# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:26:57 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: methyl (3S)-3-hydroxydodecanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC[C@H](O)CC(=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
 DK3  DK3  'methyl (3S)-3-hydroxydodecanoate'  ligand  42  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DK3
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
 DK3  C12   C  CH3   0  -0.662   8.8377  -0.2910   0.1454
 DK3  C13   C  CH3   0  -0.426  -7.3343   0.0863   0.3254
 DK3  C11   C  CH2   0  -0.419   7.5512   0.5064  -0.0180
 DK3  O3    O  OH1   0  -0.665  -2.8063   1.1490   0.6851
 DK3  C3    C  CH1   0   0.037  -2.6287   0.1016  -0.2468
 DK3  C2    C  CH2   0  -0.591  -3.8089  -0.8686  -0.1992
 DK3  C1    C  C     0   0.595  -5.1162  -0.1584  -0.4262
 DK3  O1    O  O2    0  -0.449  -6.0406  -0.5038   0.4587
 DK3  O2    O  O     0  -0.459  -5.3158   0.6245  -1.3224
 DK3  C4    C  CH2   0  -0.452  -1.3122  -0.6404  -0.0533
 DK3  C5    C  CH2   0  -0.412  -0.0804   0.2495  -0.1605
 DK3  C6    C  CH2   0  -0.413   1.2183  -0.5322  -0.0073
 DK3  C7    C  CH2   0  -0.412   2.4623   0.3398  -0.1212
 DK3  C8    C  CH2   0  -0.411   3.7595  -0.4437   0.0336
 DK3  C9    C  CH2   0  -0.411   5.0064   0.4246  -0.0783
 DK3  C10   C  CH2   0  -0.406   6.3022  -0.3618   0.0741
 DK3  H12   H  HCH3  0   0.215   8.9296  -1.0557  -0.6284
 DK3  H12A  H  HCH3  0   0.225   9.7194   0.3482   0.0837
 DK3  H12B  H  HCH3  0   0.215   8.8652  -0.7985   1.1117
 DK3  H13   H  HCH3  0   0.251  -7.9344  -0.3249   1.1319
 DK3  H13A  H  HCH3  0   0.239  -7.2896   1.1705   0.4259
 DK3  H13B  H  HCH3  0   0.239  -7.7922  -0.1677  -0.6303
 DK3  H11   H  HCH2  0   0.210   7.5052   1.2878   0.7469
 DK3  H11A  H  HCH2  0   0.210   7.5604   1.0264  -0.9813
 DK3  H3    H  HCH1  0   0.231  -2.6151   0.5855  -1.2279
 DK3  H2    H  HCH2  0   0.283  -3.6966  -1.6156  -0.9906
 DK3  H2A   H  HCH2  0   0.261  -3.8205  -1.4104   0.7493
 DK3  H4    H  HCH2  0   0.220  -1.3196  -1.1481   0.9197
 DK3  H4A   H  HCH2  0   0.226  -1.2519  -1.4332  -0.8057
 DK3  H5    H  HCH2  0   0.211  -0.0849   0.7592  -1.1306
 DK3  H5A   H  HCH2  0   0.214  -0.1208   1.0357   0.5987
 DK3  H6    H  HCH2  0   0.208   1.2215  -1.0434   0.9622
 DK3  H6A   H  HCH2  0   0.208   1.2589  -1.3225  -0.7653
 DK3  H7    H  HCH2  0   0.207   2.4599   0.8507  -1.0908
 DK3  H7A   H  HCH2  0   0.207   2.4227   1.1302   0.6367
 DK3  H8    H  HCH2  0   0.206   3.7602  -0.9553   1.0028
 DK3  H8A   H  HCH2  0   0.206   3.7984  -1.2340  -0.7246
 DK3  H9    H  HCH2  0   0.206   5.0051   0.9388  -1.0464
 DK3  H9A   H  HCH2  0   0.206   4.9688   1.2129   0.6820
 DK3  H10   H  HCH2  0   0.206   6.3467  -1.1418  -0.6944
 DK3  H10A  H  HCH2  0   0.205   6.2975  -0.8868   1.0364
