# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:40:57 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl (2E,6E)-9-[(2R,3S)-3-ethyl-3-methyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@]1(C)O[C@@H]1CC/C(C)=C/CC/C(C)=C/C(=O)OC
#
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
 JH2  JH2  'methyl (2E,6E)-9-[(2R,3S)-3-ethyl-3-methyloxiran-2-yl]-3,7-dimethylnona-2,6-dienoate'  ligand  48  20  .  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_JH2
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
 JH2  C1    C  C     0   0.578  -5.4907   0.7399  -0.0472
 JH2  O1    O  O2    0  -0.468  -5.7793   1.7629   0.7593
 JH2  C2    C  C1    0  -0.446  -4.0401   0.5666  -0.1607
 JH2  O2    O  O     0  -0.462  -6.3453   0.0728  -0.5860
 JH2  C3    C  C     0   0.190  -3.4290  -0.3568  -0.9205
 JH2  O3    O  O2    0  -0.513   5.0929  -0.4296  -0.6129
 JH2  C4    C  CH2   0  -0.506  -1.9315  -0.4372  -0.9037
 JH2  C5    C  CH2   0  -0.493  -1.4314  -1.7260  -0.2278
 JH2  C6    C  C1    0  -0.274   0.0640  -1.7943  -0.2415
 JH2  C7    C  C     0   0.121   0.8950  -1.6127   0.7885
 JH2  C8    C  CH2   0  -0.495   2.3853  -1.6647   0.5835
 JH2  C9    C  CH2   0  -0.478   3.0729  -0.3273   0.8785
 JH2  C10   C  CH1   0  -0.002   4.5625  -0.4178   0.7095
 JH2  C11   C  CT    0   0.252   5.4418   0.6591   0.2445
 JH2  C12   C  CH2   0  -0.462   4.8997   2.0109  -0.1611
 JH2  C13   C  CH3   0  -0.675   5.6641   2.6458  -1.3187
 JH2  C14   C  CH3   0  -0.727  -4.1281  -1.3608  -1.7885
 JH2  C15   C  CH3   0  -0.736   0.4513  -1.3304   2.1946
 JH2  C16   C  CH3   0  -0.700   6.8783   0.6578   0.7056
 JH2  C17   C  CH3   0  -0.423  -7.1555   2.0576   0.9782
 JH2  H2    H  H     0   0.256  -3.4324   1.2494   0.4215
 JH2  H4    H  HCH2  0   0.251  -1.5635  -0.4121  -1.9347
 JH2  H4A   H  HCH2  0   0.250  -1.5039   0.4242  -0.3878
 JH2  H5    H  HCH2  0   0.245  -1.8249  -1.7694   0.7887
 JH2  H5A   H  HCH2  0   0.244  -1.8388  -2.5933  -0.7554
 JH2  H6    H  H     0   0.226   0.5051  -1.9813  -1.2184
 JH2  H8    H  HCH2  0   0.230   2.8154  -2.4333   1.2367
 JH2  H8A   H  HCH2  0   0.239   2.6079  -1.9651  -0.4433
 JH2  H9    H  HCH2  0   0.243   2.6417   0.4472   0.2415
 JH2  H9A   H  HCH2  0   0.239   2.8807  -0.0254   1.9118
 JH2  H10   H  HCH1  0   0.230   5.0214  -1.1588   1.3685
 JH2  H12   H  HCH2  0   0.236   3.8480   1.9282  -0.4369
 JH2  H12A  H  HCH2  0   0.230   4.9383   2.6699   0.7105
 JH2  H13   H  HCH3  0   0.236   5.1827   3.5738  -1.6264
 JH2  H13A  H  HCH3  0   0.226   6.6925   2.8876  -1.0502
 JH2  H13B  H  HCH3  0   0.225   5.6922   1.9847  -2.1861
 JH2  H14   H  HCH3  0   0.260  -4.8335  -0.8847  -2.4678
 JH2  H14A  H  HCH3  0   0.243  -3.4098  -1.9209  -2.3850
 JH2  H14B  H  HCH3  0   0.256  -4.6964  -2.0762  -1.1932
 JH2  H15   H  HCH3  0   0.236   1.0005  -1.9528   2.9047
 JH2  H15A  H  HCH3  0   0.242   0.6517  -0.2929   2.4727
 JH2  H15B  H  HCH3  0   0.244  -0.6107  -1.5061   2.3511
 JH2  H16   H  HCH3  0   0.239   7.5524   0.9722  -0.0928
 JH2  H16A  H  HCH3  0   0.233   7.0099   1.3507   1.5380
 JH2  H16B  H  HCH3  0   0.240   7.1908  -0.3316   1.0396
 JH2  H17   H  HCH3  0   0.249  -7.1762   2.9005   1.6629
 JH2  H17A  H  HCH3  0   0.235  -7.6597   2.3364   0.0526
 JH2  H17B  H  HCH3  0   0.235  -7.6812   1.2159   1.4292

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
 JH2  C1   O1    single  1.334  0.020  1.334
