# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:53:47 2020
#   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  35  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.612  -6.6281  -1.2371  -0.2098
 MDX  C11   C  C      0   0.409  -6.6148  -0.0057  -0.0096
 MDX  O2    O  OC    -1  -0.634  -7.6145   0.7199   0.1774
 MDX  C10   C  CH2    0  -0.580  -5.2508   0.7072  -0.0043
 MDX  C9    C  CH2    0  -0.403  -4.0254  -0.1929  -0.0071
 MDX  C8    C  CH2    0  -0.409  -2.7172   0.5895  -0.0056
 MDX  C7    C  CH2    0  -0.410  -1.4822  -0.3034  -0.0009
 MDX  C6    C  CH2    0  -0.411  -0.1734   0.4764  -0.0030
 MDX  C5    C  CH2    0  -0.413   1.0605  -0.4180   0.0085
 MDX  C4    C  CH2    0  -0.413   2.3685   0.3630   0.0007
 MDX  C3    C  CH2    0  -0.411   3.6005  -0.5338   0.0202
 MDX  C2    C  CH2    0  -0.416   4.9050   0.2551   0.0040
 MDX  C1    C  CH2    0  -0.549   6.1193  -0.6599   0.0399
 MDX  S1    S  S2     0  -0.262   7.6384   0.3510  -0.0037
 MDX  H101  H  HCH2   0   0.218  -5.2158   1.3703  -0.8781
 MDX  H102  H  HCH2   0   0.211  -5.2134   1.3803   0.8597
 MDX  H91   H  HCH2   0   0.199  -4.0486  -0.8537   0.8658
 MDX  H92   H  HCH2   0   0.201  -4.0513  -0.8502  -0.8810
 MDX  H81   H  HCH2   0   0.202  -2.6840   1.2475  -0.8820
 MDX  H82   H  HCH2   0   0.202  -2.6868   1.2519   0.8674
 MDX  H71   H  HCH2   0   0.204  -1.5128  -0.9589   0.8770
 MDX  H72   H  HCH2   0   0.204  -1.5111  -0.9663  -0.8732
 MDX  H61   H  HCH2   0   0.206  -0.1404   1.1282  -0.8835
 MDX  H62   H  HCH2   0   0.206  -0.1459   1.1424   0.8669
 MDX  H51   H  HCH2   0   0.207   1.0297  -1.0665   0.8914
 MDX  H52   H  HCH2   0   0.207   1.0317  -1.0869  -0.8590
 MDX  H41   H  HCH2   0   0.210   2.4023   1.0068  -0.8853
 MDX  H42   H  HCH2   0   0.210   2.3962   1.0353   0.8654
 MDX  H31   H  HCH2   0   0.214   3.5714  -1.1720   0.9099
 MDX  H32   H  HCH2   0   0.215   3.5725  -1.2091  -0.8417
 MDX  H21   H  HCH2   0   0.228   4.9417   0.8812  -0.8930
 MDX  H22   H  HCH2   0   0.228   4.9337   0.9344   0.8613
 MDX  H11   H  HCH2   0   0.262   6.1146  -1.2609   0.9496
 MDX  H12   H  HCH2   0   0.261   6.1111  -1.3368  -0.8149
 MDX  HS1   H  HSH1   0   0.220   8.5268  -0.6416   0.1151

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   deloc   1.248  0.020  1.248
 MDX  C11  C10   single  1.539  0.020  1.539
 MDX  C11  O2    deloc   1.249  0.020  1.249
 MDX  C10  C9    single  1.521  0.020  1.521
 MDX  C10  H101  single  0.970  0.020  1.090
 MDX  C10  H102  single  0.970  0.020  1.090
 MDX  C9   C8    single  1.524  0.020  1.524
 MDX  C9   H91   single  0.970  0.020  1.090
 MDX  C9   H92   single  0.970  0.020  1.090
 MDX  C8   C7    single  1.524  0.020  1.524
 MDX  C8   H81   single  0.970  0.020  1.090
 MDX  C8   H82   single  0.970  0.020  1.090
 MDX  C7   C6    single  1.523  0.020  1.523
 MDX  C7   H71   single  0.970  0.020  1.090
 MDX  C7   H72   single  0.970  0.020  1.090
 MDX  C6   C5    single  1.524  0.020  1.524
 MDX  C6   H61   single  0.970  0.020  1.090
 MDX  C6   H62   single  0.970  0.020  1.090
 MDX  C5   C4    single  1.523  0.020  1.523
 MDX  C5   H51   single  0.970  0.020  1.090
 MDX  C5   H52   single  0.970  0.020  1.090
