# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:40:45 2022
#   Inital geometry file: a 108 line input string
#   Ligand name: methyl (2E,6E)-9-[(2R)-3,3-dimethyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)\C=C(/C)CC\C=C(/C)CC[C@H]1OC1(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
 JH3  JH3  'methyl (2E,6E)-9-[(2R)-3,3-dimethyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate'  ligand  45  19  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JH3
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
 JH3  C1    C  C     0   0.578   5.2684   0.6044   0.2481
 JH3  O2    O  O     0  -0.462   6.0618  -0.2642   0.5346
 JH3  O1    O  O2    0  -0.468   5.6461   1.8123  -0.1735
 JH3  CM    C  CH3   0  -0.422   7.0441   2.0581  -0.2927
 JH3  C2    C  C1    0  -0.449   3.8069   0.5086   0.2966
 JH3  C3    C  C     0   0.193   3.1145  -0.5504   0.7460
 JH3  C3'   C  CH3   0  -0.729   3.7161  -1.8128   1.2869
 JH3  C4    C  CH2   0  -0.508   1.6162  -0.5159   0.6978
 JH3  C5    C  CH2   0  -0.493   1.0453  -1.5438  -0.2941
 JH3  C6    C  C1    0  -0.262  -0.4496  -1.5681  -0.2392
 JH3  C7    C  C     0   0.104  -1.3179  -1.2187  -1.1914
 JH3  C7'   C  CH3   0  -0.729  -0.9385  -0.7564  -2.5677
 JH3  C8    C  CH2   0  -0.493  -2.7983  -1.2671  -0.9149
 JH3  C9    C  CH2   0  -0.468  -3.4020   0.1238  -0.6968
 JH3  CA    C  CH1   0  -0.005  -4.8827   0.0573  -0.4536
 JH3  O3    O  O2    0  -0.512  -5.3285  -0.3712   0.8306
 JH3  CB    C  CT    0   0.236  -5.6396   0.9597   0.4174
 JH3  CB'   C  CH3   0  -0.684  -7.0974   1.2034   0.1208
 JH3  CC    C  CH3   0  -0.694  -4.9736   2.0702   1.1876
 JH3  HM    H  HCH3  0   0.249   7.1391   3.0826  -0.6409
 JH3  HMA   H  HCH3  0   0.235   7.5548   1.9561   0.6650
 JH3  HMB   H  HCH3  0   0.235   7.5083   1.3885  -1.0171
 JH3  H2    H  H     0   0.257   3.2608   1.3714  -0.0665
 JH3  H3'   H  HCH3  0   0.261   4.5076  -1.6160   2.0065
 JH3  H3'A  H  HCH3  0   0.242   2.9552  -2.4224   1.7728
 JH3  H3'B  H  HCH3  0   0.257   4.1570  -2.4111   0.4877
 JH3  H4    H  HCH2  0   0.251   1.2273  -0.7372   1.6977
 JH3  H4A   H  HCH2  0   0.250   1.2620   0.4793   0.4235
 JH3  H5    H  HCH2  0   0.247   1.4136  -1.3146  -1.2951
 JH3  H5A   H  HCH2  0   0.244   1.4276  -2.5378  -0.0418
 JH3  H6    H  H     0   0.225  -0.8582  -1.8954   0.7153
 JH3  H7'   H  HCH3  0   0.238  -1.2903  -1.4706  -3.3169
 JH3  H7'A  H  HCH3  0   0.237  -1.4101   0.1982  -2.8096
 JH3  H7'B  H  HCH3  0   0.242   0.1337  -0.6343  -2.7052
 JH3  H8    H  HCH2  0   0.230  -3.3137  -1.7543  -1.7506
 JH3  H8A   H  HCH2  0   0.240  -2.9881  -1.8778  -0.0293
 JH3  H9    H  HCH2  0   0.239  -2.8854   0.6093   0.1331
 JH3  H9A   H  HCH2  0   0.235  -3.2402   0.7505  -1.5782
 JH3  HA    H  HCH1  0   0.232  -5.4368  -0.3924  -1.2809
 JH3  HB'   H  HCH3  0   0.238  -7.5330   0.3922  -0.4629
 JH3  HB'A  H  HCH3  0   0.234  -7.6707   1.3043   1.0444
 JH3  HB'B  H  HCH3  0   0.233  -7.2204   2.1279  -0.4446
 JH3  HC    H  HCH3  0   0.236  -4.9399   2.9778   0.5834
 JH3  HCA   H  HCH3  0   0.238  -5.5399   2.2997   2.0921
 JH3  HCB   H  HCH3  0   0.240  -3.9554   1.8276   1.4856

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
 JH3  C1   O2    double  1.211  0.020  1.211
