0  3
 AZE  Var_20  H151  C15  C14  C13  -172.67  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
 AZE  plan-1  C6   0.020
 AZE  plan-1  C7   0.020
 AZE  plan-1  C8   0.020
 AZE  plan-1  C9   0.020
 AZE  plan-1  H7   0.020
 AZE  plan-1  H8   0.020
 AZE  plan-2  C8   0.020
 AZE  plan-2  C9   0.020
 AZE  plan-2  C10  0.020
 AZE  plan-2  C11  0.020
 AZE  plan-2  C19  0.020
 AZE  plan-2  H10  0.020
 AZE  plan-3  C10  0.020
 AZE  plan-3  C11  0.020
 AZE  plan-3  C12  0.020
 AZE  plan-3  C13  0.020
 AZE  plan-3  H11  0.020
 AZE  plan-3  H12  0.020
 AZE  plan-4  C12  0.020
 AZE  plan-4  C13  0.020
 AZE  plan-4  C14  0.020
 AZE  plan-4  C15  0.020
 AZE  plan-4  C20  0.020
 AZE  plan-4  H14  0.020

