# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 23:23:27 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: (11Z)-octadec-11-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC\C=C/CCCCCCCCCC(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
 VCA  VCA  '(11Z)-octadec-11-enoic acid'  ligand  53  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VCA
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
 VCA  O2    O  OC    -1  -0.636    9.5224  -1.9507   0.0871
 VCA  C1    C  C      0   0.409    8.5799  -1.3674  -0.4911
 VCA  O1    O  O      0  -0.610    8.6016  -0.9043  -1.6486
 VCA  C2    C  CH2    0  -0.581    7.2816  -1.2202   0.3212
 VCA  C3    C  CH2    0  -0.402    6.1415  -0.4791  -0.3576
 VCA  C4    C  CH2    0  -0.409    4.9039  -0.3702   0.5255
 VCA  C5    C  CH2    0  -0.410    3.7512   0.3739  -0.1369
 VCA  C6    C  CH2    0  -0.411    2.5039   0.4487   0.7346
 VCA  C7    C  CH2    0  -0.412    1.3541   1.2059   0.0817
 VCA  C8    C  CH2    0  -0.413    0.0807   1.2007   0.9178
 VCA  C9    C  CH2    0  -0.411   -1.0539   2.0012   0.2908
 VCA  C10   C  CH2    0  -0.489   -2.3664   1.8791   1.0679
 VCA  C11   C  C1     0  -0.220   -3.4369   2.7726   0.5220
 VCA  C12   C  C1     0  -0.211   -4.4806   2.4160  -0.2255
 VCA  C13   C  CH2    0  -0.487   -4.8484   1.0381  -0.6799
 VCA  C14   C  CH2    0  -0.413   -6.1653   0.5526  -0.0715
 VCA  C15   C  CH2    0  -0.412   -6.6225  -0.7832  -0.6440
 VCA  C16   C  CH2    0  -0.407   -7.9208  -1.2925  -0.0311
 VCA  C17   C  CH2    0  -0.419   -8.3980  -2.6050  -0.6415
 VCA  C18   C  CH3    0  -0.662   -9.6935  -3.1146  -0.0251
 VCA  H21   H  HCH2   0   0.216    6.9442  -2.2232   0.6096
 VCA  H22   H  HCH2   0   0.214    7.5264  -0.7261   1.2691
 VCA  H31   H  HCH2   0   0.200    6.4703   0.5247  -0.6427
 VCA  H32   H  HCH2   0   0.200    5.8733  -0.9832  -1.2910
 VCA  H41   H  HCH2   0   0.201    4.5687  -1.3746   0.8092
 VCA  H42   H  HCH2   0   0.202    5.1670   0.1331   1.4632
 VCA  H51   H  HCH2   0   0.204    4.0764   1.3871  -0.3983
 VCA  H52   H  HCH2   0   0.204    3.5001  -0.1161  -1.0845
 VCA  H61   H  HCH2   0   0.205    2.1743  -0.5672   0.9801
 VCA  H62   H  HCH2   0   0.206    2.7542   0.9235   1.6899
 VCA  H71   H  HCH2   0   0.207    1.6636   2.2390  -0.1113
 VCA  H72   H  HCH2   0   0.206    1.1410   0.7662  -0.8991
 VCA  H81   H  HCH2   0   0.208   -0.2463   0.1657   1.0683
 VCA  H82   H  HCH2   0   0.209    0.2944   1.5981   1.9162
 VCA  H91   H  HCH2   0   0.214   -0.7632   3.0548   0.2228
 VCA  H92   H  HCH2   0   0.213   -1.2194   1.6641  -0.7375
 VCA  H101  H  HCH2   0   0.228   -2.6872   0.8346   1.0679
 VCA  H102  H  HCH2   0   0.227   -2.1841   2.1450   2.1142