 JH3  C1   O1    single  1.334  0.020  1.334
 JH3  C1   C2    single  1.465  0.020  1.465
 JH3  O1   CM    single  1.424  0.020  1.424
 JH3  CM   HM    single  0.970  0.020  1.090
 JH3  CM   HMA   single  0.970  0.020  1.090
 JH3  CM   HMB   single  0.970  0.020  1.090
 JH3  C2   C3    double  1.343  0.020  1.343
 JH3  C2   H2    single  0.930  0.020  1.080
 JH3  C3   C3'   single  1.499  0.020  1.499
 JH3  C3   C4    single  1.499  0.020  1.499
 JH3  C3'  H3'   single  0.970  0.020  1.090
 JH3  C3'  H3'A  single  0.970  0.020  1.090
 JH3  C3'  H3'B  single  0.970  0.020  1.090
 JH3  C4   C5    single  1.538  0.020  1.538
 JH3  C4   H4    single  0.970  0.020  1.090
 JH3  C4   H4A   single  0.970  0.020  1.090
 JH3  C5   C6    single  1.496  0.020  1.496
 JH3  C5   H5    single  0.970  0.020  1.090
 JH3  C5   H5A   single  0.970  0.020  1.090
 JH3  C6   C7    double  1.335  0.020  1.335
 JH3  C6   H6    single  0.930  0.020  1.080
 JH3  C7   C7'   single  1.501  0.020  1.501
 JH3  C7   C8    single  1.507  0.020  1.507
 JH3  C7'  H7'   single  0.970  0.020  1.090
 JH3  C7'  H7'A  single  0.970  0.020  1.090
 JH3  C7'  H7'B  single  0.970  0.020  1.090
 JH3  C8   C9    single  1.532  0.020  1.532
 JH3  C8   H8    single  0.970  0.020  1.090
 JH3  C8   H8A   single  0.970  0.020  1.090
 JH3  C9   CA    single  1.502  0.020  1.502
 JH3  C9   H9    single  0.970  0.020  1.090
 JH3  C9   H9A   single  0.970  0.020  1.090
 JH3  CA   O3    single  1.425  0.020  1.425
 JH3  CA   CB    single  1.465  0.020  1.465
 JH3  CA   HA    single  0.970  0.020  1.090
 JH3  O3   CB    single  1.428  0.020  1.428
 JH3  CB   CB'   single  1.507  0.020  1.507
 JH3  CB   CC    single  1.507  0.020  1.507
 JH3  CB'  HB'   single  0.970  0.020  1.090
 JH3  CB'  HB'A  single  0.970  0.020  1.090
 JH3  CB'  HB'B  single  0.970  0.020  1.090
 JH3  CC   HC    single  0.970  0.020  1.090
 JH3  CC   HCA   single  0.970  0.020  1.090
 JH3  CC   HCB   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
 JH3  C2    C1   O1    110.61  3.000
 JH3  C2    C1   O2    126.78  3.000
 JH3  O1    C1   O2    122.61  3.000
 JH3  CM    O1   C1    117.42  3.000
 JH3  HMB   CM   HMA   109.08  3.000
 JH3  HMB   CM   HM    109.21  3.000
 JH3  HMA   CM   HM    109.20  3.000
 JH3  HMB   CM   O1    111.56  3.000
 JH3  HMA   CM   O1    111.72  3.000
 JH3  HM    CM   O1    105.98  3.000
 JH3  H2    C2   C3    118.70  3.000
 JH3  H2    C2   C1    116.06  3.000
 JH3  C3    C2   C1    125.23  3.000
 JH3  C4    C3   C3'   115.58  3.000
 JH3  C4    C3   C2    119.10  3.000
 JH3  C3'   C3   C2    125.30  3.000
 JH3  H3'B  C3'  H3'A  107.58  3.000
 JH3  H3'B  C3'  H3'   106.84  3.000
 JH3  H3'A  C3'  H3'   108.33  3.000
 JH3  H3'B  C3'  C3    111.07  3.000
 JH3  H3'A  C3'  C3    110.60  3.000
 JH3  H3'   C3'  C3    112.22  3.000
 JH3  H4A   C4   H4    107.36  3.000
 JH3  H4A   C4   C5    109.08  3.000
 JH3  H4    C4   C5    108.77  3.000
 JH3  H4A   C4   C3    110.69  3.000
 JH3  H4    C4   C3    108.71  3.000
 JH3  C5    C4   C3    112.10  3.000
 JH3  H5A   C5   H5    106.52  3.000
 JH3  H5A   C5   C6    109.02  3.000
 JH3  H5    C5   C6    111.99  3.000
 JH3  H5A   C5   C4    109.18  3.000
 JH3  H5    C5   C4    109.03  3.000