 JH2  C1   C2    single  1.465  0.020  1.465
 JH2  C1   O2    double  1.211  0.020  1.211
 JH2  O1   C17   single  1.424  0.020  1.424
 JH2  C2   C3    double  1.343  0.020  1.343
 JH2  C3   C4    single  1.500  0.020  1.500
 JH2  C3   C14   single  1.500  0.020  1.500
 JH2  O3   C10   single  1.425  0.020  1.425
 JH2  O3   C11   single  1.429  0.020  1.429
 JH2  C4   C5    single  1.539  0.020  1.539
 JH2  C5   C6    single  1.497  0.020  1.497
 JH2  C6   C7    double  1.336  0.020  1.336
 JH2  C7   C8    single  1.505  0.020  1.505
 JH2  C7   C15   single  1.501  0.020  1.501
 JH2  C8   C9    single  1.532  0.020  1.532
 JH2  C9   C10   single  1.502  0.020  1.502
 JH2  C10  C11   single  1.466  0.020  1.466
 JH2  C11  C12   single  1.512  0.020  1.512
 JH2  C11  C16   single  1.509  0.020  1.509
 JH2  C12  C13   single  1.526  0.020  1.526
 JH2  C2   H2    single  0.930  0.020  1.080
 JH2  C4   H4    single  0.970  0.020  1.090
 JH2  C4   H4A   single  0.970  0.020  1.090
 JH2  C5   H5    single  0.970  0.020  1.090
 JH2  C5   H5A   single  0.970  0.020  1.090
 JH2  C6   H6    single  0.930  0.020  1.080
 JH2  C8   H8    single  0.970  0.020  1.090
 JH2  C8   H8A   single  0.970  0.020  1.090
 JH2  C9   H9    single  0.970  0.020  1.090
 JH2  C9   H9A   single  0.970  0.020  1.090
 JH2  C10  H10   single  0.970  0.020  1.090
 JH2  C12  H12   single  0.970  0.020  1.090
 JH2  C12  H12A  single  0.970  0.020  1.090
 JH2  C13  H13   single  0.970  0.020  1.090
 JH2  C13  H13A  single  0.970  0.020  1.090
 JH2  C13  H13B  single  0.970  0.020  1.090
 JH2  C14  H14   single  0.970  0.020  1.090
 JH2  C14  H14A  single  0.970  0.020  1.090
 JH2  C14  H14B  single  0.970  0.020  1.090
 JH2  C15  H15   single  0.970  0.020  1.090
 JH2  C15  H15A  single  0.970  0.020  1.090
 JH2  C15  H15B  single  0.970  0.020  1.090
 JH2  C16  H16   single  0.970  0.020  1.090
 JH2  C16  H16A  single  0.970  0.020  1.090
 JH2  C16  H16B  single  0.970  0.020  1.090
 JH2  C17  H17   single  0.970  0.020  1.090
 JH2  C17  H17A  single  0.970  0.020  1.090
 JH2  C17  H17B  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
 JH2  O2    C1   C2    126.81  3.000
 JH2  O2    C1   O1    122.60  3.000
 JH2  C2    C1   O1    110.59  3.000
 JH2  C17   O1   C1    117.42  3.000
 JH2  H2    C2   C3    118.82  3.000
 JH2  H2    C2   C1    116.04  3.000
 JH2  C3    C2   C1    125.14  3.000
 JH2  C14   C3   C4    115.84  3.000
 JH2  C14   C3   C2    125.14  3.000
 JH2  C4    C3   C2    119.01  3.000
 JH2  C11   O3   C10    61.82  3.000
 JH2  H4A   C4   H4    107.17  3.000
 JH2  H4A   C4   C5    109.03  3.000
 JH2  H4    C4   C5    108.88  3.000
 JH2  H4A   C4   C3    110.74  3.000
 JH2  H4    C4   C3    108.89  3.000
 JH2  C5    C4   C3    111.98  3.000
 JH2  H5A   C5   H5    106.47  3.000
 JH2  H5A   C5   C6    109.36  3.000
 JH2  H5    C5   C6    111.53  3.000
 JH2  H5A   C5   C4    109.34  3.000
 JH2  H5    C5   C4    108.99  3.000
 JH2  C6    C5   C4    111.02  3.000
 JH2  H6    C6   C7    117.61  3.000
 JH2  H6    C6   C5    114.90  3.000
 JH2  C7    C6   C5    127.45  3.000
 JH2  C15   C7   C8    115.26  3.000
 JH2  C15   C7   C6    124.33  3.000
 JH2  C8    C7   C6    120.41  3.000
 JH2  H8A   C8   H8    106.69  3.000
 JH2  H8A   C8   C9    109.23  3.000
 JH2  H8    C8   C9    108.73  3.000
 JH2  H8A   C8   C7    109.82  3.000
 JH2  H8    C8   C7    109.35  3.000
 JH2  C9    C8   C7    112.82  3.000
