# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 21:12:00 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2E,4E)-dodeca-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC/C=C/C=C/C(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
 MH9  MH9  '(2E,4E)-dodeca-2,4-dienoic acid'  ligand  34  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MH9
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
 MH9  C     C  C     0   0.525  -5.5634   0.5204  -0.0236
 MH9  O     O  O     0  -0.457  -5.8209   0.6111   1.1564
 MH9  C1    C  C1    0  -0.422  -4.2854   0.0696  -0.5844
 MH9  C2    C  C1    0  -0.166  -3.2554  -0.2586   0.2100
 MH9  C3    C  C1    0  -0.249  -1.9691  -0.6970  -0.2762
 MH9  C4    C  C1    0  -0.186  -0.9485  -0.9841   0.5419
 MH9  C5    C  CH2   0  -0.491   0.4095  -1.3979   0.0923
 MH9  C6    C  CH2   0  -0.417   1.4620  -0.3287   0.4028
 MH9  C7    C  CH2   0  -0.414   2.8645  -0.7466  -0.0195
 MH9  C8    C  CH2   0  -0.412   3.9066   0.3381   0.2233
 MH9  C9    C  CH2   0  -0.406   5.3096  -0.0705  -0.2079
 MH9  C10   C  CH2   0  -0.418   6.3486   1.0235   0.0055
 MH9  C11   C  CH3   0  -0.663   7.7473   0.6046  -0.4257
 MH9  OXT   O  OH1   0  -0.605  -6.4365   0.8323  -0.9796
 MH9  H1    H  H     0   0.274  -4.1926   0.0170  -1.6630
 MH9  H2    H  H     0   0.270  -3.3755  -0.1898   1.2876
 MH9  H3    H  H     0   0.254  -1.8391  -0.7846  -1.3512
 MH9  H4    H  H     0   0.257  -1.0942  -0.8818   1.6149
 MH9  H51   H  HCH2  0   0.241   0.6913  -2.3274   0.5985
 MH9  H52   H  HCH2  0   0.238   0.4033  -1.6076  -0.9804
 MH9  H61   H  HCH2  0   0.221   1.1857   0.5995  -0.1067
 MH9  H62   H  HCH2  0   0.221   1.4511  -0.1056   1.4743
 MH9  H71   H  HCH2  0   0.212   3.1527  -1.6570   0.5174
 MH9  H72   H  HCH2  0   0.211   2.8589  -1.0105  -1.0825
 MH9  H81   H  HCH2  0   0.208   3.6119   1.2470  -0.3131
 MH9  H82   H  HCH2  0   0.208   3.9153   0.6035   1.2860
 MH9  H91   H  HCH2  0   0.206   5.6128  -0.9700   0.3399
 MH9  H92   H  HCH2  0   0.206   5.2950  -0.3529  -1.2664
 MH9  H101  H  HCH2  0   0.210   6.0456   1.9199  -0.5449
 MH9  H102  H  HCH2  0   0.210   6.3618   1.3086   1.0619
 MH9  H111  H  HCH3  0   0.216   8.0858  -0.2695   0.1339
 MH9  H112  H  HCH3  0   0.215   7.7735   0.3452  -1.4858
 MH9  H113  H  HCH3  0   0.226   8.4737   1.4014  -0.2623
 MH9  HXT   H  HOH1  0   0.479  -7.2667   1.1338  -0.5823

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
 MH9  C    O     double  1.211  0.020  1.211
 MH9  C    C1    single  1.467  0.020  1.467
 MH9  C1   C2    double  1.342  0.020  1.342
 MH9  C2   C3    single  1.443  0.020  1.443
 MH9  C3   C4    double  1.339  0.020  1.339
 MH9  C4   C5    single  1.489  0.020  1.489
 MH9  C5   C6    single  1.532  0.020  1.532
 MH9  C6   C7    single  1.523  0.020  1.523
 MH9  C7   C8    single  1.524  0.020  1.524
 MH9  C8   C9    single  1.524  0.020  1.524
 MH9  C9   C10   single  1.524  0.020  1.524
 MH9  C10  C11   single  1.522  0.020  1.522
 MH9  C    OXT   single  1.332  0.020  1.332
 MH9  C1   H1    single  0.930  0.020  1.080
 MH9  C2   H2    single  0.930  0.020  1.080
 MH9  C3   H3    single  0.930  0.020  1.080
 MH9  C4   H4    single  0.930  0.020  1.080
 MH9  C5   H51   single  0.970  0.020  1.090
 MH9  C5   H52   single  0.970  0.020  1.090
 MH9  C6   H61   single  0.970  0.020  1.090
 MH9  C6   H62   single  0.970  0.020  1.090
 MH9  C7   H71   single  0.970  0.020  1.090
 MH9  C7   H72   single  0.970  0.020  1.090
 MH9  C8   H81   single  0.970  0.020  1.090
 MH9  C8   H82   single  0.970  0.020  1.090
 MH9  C9   H91   single  0.970  0.020  1.090