 VCA  H11   H  H      0   0.227   -3.3185   3.8290   0.7492
 VCA  H12   H  H      0   0.226   -5.1625   3.2005  -0.5451
 VCA  H131  H  HCH2   0   0.226   -4.9515   1.0465  -1.7708
 VCA  H132  H  HCH2   0   0.229   -4.0565   0.3195  -0.4552
 VCA  H141  H  HCH2   0   0.214   -6.0493   0.4711   1.0138
 VCA  H142  H  HCH2   0   0.213   -6.9437   1.3052  -0.2383
 VCA  H151  H  HCH2   0   0.208   -6.7492  -0.6829  -1.7276
 VCA  H152  H  HCH2   0   0.209   -5.8346  -1.5314  -0.5008
 VCA  H161  H  HCH2   0   0.206   -7.7875  -1.4217   1.0486
 VCA  H162  H  HCH2   0   0.206   -8.7020  -0.5329  -0.1497
 VCA  H171  H  HCH2   0   0.210   -8.5357  -2.4712  -1.7189
 VCA  H172  H  HCH2   0   0.210   -7.6155  -3.3621  -0.5297
 VCA  H181  H  HCH3   0   0.215   -9.5750  -3.3107   1.0421
 VCA  H182  H  HCH3   0   0.215  -10.4972  -2.3843  -0.1376
 VCA  H183  H  HCH3   0   0.225  -10.0221  -4.0418  -0.4961

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
 VCA  O2   C1    deloc   1.250  0.020  1.250
 VCA  C1   O1    deloc   1.247  0.020  1.247
 VCA  C1   C2    single  1.539  0.020  1.539
 VCA  C2   C3    single  1.520  0.020  1.520
 VCA  C2   H21   single  0.970  0.020  1.090
 VCA  C2   H22   single  0.970  0.020  1.090
 VCA  C3   C4    single  1.524  0.020  1.524
 VCA  C3   H31   single  0.970  0.020  1.090
 VCA  C3   H32   single  0.970  0.020  1.090
 VCA  C4   C5    single  1.523  0.020  1.523
 VCA  C4   H41   single  0.970  0.020  1.090
 VCA  C4   H42   single  0.970  0.020  1.090
 VCA  C5   C6    single  1.523  0.020  1.523
 VCA  C5   H51   single  0.970  0.020  1.090
 VCA  C5   H52   single  0.970  0.020  1.090
 VCA  C6   C7    single  1.524  0.020  1.524
 VCA  C6   H61   single  0.970  0.020  1.090
 VCA  C6   H62   single  0.970  0.020  1.090
 VCA  C7   C8    single  1.523  0.020  1.523
 VCA  C7   H71   single  0.970  0.020  1.090
 VCA  C7   H72   single  0.970  0.020  1.090
 VCA  C8   C9    single  1.524  0.020  1.524
 VCA  C8   H81   single  0.970  0.020  1.090
 VCA  C8   H82   single  0.970  0.020  1.090
 VCA  C9   C10   single  1.530  0.020  1.530
 VCA  C9   H91   single  0.970  0.020  1.090
 VCA  C9   H92   single  0.970  0.020  1.090
 VCA  C10  C11   single  1.497  0.020  1.497
 VCA  C10  H101  single  0.970  0.020  1.090
 VCA  C10  H102  single  0.970  0.020  1.090
 VCA  C11  C12   double  1.332  0.020  1.332
 VCA  C11  H11   single  0.930  0.020  1.080
 VCA  C12  C13   single  1.497  0.020  1.497
 VCA  C12  H12   single  0.930  0.020  1.080
 VCA  C13  C14   single  1.530  0.020  1.530
 VCA  C13  H131  single  0.970  0.020  1.090
 VCA  C13  H132  single  0.970  0.020  1.090
 VCA  C14  C15   single  1.523  0.020  1.523
 VCA  C14  H141  single  0.970  0.020  1.090
 VCA  C14  H142  single  0.970  0.020  1.090