 JH3  C6    C5   C4    110.98  3.000
 JH3  H6    C6   C7    117.38  3.000
 JH3  H6    C6   C5    114.34  3.000
 JH3  C7    C6   C5    128.27  3.000
 JH3  C8    C7   C7'   115.25  3.000
 JH3  C8    C7   C6    119.98  3.000
 JH3  C7'   C7   C6    124.77  3.000
 JH3  H7'B  C7'  H7'A  107.43  3.000
 JH3  H7'B  C7'  H7'   107.69  3.000
 JH3  H7'A  C7'  H7'   106.28  3.000
 JH3  H7'B  C7'  C7    113.56  3.000
 JH3  H7'A  C7'  C7    111.31  3.000
 JH3  H7'   C7'  C7    110.24  3.000
 JH3  H8A   C8   H8    106.74  3.000
 JH3  H8A   C8   C9    108.89  3.000
 JH3  H8    C8   C9    109.08  3.000
 JH3  H8A   C8   C7    109.72  3.000
 JH3  H8    C8   C7    109.66  3.000
 JH3  C9    C8   C7    112.59  3.000
 JH3  H9A   C9   H9    106.74  3.000
 JH3  H9A   C9   CA    107.56  3.000
 JH3  H9    C9   CA    111.30  3.000
 JH3  H9A   C9   C8    110.32  3.000
 JH3  H9    C9   C8    109.01  3.000
 JH3  CA    C9   C8    111.79  3.000
 JH3  HA    CA   CB    116.21  3.000
 JH3  HA    CA   O3    113.57  3.000
 JH3  CB    CA   O3     59.19  3.000
 JH3  HA    CA   C9    113.31  3.000
 JH3  CB    CA   C9    125.33  3.000
 JH3  O3    CA   C9    117.87  3.000
 JH3  CB    O3   CA     61.78  3.000
 JH3  CC    CB   CB'   114.14  3.000
 JH3  CC    CB   O3    116.28  3.000
 JH3  CB'   CB   O3    114.73  3.000
 JH3  CC    CB   CA    121.98  3.000
 JH3  CB'   CB   CA    118.83  3.000
 JH3  O3    CB   CA     59.02  3.000
 JH3  HB'B  CB'  HB'A  107.51  3.000
 JH3  HB'B  CB'  HB'   107.95  3.000
 JH3  HB'A  CB'  HB'   108.18  3.000
 JH3  HB'B  CB'  CB    110.37  3.000
 JH3  HB'A  CB'  CB    110.87  3.000
 JH3  HB'   CB'  CB    111.81  3.000
 JH3  HCB   CC   HCA   107.78  3.000
 JH3  HCB   CC   HC    107.96  3.000
 JH3  HCA   CC   HC    107.46  3.000
 JH3  HCB   CC   CB    112.91  3.000
 JH3  HCA   CC   CB    110.44  3.000
 JH3  HC    CC   CB    110.11  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
 JH3  Var_01  CB'  CB   O3  CA   110.05  30.0  1
 JH3  Var_02  O3   CA   C9  C8    76.26  30.0  3
 JH3  Var_03  HB'  CB'  CB  CA    22.87  30.0  3
 JH3  Var_04  HC   CC   CB  CA    88.94  30.0  3
 JH3  Var_05  CA   C9   C8  C7   178.71  30.0  3
 JH3  Var_06  C3'  C3   C2  C1     0.57   0.0  2
 JH3  Var_07  C7'  C7   C6  C5     2.05   0.0  2
 JH3  Var_08  C3   C2   C1  O2     4.05  30.0  2
 JH3  Var_09  C2   C1   O1  CM  -179.17  30.0  2
 JH3  Var_10  C5   C4   C3  C2   113.25  30.0  3
 JH3  Var_11  C6   C5   C4  C3   175.27  30.0  3
 JH3  Var_12  C7   C6   C5  C4   114.56  30.0  3
 JH3  Var_13  C9   C8   C7  C6   104.51  30.0  3
 JH3  Var_14  HM   CM   O1  C1  -179.81  30.0  3
 JH3  Var_15  H3'  C3'  C3  C2    47.01  30.0  3
 JH3  Var_16  H7'  C7'  C7  C6   115.34  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JH3  chir_01  CA  C9  O3  CB  both

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
 JH3  plan-1  C1   0.020
 JH3  plan-1  O2   0.020
 JH3  plan-1  O1   0.020
 JH3  plan-1  C2   0.020
 JH3  plan-2  C1   0.020
 JH3  plan-2  C2   0.020
 JH3  plan-2  C3   0.020
 JH3  plan-2  C3'  0.020
 JH3  plan-2  C4   0.020
 JH3  plan-2  H2   0.020
 JH3  plan-3  C5   0.020
 JH3  plan-3  C6   0.020
 JH3  plan-3  C7   0.020
 JH3  plan-3  C7'  0.020
 JH3  plan-3  C8   0.020
 JH3  plan-3  H6   0.020

