# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:55:43 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: O-(hexadecylsulfonyl)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC[S](=O)(=O)OC[C@H](N)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
 S1H  S1H  O-(hexadecylsulfonyl)-L-serine  L-peptide  64  26  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_S1H
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
 S1H  N     N  NH2    0  -0.788  11.3577  16.8504  16.3754
 S1H  CA    C  CH1    0  -0.253  12.6175  16.1391  16.2938
 S1H  C     C  C      0   0.406  12.4434  14.6053  16.4836
 S1H  O     O  O      0  -0.589  11.3280  14.1950  16.8470
 S1H  CB    C  CH2    0  -0.193  13.6908  16.6408  17.2493
 S1H  OG    O  OC2    0  -0.588  13.2396  16.3349  18.5911
 S1H  OXT   O  OC    -1  -0.609  13.4676  13.9300  16.2640
 S1H  C1    C  CH2    0  -0.632  12.9458  16.4207  21.1318
 S1H  C2    C  CH2    0  -0.436  11.5393  16.9952  21.0622
 S1H  C3    C  CH2    0  -0.416  10.7091  16.5413  22.2586
 S1H  C4    C  CH2    0  -0.413   9.2889  17.0904  22.2204
 S1H  C5    C  CH2    0  -0.411   8.4404  16.6431  23.4044
 S1H  C6    C  CH2    0  -0.410   7.0217  17.1973  23.3647
 S1H  C7    C  CH2    0  -0.410   6.1544  16.7349  24.5291
 S1H  C8    C  CH2    0  -0.409   4.7366  17.2909  24.4770
 S1H  C9    C  CH2    0  -0.408   3.8477  16.8016  25.6137
 S1H  C10   C  CH2    0  -0.415   2.4307  17.3591  25.5498
 S1H  C11   C  CH2    0  -0.420   1.5274  16.8315  26.6592
 S1H  C12   C  CH2    0  -0.420   0.0835  17.3197  26.5793
 S1H  C13   C  CH2    0  -0.415  -0.0909  18.8140  26.8287
 S1H  C14   C  CH2    0  -0.402  -1.5484  19.2559  26.7915
 S1H  C15   C  CH2    0  -0.417  -1.7367  20.7429  27.0665
 S1H  C16   C  CH3    0  -0.659  -3.1951  21.1763  27.0125
 S1H  S1    S  S      0   1.456  14.0232  16.9755  19.8270
 S1H  O1S   O  OS     0  -0.659  13.9884  18.4251  19.7254
 S1H  O2S   O  OS     0  -0.654  15.3226  16.3389  19.9518
 S1H  H     H  HNH2   0   0.334  11.5179  17.8493  16.4235
 S1H  H2    H  HNH2   0   0.333  10.8727  16.5867  17.2226
 S1H  HA    H  HCH1   0   0.236  13.0393  16.2976  15.2940
 S1H  HB2   H  HCH2   0   0.239  14.6432  16.1434  17.0627
 S1H  HB3   H  HCH2   0   0.244  13.8280  17.7202  17.1454
 S1H  H11   H  HCH2   0   0.308  13.4551  16.7253  22.0501
 S1H  H12   H  HCH2   0   0.307  12.9484  15.3296  21.0969
 S1H  H21   H  HCH2   0   0.243  11.5859  18.0860  21.0454
 S1H  H22   H  HCH2   0   0.248  11.0512  16.6791  20.1379
 S1H  H31   H  HCH2   0   0.221  10.6769  15.4475  22.2871
 S1H  H32   H  HCH2   0   0.221  11.2003  16.8589  23.1840
 S1H  H41   H  HCH2   0   0.212   9.3238  18.1846  22.1914
 S1H  H42   H  HCH2   0   0.212   8.8047  16.7767  21.2895
 S1H  H51   H  HCH2   0   0.208   8.4015  15.5487  23.4286
 S1H  H52   H  HCH2   0   0.208   8.9261  16.9500  24.3371
 S1H  H61   H  HCH2   0   0.206   7.0604  18.2921  23.3535
 S1H  H62   H  HCH2   0   0.206   6.5457  16.9024  22.4229
