# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 17:09:43 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: 11-sulfanylundecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCCCCCCS
#
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
 MDX  MDX  '11-sulfanylundecanoic acid'  ligand  36  14  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MDX
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
 MDX  O1    O  O     0  -0.446  27.3882  46.1016  22.0832
 MDX  C11   C  C     0   0.553  27.0850  47.2435  21.8409
 MDX  O2    O  OH1   0  -0.598  27.7134  48.2857  22.3798
 MDX  C10   C  CH2   0  -0.584  25.9816  47.6754  20.9158
 MDX  C9    C  CH2   0  -0.432  25.2392  46.5198  20.2639
 MDX  C8    C  CH2   0  -0.446  24.2301  46.9836  19.2164
 MDX  C7    C  CH2   0  -0.453  23.1188  47.8973  19.7301
 MDX  C6    C  CH2   0  -0.435  22.2831  47.3440  20.8833
 MDX  C5    C  CH2   0  -0.436  21.5410  46.0264  20.6518
 MDX  C4    C  CH2   0  -0.446  20.4474  46.0604  19.5792
 MDX  C3    C  CH2   0  -0.450  20.8946  45.8036  18.1388
 MDX  C2    C  CH2   0  -0.414  21.4455  44.4033  17.8710
 MDX  C1    C  CH2   0  -0.562  20.3916  43.3156  18.0064
 MDX  S1    S  S2    0  -0.249  21.0147  41.6496  17.6136
 MDX  HO2   H  HOH1  0   0.478  28.4247  47.9769  22.9603
 MDX  H101  H  HCH2  0   0.276  25.3017  48.3163  21.4852
 MDX  H102  H  HCH2  0   0.274  26.4205  48.3251  20.1511
 MDX  H91   H  HCH2  0   0.236  25.9574  45.8561  19.7775
 MDX  H92   H  HCH2  0   0.228  24.7419  45.9183  21.0288
 MDX  H81   H  HCH2  0   0.223  24.7678  47.5092  18.4206
 MDX  H82   H  HCH2  0   0.233  23.7991  46.0979  18.7412
 MDX  H71   H  HCH2  0   0.226  23.5516  48.8487  20.0548
 MDX  H72   H  HCH2  0   0.228  22.4677  48.1582  18.8911
 MDX  H61   H  HCH2  0   0.216  22.9243  47.2238  21.7622
 MDX  H62   H  HCH2  0   0.220  21.5461  48.1039  21.1629
 MDX  H51   H  HCH2  0   0.217  22.2496  45.2165  20.4539
 MDX  H52   H  HCH2  0   0.227  21.0733  45.7591  21.6034
 MDX  H41   H  HCH2  0   0.222  19.6784  45.3270  19.8393
 MDX  H42   H  HCH2  0   0.223  19.9418  47.0308  19.6210
 MDX  H31   H  HCH2  0   0.225  20.0421  45.9757  17.4739
 MDX  H32   H  HCH2  0   0.235  21.6492  46.5344  17.8423
 MDX  H21   H  HCH2  0   0.232  21.8529  44.3775  16.8569
 MDX  H22   H  HCH2  0   0.226  22.2807  44.1810  18.5405
 MDX  H11   H  HCH2  0   0.272  20.0283  43.2372  19.0320
 MDX  H12   H  HCH2  0   0.264  19.5273  43.5308  17.3765
 MDX  HS1   H  HSH1  0   0.214  21.2902  41.8693  16.3227

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
 MDX  O1   C11   double  1.206  0.020  1.206
 MDX  C11  C10   single  1.503  0.020  1.503
 MDX  C11  O2    single  1.331  0.020  1.331
 MDX  O2   HO2   single  0.850  0.020  0.980
 MDX  C10  C9    single  1.520  0.020  1.520
 MDX  C10  H101  single  0.970  0.020  1.090
 MDX  C10  H102  single  0.970  0.020  1.090
 MDX  C9   C8    single  1.527  0.020  1.527
 MDX  C9   H91   single  0.970  0.020  1.090
 MDX  C9   H92   single  0.970  0.020  1.090
 MDX  C8   C7    single  1.528  0.020  1.528
 MDX  C8   H81   single  0.970  0.020  1.090
 MDX  C8   H82   single  0.970  0.020  1.090
 MDX  C7   C6    single  1.528  0.020  1.528
 MDX  C7   H71   single  0.970  0.020  1.090
 MDX  C7   H72   single  0.970  0.020  1.090
 MDX  C6   C5    single  1.530  0.020  1.530
 MDX  C6   H61   single  0.970  0.020  1.090
 MDX  C6   H62   single  0.970  0.020  1.090
 MDX  C5   C4    single  1.532  0.020  1.532
 MDX  C5   H51   single  0.970  0.020  1.090
 MDX  C5   H52   single  0.970  0.020  1.090
 MDX  C4   C3    single  1.530  0.020  1.530
 MDX  C4   H41   single  0.970  0.020  1.090
 MDX  C4   H42   single  0.970  0.020  1.090