 VCA  C15  C16   single  1.523  0.020  1.523
 VCA  C15  H151  single  0.970  0.020  1.090
 VCA  C15  H152  single  0.970  0.020  1.090
 VCA  C16  C17   single  1.524  0.020  1.524
 VCA  C16  H161  single  0.970  0.020  1.090
 VCA  C16  H162  single  0.970  0.020  1.090
 VCA  C17  C18   single  1.522  0.020  1.522
 VCA  C17  H171  single  0.970  0.020  1.090
 VCA  C17  H172  single  0.970  0.020  1.090
 VCA  C18  H181  single  0.970  0.020  1.090
 VCA  C18  H182  single  0.970  0.020  1.090
 VCA  C18  H183  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
 VCA  C2    C1   O1    117.99  3.000
 VCA  C2    C1   O2    115.89  3.000
 VCA  O1    C1   O2    126.12  3.000
 VCA  H22   C2   H21   104.69  3.000
 VCA  H22   C2   C3    109.50  3.000
 VCA  H21   C2   C3    109.43  3.000
 VCA  H22   C2   C1    108.12  3.000
 VCA  H21   C2   C1    108.11  3.000
 VCA  C3    C2   C1    116.35  3.000
 VCA  H32   C3   H31   105.90  3.000
 VCA  H32   C3   C4    109.15  3.000
 VCA  H31   C3   C4    109.23  3.000
 VCA  H32   C3   C2    109.89  3.000
 VCA  H31   C3   C2    109.78  3.000
 VCA  C4    C3   C2    112.65  3.000
 VCA  H42   C4   H41   105.82  3.000
 VCA  H42   C4   C5    109.22  3.000
 VCA  H41   C4   C5    109.19  3.000
 VCA  H42   C4   C3    109.48  3.000
 VCA  H41   C4   C3    109.44  3.000
 VCA  C5    C4   C3    113.41  3.000
 VCA  H52   C5   H51   105.97  3.000
 VCA  H52   C5   C6    109.20  3.000
 VCA  H51   C5   C6    109.51  3.000
 VCA  H52   C5   C4    109.33  3.000
 VCA  H51   C5   C4    109.32  3.000
 VCA  C6    C5   C4    113.25  3.000
 VCA  H62   C6   H61   105.96  3.000
 VCA  H62   C6   C7    109.30  3.000
 VCA  H61   C6   C7    109.25  3.000
 VCA  H62   C6   C5    109.46  3.000
 VCA  H61   C6   C5    109.20  3.000
 VCA  C7    C6   C5    113.40  3.000
 VCA  H72   C7   H71   106.00  3.000
 VCA  H72   C7   C8    109.10  3.000
 VCA  H71   C7   C8    109.64  3.000
 VCA  H72   C7   C6    109.32  3.000
 VCA  H71   C7   C6    109.33  3.000
 VCA  C8    C7   C6    113.20  3.000
 VCA  H82   C8   H81   106.00  3.000
 VCA  H82   C8   C9    109.24  3.000
 VCA  H81   C8   C9    109.30  3.000
 VCA  H82   C8   C7    109.63  3.000
 VCA  H81   C8   C7    109.16  3.000
 VCA  C9    C8   C7    113.26  3.000
 VCA  H92   C9   H91   106.15  3.000
 VCA  H92   C9   C10   108.83  3.000
 VCA  H91   C9   C10   109.63  3.000
 VCA  H92   C9   C8    109.71  3.000
 VCA  H91   C9   C8    109.48  3.000
 VCA  C10   C9   C8    112.82  3.000
 VCA  H102  C10  H101  106.32  3.000
 VCA  H102  C10  C11   108.81  3.000
 VCA  H101  C10  C11   111.13  3.000
 VCA  H102  C10  C9    108.86  3.000
 VCA  H101  C10  C9    109.16  3.000
 VCA  C11   C10  C9    112.36  3.000
 VCA  H11   C11  C12   117.56  3.000
