# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 12:49:50 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: (3R,7S,11S)-3,7,11,15-tetramethylhexadecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[C@H](C)CCC[C@H](C)CCC[C@@H](C)CC(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
 VGJ  VGJ  '(3R,7S,11S)-3,7,11,15-tetramethylhexadecanoic acid'  ligand  61  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VGJ
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
 VGJ  O1    O  OC    -1  -0.627    9.4419  -1.9940  -0.0318
 VGJ  C15   C  C      0   0.402    8.6389  -1.0407  -0.1188
 VGJ  O2    O  O      0  -0.614    8.9311   0.1716  -0.0590
 VGJ  C14   C  CH2    0  -0.553    7.1649  -1.3996  -0.3774
 VGJ  C13   C  CH1    0  -0.212    6.1349  -0.4333   0.1997
 VGJ  C16   C  CH3    0  -0.668    6.1947  -0.4201   1.7243
 VGJ  C12   C  CH2    0  -0.392    4.7339  -0.7834  -0.3073
 VGJ  C11   C  CH2    0  -0.428    3.6375   0.1942   0.1027
 VGJ  C10   C  CH2    0  -0.395    2.3011  -0.1283  -0.5577
 VGJ  C9    C  CH1    0  -0.224    1.1148   0.7080  -0.0729
 VGJ  C17   C  CH3    0  -0.668    1.3166   2.1916  -0.3693
 VGJ  C8    C  CH2    0  -0.398   -0.1843   0.1760  -0.6833
 VGJ  C7    C  CH2    0  -0.429   -1.4596   0.7885  -0.1158
 VGJ  C6    C  CH2    0  -0.401   -2.7189   0.1074  -0.6411
 VGJ  C5    C  CH1    0  -0.219   -4.0271   0.6579  -0.0668
 VGJ  C18   C  CH3    0  -0.672   -4.3265   2.0589  -0.5946
 VGJ  C4    C  CH2    0  -0.397   -5.1790  -0.3110  -0.3446
 VGJ  C3    C  CH2    0  -0.430   -6.5305   0.1251   0.2122
 VGJ  C2    C  CH2    0  -0.394   -7.5941  -0.9607   0.0932
 VGJ  C1    C  CH1    0  -0.231   -8.9532  -0.5905   0.6906
 VGJ  C19   C  CH3    0  -0.657   -9.6162   0.5686  -0.0480
 VGJ  C20   C  CH3    0  -0.651   -9.8827  -1.8004   0.7071
 VGJ  H141  H  HCH2   0   0.222    7.0341  -1.4447  -1.4672
 VGJ  H142  H  HCH2   0   0.196    6.9626  -2.4139  -0.0166
 VGJ  H13   H  HCH1   0   0.197    6.3831   0.5707  -0.1601
 VGJ  H161  H  HCH3   0   0.203    5.9217  -1.3973   2.1335
 VGJ  H162  H  HCH3   0   0.227    7.1984  -0.1797   2.0760
 VGJ  H163  H  HCH3   0   0.223    5.5169   0.3177   2.1566
 VGJ  H121  H  HCH2   0   0.206    4.7609  -0.8368  -1.4020
 VGJ  H122  H  HCH2   0   0.198    4.4673  -1.7915   0.0335
 VGJ  H111  H  HCH2   0   0.209    3.5087   0.1819   1.1897
 VGJ  H112  H  HCH2   0   0.209    3.9547   1.2097  -0.1558
 VGJ  H101  H  HCH2   0   0.202    2.3973  -0.0161  -1.6447
 VGJ  H102  H  HCH2   0   0.209    2.0756  -1.1868  -0.3835
 VGJ  H9    H  HCH1   0   0.201    1.0397   0.5833   1.0160
 VGJ  H171  H  HCH3   0   0.228    0.4798   2.7965  -0.0184
 VGJ  H172  H  HCH3   0   0.230    2.2143   2.5811   0.1116
 VGJ  H173  H  HCH3   0   0.209    1.4178   2.3585  -1.4451
 VGJ  H81C  H  HCH2   0   0.203   -0.1604   0.3208  -1.7704
 VGJ  H82C  H  HCH2   0   0.210   -0.2226  -0.9085  -0.5272
 VGJ  H71C  H  HCH2   0   0.205   -1.4413   0.7066   0.9774
 VGJ  H72C  H  HCH2   0   0.215   -1.4931   1.8586  -0.3372
