# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:37:16 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: N,N,N-trimethyl-13-[(methylsulfonyl)sulfanyl]tridecan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCCCCCCCCCCCCS[S](C)(=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
 X13  X13  N,N,N-trimethyl-13-[(methylsulfonyl)sulfanyl]tridecan-1-aminium  ligand  60  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X13
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
 X13  C4    C  CH2   0  -0.602    6.1716   1.2940  -0.3144
 X13  C5    C  CH2   0  -0.397    4.9315   0.7052   0.3329
 X13  C6    C  CH2   0  -0.418    3.6582   1.1377  -0.3859
 X13  C7    C  CH2   0  -0.414    2.4151   0.4975   0.2191
 X13  C8    C  CH2   0  -0.413    1.1129   0.9693  -0.4146
 X13  C9    C  CH2   0  -0.413   -0.1135   0.3084   0.2021
 X13  C10   C  CH2   0  -0.413   -1.4321   0.7960  -0.3836
 X13  C11   C  CH2   0  -0.413   -2.6467   0.1230   0.2434
 X13  C12   C  CH2   0  -0.415   -3.9708   0.6115  -0.3285
 X13  C13   C  CH2   0  -0.416   -5.1823  -0.0709   0.2941
 X13  C14   C  CH2   0  -0.417   -6.4984   0.4085  -0.3031
 X13  C15   C  CH2   0  -0.475   -7.7119  -0.2925   0.3023
 X13  C16   C  CH2   0  -0.304   -8.9662   0.1785  -0.4078
 X13  N1    N  NT    1  -0.385  -10.2642  -0.3925   0.1009
 X13  C19   C  CH3   0  -0.552  -10.2503  -1.8796   0.0524
 X13  S18   S  S2    0  -0.035    7.7064   0.9605   0.6150
 X13  S19   S  S     0   1.101    8.2561  -0.9198  -0.0941
 X13  O1    O  OS    0  -0.650    9.2419  -1.3861   0.8703
 X13  O2    O  OS    0  -0.634    7.0753  -1.7283  -0.3639
 X13  C20   C  CH3   0  -0.788    9.0701  -0.5915  -1.6404
 X13  C17   C  CH3   0  -0.548  -10.5284   0.0575   1.4950
 X13  C18   C  CH3   0  -0.546  -11.3569   0.1082  -0.7792
 X13  H41C  H  HCH2  0   0.288    6.2940   0.9657  -1.3481
 X13  H42C  H  HCH2  0   0.303    6.1226   2.3847  -0.3394
 X13  H51C  H  HCH2  0   0.238    5.0021  -0.3835   0.3357
 X13  H52C  H  HCH2  0   0.232    4.8838   1.0205   1.3785
 X13  H61C  H  HCH2  0   0.216    3.5679   2.2283  -0.3426
 X13  H62C  H  HCH2  0   0.218    3.7253   0.8783  -1.4477
 X13  H71C  H  HCH2  0   0.212    2.4904  -0.5914   0.1272
 X13  H72C  H  HCH2  0   0.211    2.3875   0.7075   1.2940
 X13  H81C  H  HCH2  0   0.208    1.0320   2.0569  -0.3104
 X13  H82C  H  HCH2  0   0.209    1.1341   0.7693  -1.4915
 X13  H91C  H  HCH2  0   0.207   -0.0404  -0.7776   0.0762
 X13  H92C  H  HCH2  0   0.207   -0.1120   0.4854   1.2836
 X13  H101  H  HCH2  0   0.207   -1.5091   1.8810  -0.2517
 X13  H102  H  HCH2  0   0.207   -1.4385   0.6227  -1.4655
 X13  H111  H  HCH2  0   0.208   -2.5706  -0.9615   0.1058
 X13  H112  H  HCH2  0   0.208   -2.6342   0.2903   1.3262
 X13  H121  H  HCH2  0   0.210   -4.0509   1.6949  -0.1872
 X13  H122  H  HCH2  0   0.209   -3.9813   0.4472  -1.4117
 X13  H131  H  HCH2  0   0.214   -5.0976  -1.1546   0.1602
 X13  H132  H  HCH2  0   0.215   -5.1849   0.1028   1.3754
