# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:30:20 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (3R)-3-hydroxydodecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC[C@@H](O)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
 HXD  HXD  '(3R)-3-hydroxydodecanoic acid'  ligand  38  15  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HXD
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
 HXD  C11   C  CH2    0  -0.418   7.0748  -0.5306  -0.1638
 HXD  C10   C  CH2    0  -0.406   5.8344   0.3375   0.0079
 HXD  C12   C  CH3    0  -0.662   8.3711   0.2489   0.0077
 HXD  C9    C  CH2    0  -0.411   4.5298  -0.4321  -0.1533
 HXD  C8    C  CH2    0  -0.411   3.2920   0.4366   0.0318
 HXD  C7    C  CH2    0  -0.411   1.9858  -0.3317  -0.1231
 HXD  C6    C  CH2    0  -0.412   0.7500   0.5372   0.0731
 HXD  C5    C  CH2    0  -0.408  -0.5572  -0.2301  -0.0810
 HXD  C4    C  CH2    0  -0.437  -1.7843   0.6468   0.1321
 HXD  C3    C  CH1    0   0.041  -3.1136  -0.0751  -0.0668
 HXD  O8    O  OH1    0  -0.673  -3.2281  -1.2114   0.7749
 HXD  C2    C  CH2    0  -0.581  -4.2989   0.8624   0.1192
 HXD  C1    C  C      0   0.406  -5.6538   0.1814  -0.1368
 HXD  O1    O  OC    -1  -0.620  -6.5443   0.3289   0.7246
 HXD  O     O  O      0  -0.623  -5.7622  -0.4513  -1.2080
 HXD  H111  H  HCH2   0   0.209   7.0554  -0.9988  -1.1531
 HXD  H112  H  HCH2   0   0.209   7.0444  -1.3518   0.5592
 HXD  H101  H  HCH2   0   0.205   5.8569   0.8085   0.9973
 HXD  H102  H  HCH2   0   0.205   5.8638   1.1587  -0.7173
 HXD  H121  H  HCH3   0   0.215   8.4514   1.0504  -0.7291
 HXD  H122  H  HCH3   0   0.215   8.4257   0.7069   0.9972
 HXD  H123  H  HCH3   0   0.225   9.2452  -0.3935  -0.1069
 HXD  H91   H  HCH2   0   0.206   4.5031  -0.8978  -1.1450
 HXD  H92   H  HCH2   0   0.205   4.5052  -1.2568   0.5680
 HXD  H81   H  HCH2   0   0.205   3.3215   0.9033   1.0229
 HXD  H82   H  HCH2   0   0.206   3.3152   1.2606  -0.6902
 HXD  H71   H  HCH2   0   0.206   1.9523  -0.7939  -1.1161
 HXD  H72   H  HCH2   0   0.205   1.9653  -1.1588   0.5955
 HXD  H61   H  HCH2   0   0.205   0.7844   0.9973   1.0672
 HXD  H62   H  HCH2   0   0.205   0.7717   1.3664  -0.6432
 HXD  H51   H  HCH2   0   0.205  -0.5981  -0.6770  -1.0810
 HXD  H52   H  HCH2   0   0.209  -0.5707  -1.0647   0.6258
 HXD  H41   H  HCH2   0   0.207  -1.7549   1.0859   1.1377
 HXD  H42   H  HCH2   0   0.213  -1.7497   1.4916  -0.5640
 HXD  H3    H  HCH1   0   0.204  -3.1430  -0.4720  -1.0859
 HXD  HO8   H  HOH1   0   0.435  -3.2343  -0.9020   1.6871
 HXD  H21   H  HCH2   0   0.200  -4.2680   1.2991   1.1238
 HXD  H22   H  HCH2   0   0.223  -4.1953   1.6982  -0.5824

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
 HXD  C11  C10   single  1.524  0.020  1.524
 HXD  C11  C12   single  1.522  0.020  1.522
 HXD  C11  H111  single  0.970  0.020  1.090
 HXD  C11  H112  single  0.970  0.020  1.090
 HXD  C10  C9    single  1.523  0.020  1.523
 HXD  C10  H101  single  0.970  0.020  1.090
 HXD  C10  H102  single  0.970  0.020  1.090
 HXD  C12  H121  single  0.970  0.020  1.090
 HXD  C12  H122  single  0.970  0.020  1.090
 HXD  C12  H123  single  0.970  0.020  1.090
 HXD  C9   C8    single  1.524  0.020  1.524
 HXD  C9   H91   single  0.970  0.020  1.090
 HXD  C9   H92   single  0.970  0.020  1.090
 HXD  C8   C7    single  1.523  0.020  1.523
 HXD  C8   H81   single  0.970  0.020  1.090
 HXD  C8   H82   single  0.970  0.020  1.090
 HXD  C7   C6    single  1.523  0.020  1.523
 HXD  C7   H71   single  0.970  0.020  1.090
 HXD  C7   H72   single  0.970  0.020  1.090
 HXD  C6   C5    single  1.524  0.020  1.524
 HXD  C6   H61   single  0.970  0.020  1.090
 HXD  C6   H62   single  0.970  0.020  1.090
 HXD  C5   C4    single  1.523  0.020  1.523
 HXD  C5   H51   single  0.970  0.020  1.090
 HXD  C5   H52   single  0.970  0.020  1.090
 HXD  C4   C3    single  1.526  0.020  1.526