 JH2  H9A   C9   H9    106.62  3.000
 JH2  H9A   C9   C10   107.29  3.000
 JH2  H9    C9   C10   111.64  3.000
 JH2  H9A   C9   C8    110.12  3.000
 JH2  H9    C9   C8    109.25  3.000
 JH2  C10   C9   C8    111.76  3.000
 JH2  H10   C10  C11   115.95  3.000
 JH2  H10   C10  C9    112.93  3.000
 JH2  C11   C10  C9    125.90  3.000
 JH2  H10   C10  O3    113.44  3.000
 JH2  C11   C10  O3     59.23  3.000
 JH2  C9    C10  O3    118.30  3.000
 JH2  C16   C11  C12   115.10  3.000
 JH2  C16   C11  C10   118.27  3.000
 JH2  C12   C11  C10   121.79  3.000
 JH2  C16   C11  O3    114.53  3.000
 JH2  C12   C11  O3    115.64  3.000
 JH2  C10   C11  O3     58.95  3.000
 JH2  H12A  C12  H12   106.35  3.000
 JH2  H12A  C12  C13   109.65  3.000
 JH2  H12   C12  C13   108.84  3.000
 JH2  H12A  C12  C11   108.21  3.000
 JH2  H12   C12  C11   110.24  3.000
 JH2  C13   C12  C11   113.32  3.000
 JH2  H13B  C13  H13A  107.82  3.000
 JH2  H13B  C13  H13   107.63  3.000
 JH2  H13A  C13  H13   107.30  3.000
 JH2  H13B  C13  C12   111.35  3.000
 JH2  H13A  C13  C12   112.22  3.000
 JH2  H13   C13  C12   110.32  3.000
 JH2  H14B  C14  H14A  107.78  3.000
 JH2  H14B  C14  H14   106.85  3.000
 JH2  H14A  C14  H14   108.09  3.000
 JH2  H14B  C14  C3    111.48  3.000
 JH2  H14A  C14  C3    110.73  3.000
 JH2  H14   C14  C3    111.73  3.000
 JH2  H15B  C15  H15A  107.21  3.000
 JH2  H15B  C15  H15   107.78  3.000
 JH2  H15A  C15  H15   106.46  3.000
 JH2  H15B  C15  C7    113.13  3.000
 JH2  H15A  C15  C7    111.27  3.000
 JH2  H15   C15  C7    110.68  3.000
 JH2  H16B  C16  H16A  107.95  3.000
 JH2  H16B  C16  H16   107.98  3.000
 JH2  H16A  C16  H16   107.51  3.000
 JH2  H16B  C16  C11   111.55  3.000
 JH2  H16A  C16  C11   110.33  3.000
 JH2  H16   C16  C11   111.37  3.000
 JH2  H17B  C17  H17A  109.01  3.000
 JH2  H17B  C17  H17   109.22  3.000
 JH2  H17A  C17  H17   109.15  3.000
 JH2  H17B  C17  O1    111.70  3.000
 JH2  H17A  C17  O1    111.67  3.000
 JH2  H17   C17  O1    106.01  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
 JH2  Var_01  C12  C11  C10  O3    102.77  30.0  1
 JH2  Var_02  C8   C9   C10  O3     76.23  30.0  1
 JH2  Var_03  C13  C12  C11  O3    -76.93  30.0  3
 JH2  Var_04  H16  C16  C11  O3     74.95  30.0  3
 JH2  Var_05  C10  C9   C8   C7    178.16  30.0  3
 JH2  Var_06  H13  C13  C12  C11   175.14  30.0  3
 JH2  Var_07  C4   C3   C2   C1   -178.27   0.0  2
 JH2  Var_08  C8   C7   C6   C5   -177.57   0.0  2
 JH2  Var_09  C3   C2   C1   O1   -178.46  30.0  2
 JH2  Var_10  C5   C4   C3   C2    111.24  30.0  3
 JH2  Var_11  C6   C5   C4   C3    179.13  30.0  3
 JH2  Var_12  C7   C6   C5   C4    106.37  30.0  3
 JH2  Var_13  C9   C8   C7   C6    116.11  30.0  3
 JH2  Var_14  H17  C17  O1   C1    179.23  30.0  3
 JH2  Var_15  H14  C14  C3   C2     53.15  30.0  3
 JH2  Var_16  H15  C15  C7   C6    134.07  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
 JH2  chir_01  C10  O3   C9   C11  both
 JH2  chir_02  C11  C16  C12  C10  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
 JH2  plan-1  C1   0.020
 JH2  plan-1  O1   0.020
 JH2  plan-1  C2   0.020
 JH2  plan-1  O2   0.020
 JH2  plan-2  C1   0.020
 JH2  plan-2  C2   0.020
 JH2  plan-2  C3   0.020
 JH2  plan-2  C4   0.020
 JH2  plan-2  C14  0.020
 JH2  plan-2  H2   0.020
 JH2  plan-3  C5   0.020
 JH2  plan-3  C6   0.020
 JH2  plan-3  C7   0.020
 JH2  plan-3  C8   0.020
 JH2  plan-3  C15  0.020
 JH2  plan-3  H6   0.020