 VGJ  H61C  H  HCH2   0   0.203   -2.7462   0.1774  -1.7354
 VGJ  H62C  H  HCH2   0   0.211   -2.6517  -0.9623  -0.4123
 VGJ  H5    H  HCH1   0   0.202   -3.9073   0.7230   1.0229
 VGJ  H181  H  HCH3   0   0.229   -5.1754   2.5139  -0.0837
 VGJ  H182  H  HCH3   0   0.229   -3.4783   2.7311  -0.4621
 VGJ  H183  H  HCH3   0   0.211   -4.5603   2.0292  -1.6623
 VGJ  H41C  H  HCH2   0   0.202   -5.2667  -0.4652  -1.4270
 VGJ  H42C  H  HCH2   0   0.210   -4.9197  -1.2878   0.0791
 VGJ  H31C  H  HCH2   0   0.204   -6.4153   0.4004   1.2670
 VGJ  H32C  H  HCH2   0   0.218   -6.8648   1.0289  -0.3030
 VGJ  H21C  H  HCH2   0   0.201   -7.7279  -1.2294  -0.9621
 VGJ  H22C  H  HCH2   0   0.211   -7.2276  -1.8657   0.5909
 VGJ  HA    H  HCH1   0   0.207   -8.7866  -0.2802   1.7296
 VGJ  H191  H  HCH3   0   0.210   -9.8146   0.2997  -1.0888
 VGJ  H192  H  HCH3   0   0.224  -10.5710   0.8288   0.4122
 VGJ  H193  H  HCH3   0   0.226   -8.9992   1.4680  -0.0511
 VGJ  H201  H  HCH3   0   0.222   -9.4484  -2.6334   1.2630
 VGJ  H202  H  HCH3   0   0.222  -10.8416  -1.5567   1.1687
 VGJ  H203  H  HCH3   0   0.211  -10.0863  -2.1500  -0.3082

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
 VGJ  O1   C15   deloc   1.249  0.020  1.249
 VGJ  C15  O2    deloc   1.248  0.020  1.248
 VGJ  C15  C14   single  1.539  0.020  1.539
 VGJ  C14  C13   single  1.526  0.020  1.526
 VGJ  C13  C16   single  1.526  0.020  1.526
 VGJ  C13  C12   single  1.531  0.020  1.531
 VGJ  C12  C11   single  1.525  0.020  1.525
 VGJ  C11  C10   single  1.525  0.020  1.525
 VGJ  C10  C9    single  1.530  0.020  1.530
 VGJ  C9   C17   single  1.526  0.020  1.526
 VGJ  C9   C8    single  1.531  0.020  1.531
 VGJ  C8   C7    single  1.524  0.020  1.524
 VGJ  C7   C6    single  1.525  0.020  1.525
 VGJ  C6   C5    single  1.531  0.020  1.531
 VGJ  C5   C18   single  1.527  0.020  1.527
 VGJ  C5   C4    single  1.531  0.020  1.531
 VGJ  C4   C3    single  1.525  0.020  1.525
 VGJ  C3   C2    single  1.525  0.020  1.525
 VGJ  C2   C1    single  1.530  0.020  1.530
 VGJ  C1   C19   single  1.526  0.020  1.526
 VGJ  C1   C20   single  1.526  0.020  1.526
 VGJ  C14  H141  single  0.970  0.020  1.090
 VGJ  C14  H142  single  0.970  0.020  1.090
 VGJ  C13  H13   single  0.970  0.020  1.090
 VGJ  C16  H161  single  0.970  0.020  1.090
 VGJ  C16  H162  single  0.970  0.020  1.090
 VGJ  C16  H163  single  0.970  0.020  1.090
 VGJ  C12  H121  single  0.970  0.020  1.090
 VGJ  C12  H122  single  0.970  0.020  1.090
 VGJ  C11  H111  single  0.970  0.020  1.090
 VGJ  C11  H112  single  0.970  0.020  1.090
 VGJ  C10  H101  single  0.970  0.020  1.090
 VGJ  C10  H102  single  0.970  0.020  1.090
 VGJ  C9   H9    single  0.970  0.020  1.090
 VGJ  C17  H171  single  0.970  0.020  1.090
 VGJ  C17  H172  single  0.970  0.020  1.090
 VGJ  C17  H173  single  0.970  0.020  1.090
 VGJ  C8   H81C  single  0.970  0.020  1.090
 VGJ  C8   H82C  single  0.970  0.020  1.090
 VGJ  C7   H71C  single  0.970  0.020  1.090
 VGJ  C7   H72C  single  0.970  0.020  1.090
 VGJ  C6   H61C  single  0.970  0.020  1.090