 S1H  H71   H  HCH2   0   0.205   6.1139  15.6401  24.5368
 S1H  H72   H  HCH2   0   0.206   6.6260  17.0268  25.4739
 S1H  H81   H  HCH2   0   0.205   4.7757  18.3856  24.4922
 S1H  H82   H  HCH2   0   0.205   4.2778  17.0187  23.5199
 S1H  H91   H  HCH2   0   0.204   3.8078  15.7069  25.5951
 S1H  H92   H  HCH2   0   0.205   4.3012  17.0710  26.5741
 S1H  H101  H  HCH2   0   0.211   2.4756  18.4519  25.5882
 S1H  H102  H  HCH2   0   0.203   1.9882  17.1088  24.5787
 S1H  H111  H  HCH2   0   0.214   1.5347  15.7373  26.6253
 S1H  H112  H  HCH2   0   0.205   1.9487  17.1042  27.6334
 S1H  H121  H  HCH2   0   0.204  -0.3317  17.0653  25.5976
 S1H  H122  H  HCH2   0   0.214  -0.5179  16.7708  27.3111
 S1H  H131  H  HCH2   0   0.204   0.3411  19.0674  27.8035
 S1H  H132  H  HCH2   0   0.211   0.4747  19.3885  26.0887
 S1H  H141  H  HCH2   0   0.205  -1.9755  19.0125  25.8123
 S1H  H142  H  HCH2   0   0.204  -2.1228  18.6768  27.5232
 S1H  H151  H  HCH2   0   0.209  -1.3178  20.9830  28.0487
 S1H  H152  H  HCH2   0   0.208  -1.1557  21.3205  26.3409
 S1H  H161  H  HCH3   0   0.224  -3.3062  22.2426  27.2126
 S1H  H162  H  HCH3   0   0.214  -3.6273  20.9782  26.0300
 S1H  H163  H  HCH3   0   0.214  -3.7943  20.6378  27.7490

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
 S1H  N    CA    single  1.458  0.019  1.458
 S1H  N    H     single  0.860  0.020  0.860
 S1H  N    H2    single  0.890  0.020  1.040
 S1H  CA   C     single  1.525  0.021  1.525
 S1H  CA   CB    single  1.530  0.020  1.530
 S1H  CA   HA    single  0.970  0.020  0.970
 S1H  C    O     deloc   1.231  0.020  1.231
 S1H  C    OXT   deloc   1.246  0.020  1.246
 S1H  CB   OG    single  1.448  0.020  1.448
 S1H  CB   HB2   single  0.970  0.020  1.090
 S1H  CB   HB3   single  0.970  0.020  1.090
 S1H  OG   S1    single  1.597  0.020  1.597
 S1H  C1   C2    single  1.521  0.020  1.521
 S1H  C1   S1    single  1.781  0.020  1.781
 S1H  C1   H11   single  0.970  0.020  1.090
 S1H  C1   H12   single  0.970  0.020  1.090
 S1H  C2   C3    single  1.525  0.020  1.525
 S1H  C2   H21   single  0.970  0.020  1.090
 S1H  C2   H22   single  0.970  0.020  1.090
 S1H  C3   C4    single  1.523  0.020  1.523
 S1H  C3   H31   single  0.970  0.020  1.090
 S1H  C3   H32   single  0.970  0.020  1.090
 S1H  C4   C5    single  1.524  0.020  1.524
 S1H  C4   H41   single  0.970  0.020  1.090
 S1H  C4   H42   single  0.970  0.020  1.090
 S1H  C5   C6    single  1.524  0.020  1.524
 S1H  C5   H51   single  0.970  0.020  1.090
 S1H  C5   H52   single  0.970  0.020  1.090
 S1H  C6   C7    single  1.524  0.020  1.524
 S1H  C6   H61   single  0.970  0.020  1.090
 S1H  C6   H62   single  0.970  0.020  1.090
 S1H  C7   C8    single  1.524  0.020  1.524
 S1H  C7   H71   single  0.970  0.020  1.090
 S1H  C7   H72   single  0.970  0.020  1.090
 S1H  C8   C9    single  1.524  0.020  1.524
 S1H  C8   H81   single  0.970  0.020  1.090
 S1H  C8   H82   single  0.970  0.020  1.090
 S1H  C9   C10   single  1.524  0.020  1.524