 X13  H141  H  HCH2  0   0.227   -6.5925   1.4898  -0.1625
 X13  H142  H  HCH2  0   0.225   -6.4854   0.2399  -1.3849
 X13  H151  H  HCH2  0   0.251   -7.5881  -1.3723   0.1929
 X13  H152  H  HCH2  0   0.253   -7.7584  -0.0776   1.3722
 X13  H161  H  HCH2  0   0.296   -9.0663   1.2617  -0.3323
 X13  H162  H  HCH2  0   0.298   -8.9169  -0.0780  -1.4667
 X13  H171  H  HCH3  0   0.294  -10.5382   1.1440   1.5223
 X13  H172  H  HCH3  0   0.296  -11.4939  -0.3262   1.8124
 X13  H173  H  HCH3  0   0.295   -9.7563  -0.3212   2.1573
 X13  H181  H  HCH3  0   0.296  -11.1812  -0.2336  -1.7957
 X13  H182  H  HCH3  0   0.294  -12.3081  -0.2767  -0.4221
 X13  H183  H  HCH3  0   0.295  -11.3654   1.1947  -0.7525
 X13  H191  H  HCH3  0   0.295   -9.5286  -2.2662   0.7648
 X13  H192  H  HCH3  0   0.298  -11.2398  -2.2484   0.3098
 X13  H193  H  HCH3  0   0.296   -9.9887  -2.2043  -0.9516
 X13  H201  H  HCH3  0   0.302    9.9255   0.0533  -1.4597
 X13  H202  H  HCH3  0   0.317    9.3938  -1.5508  -2.0435
 X13  H203  H  HCH3  0   0.297    8.3719  -0.1180  -2.3264

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
 X13  C4   C5    single  1.518  0.020  1.518
 X13  C4   S18   single  1.825  0.020  1.825
 X13  C5   C6    single  1.525  0.020  1.525
 X13  C6   C7    single  1.523  0.020  1.523
 X13  C7   C8    single  1.523  0.020  1.523
 X13  C8   C9    single  1.524  0.020  1.524
 X13  C9   C10   single  1.523  0.020  1.523
 X13  C10  C11   single  1.524  0.020  1.524
 X13  C11  C12   single  1.523  0.020  1.523
 X13  C12  C13   single  1.523  0.020  1.523
 X13  C13  C14   single  1.523  0.020  1.523
 X13  C14  C15   single  1.527  0.020  1.527
 X13  C15  C16   single  1.516  0.020  1.516
 X13  C16  N1    single  1.507  0.020  1.507
 X13  N1   C17   single  1.488  0.020  1.488
 X13  N1   C18   single  1.490  0.020  1.490
 X13  N1   C19   single  1.488  0.020  1.488
 X13  C4   H41C  single  0.970  0.020  1.090
 X13  C4   H42C  single  0.970  0.020  1.090
 X13  C5   H51C  single  0.970  0.020  1.090
 X13  C5   H52C  single  0.970  0.020  1.090
 X13  C6   H61C  single  0.970  0.020  1.090
 X13  C6   H62C  single  0.970  0.020  1.090
 X13  C7   H71C  single  0.970  0.020  1.090
 X13  C7   H72C  single  0.970  0.020  1.090
 X13  C8   H81C  single  0.970  0.020  1.090
 X13  C8   H82C  single  0.970  0.020  1.090
 X13  C9   H91C  single  0.970  0.020  1.090
 X13  C9   H92C  single  0.970  0.020  1.090
 X13  C10  H101  single  0.970  0.020  1.090
 X13  C10  H102  single  0.970  0.020  1.090
 X13  C11  H111  single  0.970  0.020  1.090
 X13  C11  H112  single  0.970  0.020  1.090
 X13  C12  H121  single  0.970  0.020  1.090
 X13  C12  H122  single  0.970  0.020  1.090
 X13  C13  H131  single  0.970  0.020  1.090
 X13  C13  H132  single  0.970  0.020  1.090
 X13  C14  H141  single  0.970  0.020  1.090
 X13  C14  H142  single  0.970  0.020  1.090
 X13  C15  H151  single  0.970  0.020  1.090
 X13  C15  H152  single  0.970  0.020  1.090
 X13  C16  H161  single  0.970  0.020  1.090