 VGJ  C6   H62C  single  0.970  0.020  1.090
 VGJ  C5   H5    single  0.970  0.020  1.090
 VGJ  C18  H181  single  0.970  0.020  1.090
 VGJ  C18  H182  single  0.970  0.020  1.090
 VGJ  C18  H183  single  0.970  0.020  1.090
 VGJ  C4   H41C  single  0.970  0.020  1.090
 VGJ  C4   H42C  single  0.970  0.020  1.090
 VGJ  C3   H31C  single  0.970  0.020  1.090
 VGJ  C3   H32C  single  0.970  0.020  1.090
 VGJ  C2   H21C  single  0.970  0.020  1.090
 VGJ  C2   H22C  single  0.970  0.020  1.090
 VGJ  C1   HA    single  0.970  0.020  1.090
 VGJ  C19  H191  single  0.970  0.020  1.090
 VGJ  C19  H192  single  0.970  0.020  1.090
 VGJ  C19  H193  single  0.970  0.020  1.090
 VGJ  C20  H201  single  0.970  0.020  1.090
 VGJ  C20  H202  single  0.970  0.020  1.090
 VGJ  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
 VGJ  C14   C15  O2    117.30  3.000
 VGJ  C14   C15  O1    116.70  3.000
 VGJ  O2    C15  O1    125.96  3.000
 VGJ  H142  C14  H141  105.47  3.000
 VGJ  H142  C14  C13   109.71  3.000
 VGJ  H141  C14  C13   108.71  3.000
 VGJ  H142  C14  C15   109.72  3.000
 VGJ  H141  C14  C15   106.88  3.000
 VGJ  C13   C14  C15   115.81  3.000
 VGJ  H13   C13  C12   107.96  3.000
 VGJ  H13   C13  C16   108.15  3.000
 VGJ  C12   C13  C16   111.64  3.000
 VGJ  H13   C13  C14   107.66  3.000
 VGJ  C12   C13  C14   110.36  3.000
 VGJ  C16   C13  C14   110.91  3.000
 VGJ  H163  C16  H162  107.15  3.000
 VGJ  H163  C16  H161  107.51  3.000
 VGJ  H162  C16  H161  107.82  3.000
 VGJ  H163  C16  C13   112.17  3.000
 VGJ  H162  C16  C13   111.11  3.000
 VGJ  H161  C16  C13   110.87  3.000
 VGJ  H122  C12  H121  105.76  3.000
 VGJ  H122  C12  C11   109.32  3.000
 VGJ  H121  C12  C11   108.50  3.000
 VGJ  H122  C12  C13   109.25  3.000
 VGJ  H121  C12  C13   108.62  3.000
 VGJ  C11   C12  C13   114.98  3.000
 VGJ  H112  C11  H111  106.20  3.000
 VGJ  H112  C11  C10   110.35  3.000
 VGJ  H111  C11  C10   108.93  3.000
 VGJ  H112  C11  C12   108.84  3.000
 VGJ  H111  C11  C12   110.14  3.000
 VGJ  C10   C11  C12   112.21  3.000
 VGJ  H102  C10  H101  105.92  3.000
 VGJ  H102  C10  C9    108.54  3.000
 VGJ  H101  C10  C9    109.03  3.000
 VGJ  H102  C10  C11   108.39  3.000
 VGJ  H101  C10  C11   109.30  3.000
 VGJ  C9    C10  C11   115.25  3.000
 VGJ  H9    C9   C8    107.33  3.000
 VGJ  H9    C9   C17   108.17  3.000
 VGJ  C8    C9   C17   111.88  3.000
 VGJ  H9    C9   C10   107.75  3.000
 VGJ  C8    C9   C10   109.97  3.000
 VGJ  C17   C9   C10   111.54  3.000
 VGJ  H173  C17  H172  107.65  3.000
 VGJ  H173  C17  H171  107.64  3.000
 VGJ  H172  C17  H171  106.96  3.000
 VGJ  H173  C17  C9    110.59  3.000
 VGJ  H172  C17  C9    111.74  3.000
 VGJ  H171  C17  C9    112.04  3.000
 VGJ  H82C  C8   H81C  105.81  3.000
 VGJ  H82C  C8   C7    108.38  3.000
 VGJ  H81C  C8   C7    109.52  3.000
 VGJ  H82C  C8   C9    108.46  3.000
 VGJ  H81C  C8   C9    109.32  3.000
 VGJ  C7    C8   C9    114.95  3.000
 VGJ  H72C  C7   H71C  105.99  3.000
 VGJ  H72C  C7   C6    110.01  3.000