 MDX  C4   C3    single  1.524  0.020  1.524
 MDX  C4   H41   single  0.970  0.020  1.090
 MDX  C4   H42   single  0.970  0.020  1.090
 MDX  C3   C2    single  1.525  0.020  1.525
 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  1.825  0.020  1.825
 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    116.08  3.000
 MDX  O2    C11  O1    126.07  3.000
 MDX  C10   C11  O1    117.85  3.000
 MDX  H102  C10  H101  104.81  3.000
 MDX  H102  C10  C9    109.73  3.000
 MDX  H101  C10  C9    109.29  3.000
 MDX  H102  C10  C11   108.52  3.000
 MDX  H101  C10  C11   107.78  3.000
 MDX  C9    C10  C11   116.11  3.000
 MDX  H92   C9   H91   105.89  3.000
 MDX  H92   C9   C8    109.25  3.000
 MDX  H91   C9   C8    109.09  3.000
 MDX  H92   C9   C10   109.76  3.000
 MDX  H91   C9   C10   109.79  3.000
 MDX  C8    C9   C10   112.82  3.000
 MDX  H82   C8   H81   105.84  3.000
 MDX  H82   C8   C7    109.21  3.000
 MDX  H81   C8   C7    109.24  3.000
 MDX  H82   C8   C9    109.56  3.000
 MDX  H81   C8   C9    109.46  3.000
 MDX  C7    C8   C9    113.25  3.000
 MDX  H72   C7   H71   105.97  3.000
 MDX  H72   C7   C6    109.34  3.000
 MDX  H71   C7   C6    109.34  3.000
 MDX  H72   C7   C8    109.30  3.000
 MDX  H71   C7   C8    109.28  3.000
 MDX  C6    C7   C8    113.35  3.000
 MDX  H62   C6   H61   105.99  3.000
 MDX  H62   C6   C5    109.29  3.000
 MDX  H61   C6   C5    109.32  3.000
 MDX  H62   C6   C7    109.36  3.000
 MDX  H61   C6   C7    109.35  3.000
 MDX  C5    C6   C7    113.28  3.000
 MDX  H52   C5   H51   106.02  3.000
 MDX  H52   C5   C4    109.36  3.000
 MDX  H51   C5   C4    109.37  3.000
 MDX  H52   C5   C6    109.33  3.000
 MDX  H51   C5   C6    109.31  3.000
 MDX  C4    C5   C6    113.22  3.000
 MDX  H42   C4   H41   106.07  3.000
 MDX  H42   C4   C3    109.30  3.000
 MDX  H41   C4   C3    109.34  3.000
 MDX  H42   C4   C5    109.40  3.000
 MDX  H41   C4   C5    109.38  3.000
 MDX  C3    C4   C5    113.10  3.000
 MDX  H32   C3   H31   106.21  3.000
 MDX  H32   C3   C2    109.42  3.000
 MDX  H31   C3   C2    109.44  3.000
 MDX  H32   C3   C4    109.40  3.000
 MDX  H31   C3   C4    109.38  3.000
 MDX  C2    C3   C4    112.78  3.000
 MDX  H22   C2   H21   106.63  3.000
 MDX  H22   C2   C1    109.52  3.000
 MDX  H21   C2   C1    109.68  3.000
 MDX  H22   C2   C3    109.59  3.000
 MDX  H21   C2   C3    109.47  3.000
 MDX  C1    C2   C3    111.82  3.000
 MDX  H12   C1   H11   108.18  3.000
 MDX  H12   C1   S1    109.35  3.000
 MDX  H11   C1   S1    109.19  3.000
 MDX  H12   C1   C2    110.43  3.000
 MDX  H11   C1   C2    110.35  3.000
 MDX  S1    C1   C2    109.31  3.000
 MDX  HS1   S1   C1     98.03  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  Var_01  C9  C10  C11  O1   -10.13  30.0  3
 MDX  Var_02  C8  C9   C10  C11  179.83  30.0  3
 MDX  Var_03  C7  C8   C9   C10  179.69  30.0  3
 MDX  Var_04  C6  C7   C8   C9   179.85  30.0  3
 MDX  Var_05  C5  C6   C7   C8   179.72  30.0  3
 MDX  Var_06  C4  C5   C6   C7   179.77  30.0  3
 MDX  Var_07  C3  C4   C5   C6   179.68  30.0  3
 MDX  Var_08  C2  C3   C4   C5   179.67  30.0  3
 MDX  Var_09  C1  C2   C3   C4   179.35  30.0  3
 MDX  Var_10  S1  C1   C2   C3   179.27  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