 DK3  HO3   H  HOH1  0   0.443  -2.7320   0.7811   1.5728

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
 DK3  C11  C12   single  1.522  0.020  1.522
 DK3  C12  H12   single  0.970  0.020  1.090
 DK3  C12  H12A  single  0.970  0.020  1.090
 DK3  C12  H12B  single  0.970  0.020  1.090
 DK3  C13  O1    single  1.428  0.020  1.428
 DK3  C13  H13   single  0.970  0.020  1.090
 DK3  C13  H13A  single  0.970  0.020  1.090
 DK3  C13  H13B  single  0.970  0.020  1.090
 DK3  C10  C11   single  1.524  0.020  1.524
 DK3  C11  H11   single  0.970  0.020  1.090
 DK3  C11  H11A  single  0.970  0.020  1.090
 DK3  C3   O3    single  1.413  0.020  1.413
 DK3  O3   HO3   single  0.850  0.020  0.980
 DK3  C2   C3    single  1.528  0.020  1.528
 DK3  C3   C4    single  1.524  0.020  1.524
 DK3  C3   H3    single  0.970  0.020  1.090
 DK3  C1   C2    single  1.505  0.020  1.505
 DK3  C2   H2    single  0.970  0.020  1.090
 DK3  C2   H2A   single  0.970  0.020  1.090
 DK3  O1   C1    single  1.325  0.020  1.325
 DK3  O2   C1    double  1.207  0.020  1.207
 DK3  C4   C5    single  1.523  0.020  1.523
 DK3  C4   H4    single  0.970  0.020  1.090
 DK3  C4   H4A   single  0.970  0.020  1.090
 DK3  C5   C6    single  1.524  0.020  1.524
 DK3  C5   H5    single  0.970  0.020  1.090
 DK3  C5   H5A   single  0.970  0.020  1.090
 DK3  C6   C7    single  1.523  0.020  1.523
 DK3  C6   H6    single  0.970  0.020  1.090
 DK3  C6   H6A   single  0.970  0.020  1.090
 DK3  C7   C8    single  1.523  0.020  1.523
 DK3  C7   H7    single  0.970  0.020  1.090
 DK3  C7   H7A   single  0.970  0.020  1.090
 DK3  C8   C9    single  1.524  0.020  1.524
 DK3  C8   H8    single  0.970  0.020  1.090
 DK3  C8   H8A   single  0.970  0.020  1.090
 DK3  C9   C10   single  1.523  0.020  1.523
 DK3  C9   H9    single  0.970  0.020  1.090
 DK3  C9   H9A   single  0.970  0.020  1.090
 DK3  C10  H10   single  0.970  0.020  1.090
 DK3  C10  H10A  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
 DK3  H12B  C12  H12A  107.58  3.000
 DK3  H12B  C12  H12   107.44  3.000
 DK3  H12A  C12  H12   107.60  3.000
 DK3  H12B  C12  C11   111.08  3.000
 DK3  H12A  C12  C11   111.71  3.000
 DK3  H12   C12  C11   111.22  3.000
 DK3  H13B  C13  H13A  109.26  3.000
 DK3  H13B  C13  H13   109.32  3.000
 DK3  H13A  C13  H13   109.32  3.000
 DK3  H13B  C13  O1    111.48  3.000
 DK3  H13A  C13  O1    111.43  3.000
 DK3  H13   C13  O1    105.95  3.000
 DK3  H11A  C11  H11   106.04  3.000
 DK3  H11A  C11  C10   109.31  3.000
 DK3  H11   C11  C10   109.27  3.000
 DK3  H11A  C11  C12   109.65  3.000
 DK3  H11   C11  C12   109.54  3.000
 DK3  C10   C11  C12   112.81  3.000
 DK3  HO3   O3   C3    108.35  3.000
 DK3  H3    C3   C4    108.58  3.000
 DK3  H3    C3   C2    108.56  3.000
 DK3  C4    C3   C2    110.74  3.000
 DK3  H3    C3   O3    105.38  3.000