 HXD  C4   H41   single  0.970  0.020  1.090
 HXD  C4   H42   single  0.970  0.020  1.090
 HXD  C3   O8    single  1.419  0.020  1.419
 HXD  C3   C2    single  1.523  0.020  1.523
 HXD  C3   H3    single  0.970  0.020  1.090
 HXD  O8   HO8   single  0.850  0.020  0.980
 HXD  C2   C1    single  1.538  0.020  1.538
 HXD  C2   H21   single  0.970  0.020  1.090
 HXD  C2   H22   single  0.970  0.020  1.090
 HXD  C1   O1    deloc   1.248  0.020  1.248
 HXD  C1   O     deloc   1.249  0.020  1.249

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
 HXD  H112  C11  H111  106.00  3.000
 HXD  H112  C11  C12   109.47  3.000
 HXD  H111  C11  C12   109.63  3.000
 HXD  H112  C11  C10   109.30  3.000
 HXD  H111  C11  C10   109.33  3.000
 HXD  C12   C11  C10   112.88  3.000
 HXD  H102  C10  H101  105.95  3.000
 HXD  H102  C10  C9    109.36  3.000
 HXD  H101  C10  C9    109.28  3.000
 HXD  H102  C10  C11   109.30  3.000
 HXD  H101  C10  C11   109.26  3.000
 HXD  C9    C10  C11   113.41  3.000
 HXD  H123  C12  H122  107.59  3.000
 HXD  H123  C12  H121  107.62  3.000
 HXD  H122  C12  H121  107.46  3.000
 HXD  H123  C12  C11   111.65  3.000
 HXD  H122  C12  C11   111.07  3.000
 HXD  H121  C12  C11   111.25  3.000
 HXD  H92   C9   H91   105.98  3.000
 HXD  H92   C9   C8    109.32  3.000
 HXD  H91   C9   C8    109.41  3.000
 HXD  H92   C9   C10   109.26  3.000
 HXD  H91   C9   C10   109.35  3.000
 HXD  C8    C9   C10   113.26  3.000
 HXD  H82   C8   H81   105.96  3.000
 HXD  H82   C8   C7    109.29  3.000
 HXD  H81   C8   C7    109.26  3.000
 HXD  H82   C8   C9    109.36  3.000
 HXD  H81   C8   C9    109.32  3.000
 HXD  C7    C8   C9    113.38  3.000
 HXD  H72   C7   H71   105.98  3.000
 HXD  H72   C7   C6    109.32  3.000
 HXD  H71   C7   C6    109.42  3.000
 HXD  H72   C7   C8    109.27  3.000
 HXD  H71   C7   C8    109.33  3.000
 HXD  C6    C7   C8    113.26  3.000
 HXD  H62   C6   H61   105.94  3.000
 HXD  H62   C6   C5    109.39  3.000
 HXD  H61   C6   C5    109.28  3.000
 HXD  H62   C6   C7    109.35  3.000
 HXD  H61   C6   C7    109.31  3.000
 HXD  C5    C6   C7    113.31  3.000
 HXD  H52   C5   H51   106.15  3.000
 HXD  H52   C5   C4    109.81  3.000
 HXD  H51   C5   C4    109.41  3.000
 HXD  H52   C5   C6    109.24  3.000
 HXD  H51   C5   C6    109.25  3.000
 HXD  C4    C5   C6    112.77  3.000
 HXD  H42   C4   H41   105.83  3.000
 HXD  H42   C4   C3    108.04  3.000
 HXD  H41   C4   C3    109.39  3.000
 HXD  H42   C4   C5    109.25  3.000
 HXD  H41   C4   C5    109.69  3.000
 HXD  C3    C4   C5    114.28  3.000
 HXD  H3    C3   C2    108.44  3.000
 HXD  H3    C3   O8    105.06  3.000
 HXD  C2    C3   O8    110.97  3.000
 HXD  H3    C3   C4    108.45  3.000
 HXD  C2    C3   C4    111.78  3.000
 HXD  O8    C3   C4    111.84  3.000
 HXD  HO8   O8   C3    107.76  3.000
 HXD  H22   C2   H21   106.28  3.000
 HXD  H22   C2   C1    108.32  3.000
 HXD  H21   C2   C1    110.73  3.000
 HXD  H22   C2   C3    108.53  3.000
 HXD  H21   C2   C3    109.60  3.000
 HXD  C1    C2   C3    113.13  3.000
 HXD  O     C1   O1    126.17  3.000
 HXD  O     C1   C2    116.33  3.000
 HXD  O1    C1   C2    117.49  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
 HXD  Var_01  C8    C9   C10  C11   179.47  30.0  3
 HXD  Var_02  C7    C8   C9   C10  -179.76  30.0  3
 HXD  Var_03  C9    C10  C11  C12  -179.66  30.0  3
 HXD  Var_04  C6    C7   C8   C9    179.56  30.0  3
 HXD  Var_05  C5    C6   C7   C8   -179.98  30.0  3
 HXD  Var_06  C4    C5   C6   C7    179.39  30.0  3
 HXD  Var_07  C3    C4   C5   C6    177.78  30.0  3
 HXD  Var_08  O1    C1   C2   C3    130.64  30.0  3
 HXD  Var_09  H121  C12  C11  C10   -60.46  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
 HXD  chir_01  C3  C4  O8  C2  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
 HXD  plan-1  C2  0.020
 HXD  plan-1  C1  0.020
 HXD  plan-1  O1  0.020
 HXD  plan-1  O   0.020