 VCA  H11   C11  C10   115.20  3.000
 VCA  C12   C11  C10   127.21  3.000
 VCA  H12   C12  C13   114.89  3.000
 VCA  H12   C12  C11   117.58  3.000
 VCA  C13   C12  C11   127.53  3.000
 VCA  H132  C13  H131  106.13  3.000
 VCA  H132  C13  C14   109.47  3.000
 VCA  H131  C13  C14   108.51  3.000
 VCA  H132  C13  C12   111.40  3.000
 VCA  H131  C13  C12   108.56  3.000
 VCA  C14   C13  C12   112.52  3.000
 VCA  H142  C14  H141  106.10  3.000
 VCA  H142  C14  C15   109.38  3.000
 VCA  H141  C14  C15   109.83  3.000
 VCA  H142  C14  C13   109.46  3.000
 VCA  H141  C14  C13   109.07  3.000
 VCA  C15   C14  C13   112.78  3.000
 VCA  H152  C15  H151  105.95  3.000
 VCA  H152  C15  C16   109.38  3.000
 VCA  H151  C15  C16   109.27  3.000
 VCA  H152  C15  C14   109.50  3.000
 VCA  H151  C15  C14   109.04  3.000
 VCA  C16   C15  C14   113.43  3.000
 VCA  H162  C16  H161  105.97  3.000
 VCA  H162  C16  C17   109.29  3.000
 VCA  H161  C16  C17   109.34  3.000
 VCA  H162  C16  C15   109.40  3.000
 VCA  H161  C16  C15   109.40  3.000
 VCA  C17   C16  C15   113.18  3.000
 VCA  H172  C17  H171  105.96  3.000
 VCA  H172  C17  C18   109.60  3.000
 VCA  H171  C17  C18   109.42  3.000
 VCA  H172  C17  C16   109.33  3.000
 VCA  H171  C17  C16   109.17  3.000
 VCA  C18   C17  C16   113.11  3.000
 VCA  H183  C18  H182  107.60  3.000
 VCA  H183  C18  H181  107.59  3.000
 VCA  H182  C18  H181  107.51  3.000
 VCA  H183  C18  C17   111.47  3.000
 VCA  H182  C18  C17   111.15  3.000
 VCA  H181  C18  C17   111.32  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
 VCA  Var_01  C13   C12  C11  C10     1.14   0.0  2
 VCA  Var_02  C3    C2   C1   O2    178.38  30.0  3
 VCA  Var_03  C4    C3   C2   C1   -179.42  30.0  3
 VCA  Var_04  C5    C4   C3   C2    179.82  30.0  3
 VCA  Var_05  C6    C5   C4   C3    178.48  30.0  3
 VCA  Var_06  C7    C6   C5   C4    179.34  30.0  3
 VCA  Var_07  C8    C7   C6   C5    176.26  30.0  3
 VCA  Var_08  C9    C8   C7   C6    177.84  30.0  3
 VCA  Var_09  C10   C9   C8   C7    174.45  30.0  3
 VCA  Var_10  C11   C10  C9   C8    174.41  30.0  3
 VCA  Var_11  C12   C11  C10  C9    104.01  30.0  3
 VCA  Var_12  C14   C13  C12  C11   114.42  30.0  3
 VCA  Var_13  C15   C14  C13  C12   173.77  30.0  3
 VCA  Var_14  C16   C15  C14  C13   179.01  30.0  3
 VCA  Var_15  C17   C16  C15  C14   178.03  30.0  3
 VCA  Var_16  C18   C17  C16  C15   179.84  30.0  3
 VCA  Var_17  H181  C18  C17  C16   -61.14  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
 VCA  plan-1  O2   0.020
 VCA  plan-1  C1   0.020
 VCA  plan-1  O1   0.020
 VCA  plan-1  C2   0.020
 VCA  plan-2  C10  0.020
 VCA  plan-2  C11  0.020
 VCA  plan-2  C12  0.020
 VCA  plan-2  C13  0.020
 VCA  plan-2  H11  0.020
 VCA  plan-2  H12  0.020