 DK3  C4    C3   O3    112.70  3.000
 DK3  C2    C3   O3    110.66  3.000
 DK3  H2A   C2   H2    106.88  3.000
 DK3  H2A   C2   C1    110.84  3.000
 DK3  H2    C2   C1    107.59  3.000
 DK3  H2A   C2   C3    110.50  3.000
 DK3  H2    C2   C3    109.37  3.000
 DK3  C1    C2   C3    111.50  3.000
 DK3  O2    C1   O1    123.33  3.000
 DK3  O2    C1   C2    124.19  3.000
 DK3  O1    C1   C2    112.47  3.000
 DK3  C1    O1   C13   117.50  3.000
 DK3  H4A   C4   H4    105.94  3.000
 DK3  H4A   C4   C5    109.28  3.000
 DK3  H4    C4   C5    109.76  3.000
 DK3  H4A   C4   C3    108.24  3.000
 DK3  H4    C4   C3    109.39  3.000
 DK3  C5    C4   C3    113.91  3.000
 DK3  H5A   C5   H5    106.26  3.000
 DK3  H5A   C5   C6    109.31  3.000
 DK3  H5    C5   C6    109.34  3.000
 DK3  H5A   C5   C4    109.95  3.000
 DK3  H5    C5   C4    109.31  3.000
 DK3  C6    C5   C4    112.49  3.000
 DK3  H6A   C6   H6    105.98  3.000
 DK3  H6A   C6   C7    109.32  3.000
 DK3  H6    C6   C7    109.31  3.000
 DK3  H6A   C6   C5    109.40  3.000
 DK3  H6    C6   C5    109.31  3.000
 DK3  C7    C6   C5    113.26  3.000
 DK3  H7A   C7   H7    105.99  3.000
 DK3  H7A   C7   C8    109.36  3.000
 DK3  H7    C7   C8    109.36  3.000
 DK3  H7A   C7   C6    109.37  3.000
 DK3  H7    C7   C6    109.34  3.000
 DK3  C8    C7   C6    113.17  3.000
 DK3  H8A   C8   H8    105.97  3.000
 DK3  H8A   C8   C9    109.34  3.000
 DK3  H8    C8   C9    109.30  3.000
 DK3  H8A   C8   C7    109.32  3.000
 DK3  H8    C8   C7    109.30  3.000
 DK3  C9    C8   C7    113.35  3.000
 DK3  H9A   C9   H9    105.98  3.000
 DK3  H9A   C9   C10   109.34  3.000
 DK3  H9    C9   C10   109.36  3.000
 DK3  H9A   C9   C8    109.32  3.000
 DK3  H9    C9   C8    109.34  3.000
 DK3  C10   C9   C8    113.24  3.000
 DK3  H10A  C10  H10   105.96  3.000
 DK3  H10A  C10  C9    109.36  3.000
 DK3  H10   C10  C9    109.38  3.000
 DK3  H10A  C10  C11   109.23  3.000
 DK3  H10   C10  C11   109.26  3.000
 DK3  C9    C10  C11   113.39  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
 DK3  Var_01  C9   C10  C11  C12   179.61  30.0  1
 DK3  Var_02  C2   C1   O1   C13  -178.71  30.0  3
 DK3  Var_03  C8   C9   C10  C11  -179.20  30.0  1
 DK3  Var_04  O1   C1   C2   C3   -132.84  30.0  1
 DK3  Var_05  C6   C5   C4   C3   -178.13  30.0  3
 DK3  Var_06  C7   C6   C5   C4    179.61  30.0  3
 DK3  Var_07  C8   C7   C6   C5    179.95  30.0  3
 DK3  Var_08  C9   C8   C7   C6   -179.95  30.0  3
 DK3  Var_09  C10  C9   C8   C7   -179.89  30.0  3
 DK3  Var_10  H13  C13  O1   C1    179.78  30.0  3
 DK3  Var_11  H12  C12  C11  C10    60.17  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
 DK3  chir_01  C3  O3  C2  C4  positiv

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
 DK3  plan-1  C2  0.020
 DK3  plan-1  C1  0.020
 DK3  plan-1  O1  0.020
 DK3  plan-1  O2  0.020