 VGJ  H71C  C7   C6    108.90  3.000
 VGJ  H72C  C7   C8    110.09  3.000
 VGJ  H71C  C7   C8    109.10  3.000
 VGJ  C6    C7   C8    112.53  3.000
 VGJ  H62C  C6   H61C  105.79  3.000
 VGJ  H62C  C6   C5    108.96  3.000
 VGJ  H61C  C6   C5    109.27  3.000
 VGJ  H62C  C6   C7    108.26  3.000
 VGJ  H61C  C6   C7    109.62  3.000
 VGJ  C5    C6   C7    114.57  3.000
 VGJ  H5    C5   C4    107.44  3.000
 VGJ  H5    C5   C18   108.06  3.000
 VGJ  C4    C5   C18   111.75  3.000
 VGJ  H5    C5   C6    107.47  3.000
 VGJ  C4    C5   C6    110.32  3.000
 VGJ  C18   C5   C6    111.58  3.000
 VGJ  H183  C18  H182  107.57  3.000
 VGJ  H183  C18  H181  107.60  3.000
 VGJ  H182  C18  H181  106.95  3.000
 VGJ  H183  C18  C5    110.77  3.000
 VGJ  H182  C18  C5    111.78  3.000
 VGJ  H181  C18  C5    111.94  3.000
 VGJ  H42C  C4   H41C  105.97  3.000
 VGJ  H42C  C4   C3    108.87  3.000
 VGJ  H41C  C4   C3    109.25  3.000
 VGJ  H42C  C4   C5    108.42  3.000
 VGJ  H41C  C4   C5    109.16  3.000
 VGJ  C3    C4   C5    114.81  3.000
 VGJ  H32C  C3   H31C  106.14  3.000
 VGJ  H32C  C3   C2    109.80  3.000
 VGJ  H31C  C3   C2    109.10  3.000
 VGJ  H32C  C3   C4    109.60  3.000
 VGJ  H31C  C3   C4    109.27  3.000
 VGJ  C2    C3   C4    112.71  3.000
 VGJ  H22C  C2   H21C  105.98  3.000
 VGJ  H22C  C2   C1    108.63  3.000
 VGJ  H21C  C2   C1    109.05  3.000
 VGJ  H22C  C2   C3    108.63  3.000
 VGJ  H21C  C2   C3    109.55  3.000
 VGJ  C1    C2   C3    114.64  3.000
 VGJ  HA    C1   C20   107.85  3.000
 VGJ  HA    C1   C19   108.03  3.000
 VGJ  C20   C1   C19   110.05  3.000
 VGJ  HA    C1   C2    107.66  3.000
 VGJ  C20   C1   C2    110.70  3.000
 VGJ  C19   C1   C2    112.38  3.000
 VGJ  H193  C19  H192  107.43  3.000
 VGJ  H193  C19  H191  107.63  3.000
 VGJ  H192  C19  H191  107.54  3.000
 VGJ  H193  C19  C1    112.45  3.000
 VGJ  H192  C19  C1    110.92  3.000
 VGJ  H191  C19  C1    110.66  3.000
 VGJ  H203  C20  H202  107.49  3.000
 VGJ  H203  C20  H201  107.64  3.000
 VGJ  H202  C20  H201  107.72  3.000
 VGJ  H203  C20  C1    110.92  3.000
 VGJ  H202  C20  C1    111.26  3.000
 VGJ  H201  C20  C1    111.61  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
 VGJ  Var_01  C13   C14  C15  O1    149.81  30.0  3
 VGJ  Var_02  C10   C11  C12  C13   173.80  30.0  3
 VGJ  Var_03  C9    C10  C11  C12   173.25  30.0  3
 VGJ  Var_04  C6    C7   C8   C9   -173.28  30.0  3
 VGJ  Var_05  C5    C6   C7   C8    178.18  30.0  3
 VGJ  Var_06  C2    C3   C4   C5   -171.44  30.0  3
 VGJ  Var_07  C1    C2   C3   C4    177.62  30.0  3
 VGJ  Var_08  C19   C1   C2   C3     64.73  30.0  3
 VGJ  Var_09  H191  C19  C1   C2     62.14  30.0  3
 VGJ  Var_10  H201  C20  C1   C2     57.34  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
 VGJ  chir_01  C13  C14  C16  C12  positiv
 VGJ  chir_02  C9   C10  C17  C8   negativ
 VGJ  chir_03  C5   C6   C18  C4   negativ

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
 VGJ  plan-1  O1   0.020
 VGJ  plan-1  C15  0.020
 VGJ  plan-1  O2   0.020
 VGJ  plan-1  C14  0.020