 X13  C16  H162  single  0.970  0.020  1.090
 X13  C17  H171  single  0.970  0.020  1.090
 X13  C17  H172  single  0.970  0.020  1.090
 X13  C17  H173  single  0.970  0.020  1.090
 X13  C18  H181  single  0.970  0.020  1.090
 X13  C18  H182  single  0.970  0.020  1.090
 X13  C18  H183  single  0.970  0.020  1.090
 X13  C19  H191  single  0.970  0.020  1.090
 X13  C19  H192  single  0.970  0.020  1.090
 X13  C19  H193  single  0.970  0.020  1.090
 X13  S18  S19   single  2.083  0.020  2.083
 X13  S19  O1    double  1.456  0.020  1.456
 X13  S19  O2    double  1.456  0.020  1.456
 X13  C20  S19   single  1.778  0.020  1.778
 X13  C20  H201  single  0.970  0.020  1.090
 X13  C20  H202  single  0.970  0.020  1.090
 X13  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
 X13  H42C  C4   H41C  106.48  3.000
 X13  H42C  C4   S18   103.41  3.000
 X13  H41C  C4   S18   109.45  3.000
 X13  H42C  C4   C5    111.14  3.000
 X13  H41C  C4   C5    112.26  3.000
 X13  S18   C4   C5    113.52  3.000
 X13  H52C  C5   H51C  106.75  3.000
 X13  H52C  C5   C6    109.43  3.000
 X13  H51C  C5   C6    109.77  3.000
 X13  H52C  C5   C4    109.37  3.000
 X13  H51C  C5   C4    109.60  3.000
 X13  C6    C5   C4    111.79  3.000
 X13  H62C  C6   H61C  106.22  3.000
 X13  H62C  C6   C7    109.60  3.000
 X13  H61C  C6   C7    109.61  3.000
 X13  H62C  C6   C5    109.80  3.000
 X13  H61C  C6   C5    109.43  3.000
 X13  C7    C6   C5    112.02  3.000
 X13  H72C  C7   H71C  105.94  3.000
 X13  H72C  C7   C8    109.10  3.000
 X13  H71C  C7   C8    109.38  3.000
 X13  H72C  C7   C6    109.25  3.000
 X13  H71C  C7   C6    109.17  3.000
 X13  C8    C7   C6    113.72  3.000
 X13  H82C  C8   H81C  106.03  3.000
 X13  H82C  C8   C9    109.53  3.000
 X13  H81C  C8   C9    109.43  3.000
 X13  H82C  C8   C7    109.63  3.000
 X13  H81C  C8   C7    109.34  3.000
 X13  C9    C8   C7    112.67  3.000
 X13  H92C  C9   H91C  105.87  3.000
 X13  H92C  C9   C10   109.21  3.000
 X13  H91C  C9   C10   109.32  3.000
 X13  H92C  C9   C8    109.17  3.000
 X13  H91C  C9   C8    109.25  3.000
 X13  C10   C9   C8    113.73  3.000
 X13  H102  C10  H101  105.97  3.000
 X13  H102  C10  C11   109.38  3.000
 X13  H101  C10  C11   109.38  3.000
 X13  H102  C10  C9    109.52  3.000
 X13  H101  C10  C9    109.37  3.000
 X13  C11   C10  C9    112.99  3.000
 X13  H112  C11  H111  105.93  3.000
 X13  H112  C11  C12   109.39  3.000
 X13  H111  C11  C12   109.31  3.000
 X13  H112  C11  C10   109.28  3.000
 X13  H111  C11  C10   109.28  3.000
 X13  C12   C11  C10   113.39  3.000
 X13  H122  C12  H121  105.97  3.000
 X13  H122  C12  C13   109.22  3.000
 X13  H121  C12  C13   109.40  3.000
 X13  H122  C12  C11   109.36  3.000
 X13  H121  C12  C11   109.41  3.000
 X13  C13   C12  C11   113.22  3.000
 X13  H132  C13  H131  106.13  3.000
 X13  H132  C13  C14   109.59  3.000
 X13  H131  C13  C14   109.30  3.000
 X13  H132  C13  C12   109.54  3.000
 X13  H131  C13  C12   109.37  3.000
 X13  C14   C13  C12   112.71  3.000
 X13  H142  C14  H141  106.27  3.000