 MDX  C3   C2    single  1.528  0.020  1.528
 MDX  C3   H31   single  0.970  0.020  1.090
 MDX  C3   H32   single  0.970  0.020  1.090
 MDX  C2   C1    single  1.521  0.020  1.521
 MDX  C2   H21   single  0.970  0.020  1.090
 MDX  C2   H22   single  0.970  0.020  1.090
 MDX  C1   S1    single  1.822  0.020  1.822
 MDX  C1   H11   single  0.970  0.020  1.090
 MDX  C1   H12   single  0.970  0.020  1.090
 MDX  S1   HS1   single  1.200  0.020  1.300

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
 MDX  C10   C11  O2    111.76  3.000
 MDX  O2    C11  O1    122.78  3.000
 MDX  C10   C11  O1    125.46  3.000
 MDX  HO2   O2   C11   109.86  3.000
 MDX  H102  C10  H101  105.36  3.000
 MDX  H102  C10  C9    110.31  3.000
 MDX  H101  C10  C9    111.40  3.000
 MDX  H102  C10  C11   107.82  3.000
 MDX  H101  C10  C11   107.71  3.000
 MDX  C9    C10  C11   113.83  3.000
 MDX  H92   C9   H91   106.05  3.000
 MDX  H92   C9   C8    110.28  3.000
 MDX  H91   C9   C8    108.29  3.000
 MDX  H92   C9   C10   109.90  3.000
 MDX  H91   C9   C10   109.37  3.000
 MDX  C8    C9   C10   112.71  3.000
 MDX  H82   C8   H81   105.45  3.000
 MDX  H82   C8   C7    110.11  3.000
 MDX  H81   C8   C7    108.34  3.000
 MDX  H82   C8   C9    108.21  3.000
 MDX  H81   C8   C9    108.66  3.000
 MDX  C7    C8   C9    115.59  3.000
 MDX  H72   C7   H71   104.82  3.000
 MDX  H72   C7   C6    109.86  3.000
 MDX  H71   C7   C6    107.89  3.000
 MDX  H72   C7   C8    108.53  3.000
 MDX  H71   C7   C8    109.39  3.000
 MDX  C6    C7   C8    115.79  3.000
 MDX  H62   C6   H61   105.39  3.000
 MDX  H62   C6   C5    108.05  3.000
 MDX  H61   C6   C5    108.12  3.000
 MDX  H62   C6   C7    108.04  3.000
 MDX  H61   C6   C7    108.99  3.000
 MDX  C5    C6   C7    117.58  3.000
 MDX  H52   C5   H51   104.68  3.000
 MDX  H52   C5   C4    108.03  3.000
 MDX  H51   C5   C4    110.61  3.000
 MDX  H52   C5   C6    106.64  3.000
 MDX  H51   C5   C6    110.53  3.000
 MDX  C4    C5   C6    115.66  3.000
 MDX  H42   C4   H41   105.09  3.000
 MDX  H42   C4   C3    108.64  3.000
 MDX  H41   C4   C3    108.47  3.000
 MDX  H42   C4   C5    108.82  3.000
 MDX  H41   C4   C5    108.68  3.000
 MDX  C3    C4   C5    116.54  3.000
 MDX  H32   C3   H31   105.55  3.000
 MDX  H32   C3   C2    108.46  3.000
 MDX  H31   C3   C2    108.56  3.000
 MDX  H32   C3   C4    110.21  3.000
 MDX  H31   C3   C4    108.53  3.000
 MDX  C2    C3   C4    115.10  3.000
 MDX  H22   C2   H21   106.18  3.000
 MDX  H22   C2   C1    109.24  3.000
 MDX  H21   C2   C1    108.91  3.000
 MDX  H22   C2   C3    110.75  3.000
 MDX  H21   C2   C3    108.57  3.000
 MDX  C1    C2   C3    112.95  3.000
 MDX  H12   C1   H11   107.05  3.000
 MDX  H12   C1   S1    109.08  3.000
 MDX  H11   C1   S1    104.53  3.000
 MDX  H12   C1   C2    110.89  3.000
 MDX  H11   C1   C2    111.47  3.000
 MDX  S1    C1   C2    113.45  3.000
 MDX  HS1   S1   C1     97.37  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
 MDX  CONST_01  HO2  O2   C11  O1      0.00   0.0  0
 MDX  Var_01    C9   C10  C11  O1     -0.40  30.0  3
 MDX  Var_02    C8   C9   C10  C11  -173.69  30.0  3
 MDX  Var_03    C7   C8   C9   C10   -60.45  30.0  3
 MDX  Var_04    C6   C7   C8   C9    -55.99  30.0  3
 MDX  Var_05    C5   C6   C7   C8    -58.70  30.0  3
 MDX  Var_06    C4   C5   C6   C7    -64.29  30.0  3
 MDX  Var_07    C3   C4   C5   C6     86.57  30.0  3
 MDX  Var_08    C2   C3   C4   C5     64.84  30.0  3
 MDX  Var_09    C1   C2   C3   C4     66.56  30.0  3
 MDX  Var_10    S1   C1   C2   C3    177.28  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
 MDX  plan-1  O1   0.020
 MDX  plan-1  C11  0.020
 MDX  plan-1  O2   0.020
 MDX  plan-1  C10  0.020
 MDX  plan-1  HO2  0.020