 MH9  C9   H92   single  0.970  0.020  1.090
 MH9  C10  H101  single  0.970  0.020  1.090
 MH9  C10  H102  single  0.970  0.020  1.090
 MH9  C11  H111  single  0.970  0.020  1.090
 MH9  C11  H112  single  0.970  0.020  1.090
 MH9  C11  H113  single  0.970  0.020  1.090
 MH9  OXT  HXT   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
 MH9  OXT   C    C1    111.64  3.000
 MH9  OXT   C    O     122.85  3.000
 MH9  C1    C    O     125.51  3.000
 MH9  H1    C1   C2    120.78  3.000
 MH9  H1    C1   C     118.04  3.000
 MH9  C2    C1   C     121.18  3.000
 MH9  H2    C2   C3    116.87  3.000
 MH9  H2    C2   C1    119.14  3.000
 MH9  C3    C2   C1    123.99  3.000
 MH9  H3    C3   C4    119.73  3.000
 MH9  H3    C3   C2    117.68  3.000
 MH9  C4    C3   C2    122.59  3.000
 MH9  H4    C4   C5    116.50  3.000
 MH9  H4    C4   C3    118.71  3.000
 MH9  C5    C4   C3    124.76  3.000
 MH9  H52   C5   H51   106.99  3.000
 MH9  H52   C5   C6    109.67  3.000
 MH9  H51   C5   C6    108.78  3.000
 MH9  H52   C5   C4    110.15  3.000
 MH9  H51   C5   C4    109.32  3.000
 MH9  C6    C5   C4    111.80  3.000
 MH9  H62   C6   H61   106.29  3.000
 MH9  H62   C6   C7    109.66  3.000
 MH9  H61   C6   C7    109.64  3.000
 MH9  H62   C6   C5    109.50  3.000
 MH9  H61   C6   C5    108.92  3.000
 MH9  C7    C6   C5    112.63  3.000
 MH9  H72   C7   H71   106.07  3.000
 MH9  H72   C7   C8    109.25  3.000
 MH9  H71   C7   C8    109.49  3.000
 MH9  H72   C7   C6    109.30  3.000
 MH9  H71   C7   C6    109.53  3.000
 MH9  C8    C7   C6    112.97  3.000
 MH9  H82   C8   H81   106.03  3.000
 MH9  H82   C8   C9    109.40  3.000
 MH9  H81   C8   C9    109.37  3.000
 MH9  H82   C8   C7    109.42  3.000
 MH9  H81   C8   C7    109.18  3.000
 MH9  C9    C8   C7    113.19  3.000
 MH9  H92   C9   H91   105.97  3.000
 MH9  H92   C9   C10   109.23  3.000
 MH9  H91   C9   C10   109.30  3.000
 MH9  H92   C9   C8    109.29  3.000
 MH9  H91   C9   C8    109.48  3.000
 MH9  C10   C9   C8    113.31  3.000
 MH9  H102  C10  H101  105.98  3.000
 MH9  H102  C10  C11   109.52  3.000
 MH9  H101  C10  C11   109.71  3.000
 MH9  H102  C10  C9    109.29  3.000
 MH9  H101  C10  C9    109.19  3.000
 MH9  C11   C10  C9    112.91  3.000
 MH9  H113  C11  H112  107.64  3.000
 MH9  H113  C11  H111  107.56  3.000
 MH9  H112  C11  H111  107.46  3.000
 MH9  H113  C11  C10   111.63  3.000
 MH9  H112  C11  C10   111.25  3.000
 MH9  H111  C11  C10   111.10  3.000
 MH9  HXT   OXT  C     109.90  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
 MH9  CONST_01  HXT   OXT  C    O      0.00   0.0  0
 MH9  Var_01    C3    C2   C1   C   -179.41   0.0  2
 MH9  Var_02    C5    C4   C3   C2  -177.95   0.0  2
 MH9  Var_03    C2    C1   C    O     -1.66  30.0  2
 MH9  Var_04    C4    C3   C2   C1   178.20  30.0  2
 MH9  Var_05    C6    C5   C4   C3   112.02  30.0  3
 MH9  Var_06    C7    C6   C5   C4   178.63  30.0  3
 MH9  Var_07    C8    C7   C6   C5   177.19  30.0  3
 MH9  Var_08    C9    C8   C7   C6  -179.53  30.0  3
 MH9  Var_09    C10   C9   C8   C7   178.74  30.0  3
 MH9  Var_10    C11   C10  C9   C8   179.88  30.0  3
 MH9  Var_11    H111  C11  C10  C9   -59.84  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
 MH9  plan-1  C    0.020
 MH9  plan-1  O    0.020
 MH9  plan-1  C1   0.020
 MH9  plan-1  OXT  0.020
 MH9  plan-1  HXT  0.020
 MH9  plan-2  C    0.020
 MH9  plan-2  C1   0.020
 MH9  plan-2  C2   0.020
 MH9  plan-2  C3   0.020
 MH9  plan-2  H1   0.020
 MH9  plan-2  H2   0.020
 MH9  plan-3  C2   0.020
 MH9  plan-3  C3   0.020
 MH9  plan-3  C4   0.020
 MH9  plan-3  C5   0.020
 MH9  plan-3  H3   0.020
 MH9  plan-3  H4   0.020