 X13  H142  C14  C15   109.30  3.000
 X13  H141  C14  C15   109.53  3.000
 X13  H142  C14  C13   109.19  3.000
 X13  H141  C14  C13   109.57  3.000
 X13  C15   C14  C13   112.77  3.000
 X13  H152  C15  H151  107.30  3.000
 X13  H152  C15  C16   111.25  3.000
 X13  H151  C15  C16   110.72  3.000
 X13  H152  C15  C14   109.39  3.000
 X13  H151  C15  C14   108.91  3.000
 X13  C16   C15  C14   109.22  3.000
 X13  H162  C16  H161  107.76  3.000
 X13  H162  C16  N1    106.12  3.000
 X13  H161  C16  N1    105.90  3.000
 X13  H162  C16  C15   110.14  3.000
 X13  H161  C16  C15   110.62  3.000
 X13  N1    C16  C15   115.90  3.000
 X13  C18   N1   C17   108.76  3.000
 X13  C18   N1   C19   108.87  3.000
 X13  C17   N1   C19   109.54  3.000
 X13  C19   N1   C16   111.08  3.000
 X13  C18   N1   C16   107.76  3.000
 X13  C17   N1   C16   110.76  3.000
 X13  H193  C19  H192  109.66  3.000
 X13  H193  C19  H191  109.87  3.000
 X13  H192  C19  H191  109.22  3.000
 X13  H193  C19  N1    109.32  3.000
 X13  H192  C19  N1    108.84  3.000
 X13  H191  C19  N1    109.92  3.000
 X13  S19   S18  C4    102.33  3.000
 X13  C20   S19  O2    108.21  3.000
 X13  C20   S19  O1    108.99  3.000
 X13  O2    S19  O1    119.60  3.000
 X13  C20   S19  S18   104.48  3.000
 X13  O2    S19  S18   110.50  3.000
 X13  O1    S19  S18   104.03  3.000
 X13  H203  C20  H202  109.92  3.000
 X13  H203  C20  H201  110.62  3.000
 X13  H202  C20  H201  110.50  3.000
 X13  H203  C20  S19   109.58  3.000
 X13  H202  C20  S19   107.16  3.000
 X13  H201  C20  S19   108.98  3.000
 X13  H173  C17  H172  109.31  3.000
 X13  H173  C17  H171  109.87  3.000
 X13  H172  C17  H171  109.74  3.000
 X13  H173  C17  N1    109.86  3.000
 X13  H172  C17  N1    108.94  3.000
 X13  H171  C17  N1    109.11  3.000
 X13  H183  C18  H182  109.83  3.000
 X13  H183  C18  H181  109.79  3.000
 X13  H182  C18  H181  109.73  3.000
 X13  H183  C18  N1    109.10  3.000
 X13  H182  C18  N1    109.20  3.000
 X13  H181  C18  N1    109.17  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
 X13  Var_01  C7    C6   C5   C4    177.31  30.0  3
 X13  Var_02  O1    S19  S18  C4   -164.56  30.0  3
 X13  Var_03  C8    C7   C6   C5    176.45  30.0  3
 X13  Var_04  S18   C4   C5   C6    173.56  30.0  1
 X13  Var_05  C9    C8   C7   C6    179.66  30.0  3
 X13  Var_06  C10   C9   C8   C7    178.15  30.0  3
 X13  Var_07  C11   C10  C9   C8    179.91  30.0  3
 X13  Var_08  C12   C11  C10  C9    179.57  30.0  3
 X13  Var_09  C13   C12  C11  C10   179.59  30.0  3
 X13  Var_10  C14   C13  C12  C11  -179.00  30.0  3
 X13  Var_11  C15   C14  C13  C12   178.97  30.0  3
 X13  Var_12  C16   C15  C14  C13  -176.44  30.0  3
 X13  Var_13  N1    C16  C15  C14  -178.29  30.0  3
 X13  Var_14  C17   N1   C16  C15    65.20  30.0  3
 X13  Var_15  H171  C17  N1   C16    57.20  30.0  3
 X13  Var_16  H181  C18  N1   C16    61.00  30.0  3
 X13  Var_17  H191  C19  N1   C16    67.27  30.0  3
 X13  Var_18  H201  C20  S19  S18    59.41  30.0  3