 S1H  C9   H91   single  0.970  0.020  1.090
 S1H  C9   H92   single  0.970  0.020  1.090
 S1H  C10  C11   single  1.525  0.020  1.525
 S1H  C10  H101  single  0.970  0.020  1.090
 S1H  C10  H102  single  0.970  0.020  1.090
 S1H  C11  C12   single  1.526  0.020  1.526
 S1H  C11  H111  single  0.970  0.020  1.090
 S1H  C11  H112  single  0.970  0.020  1.090
 S1H  C12  C13   single  1.525  0.020  1.525
 S1H  C12  H121  single  0.970  0.020  1.090
 S1H  C12  H122  single  0.970  0.020  1.090
 S1H  C13  C14   single  1.524  0.020  1.524
 S1H  C13  H131  single  0.970  0.020  1.090
 S1H  C13  H132  single  0.970  0.020  1.090
 S1H  C14  C15   single  1.524  0.020  1.524
 S1H  C14  H141  single  0.970  0.020  1.090
 S1H  C14  H142  single  0.970  0.020  1.090
 S1H  C15  C16   single  1.522  0.020  1.522
 S1H  C15  H151  single  0.970  0.020  1.090
 S1H  C15  H152  single  0.970  0.020  1.090
 S1H  C16  H161  single  0.970  0.020  1.090
 S1H  C16  H162  single  0.970  0.020  1.090
 S1H  C16  H163  single  0.970  0.020  1.090
 S1H  S1   O1S   deloc   1.454  0.020  1.454
 S1H  S1   O2S   deloc   1.452  0.020  1.452

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
 S1H  H2    N    H     107.05  3.000
 S1H  H2    N    CA    109.65  3.000
 S1H  H     N    CA    114.00  3.000
 S1H  HA    CA   CB    109.00  3.000
 S1H  HA    CA   C     109.00  3.000
 S1H  CB    CA   C     110.10  1.900
 S1H  HA    CA   N     110.00  3.000
 S1H  CB    CA   N     110.50  1.700
 S1H  C     CA   N     111.00  2.800
 S1H  OXT   C    O     127.61  3.000
 S1H  OXT   C    CA    114.89  3.000
 S1H  O     C    CA    120.80  1.700
 S1H  HB3   CB   HB2   108.94  3.000
 S1H  HB3   CB   OG    109.62  3.000
 S1H  HB2   CB   OG    109.53  3.000
 S1H  HB3   CB   CA    110.75  3.000
 S1H  HB2   CB   CA    110.98  3.000
 S1H  OG    CB   CA    106.99  3.000
 S1H  S1    OG   CB    118.63  3.000
 S1H  H12   C1   H11   107.70  3.000
 S1H  H12   C1   S1    106.66  3.000
 S1H  H11   C1   S1    104.29  3.000
 S1H  H12   C1   C2    112.23  3.000
 S1H  H11   C1   C2    111.34  3.000
 S1H  S1    C1   C2    114.10  3.000
 S1H  H22   C2   H21   107.17  3.000
 S1H  H22   C2   C3    109.54  3.000
 S1H  H21   C2   C3    109.42  3.000
 S1H  H22   C2   C1    110.04  3.000
 S1H  H21   C2   C1    109.80  3.000
 S1H  C3    C2   C1    110.79  3.000
 S1H  H32   C3   H31   106.33  3.000
 S1H  H32   C3   C4    109.57  3.000
 S1H  H31   C3   C4    109.48  3.000
 S1H  H32   C3   C2    109.42  3.000
 S1H  H31   C3   C2    109.50  3.000
 S1H  C4    C3   C2    112.36  3.000
 S1H  H42   C4   H41   106.12  3.000
 S1H  H42   C4   C5    109.28  3.000
 S1H  H41   C4   C5    109.37  3.000
 S1H  H42   C4   C3    109.28  3.000
 S1H  H41   C4   C3    109.34  3.000
 S1H  C5    C4   C3    113.20  3.000
 S1H  H52   C5   H51   106.07  3.000
 S1H  H52   C5   C6    109.46  3.000
 S1H  H51   C5   C6    109.33  3.000
 S1H  H52   C5   C4    109.41  3.000
 S1H  H51   C5   C4    109.28  3.000
 S1H  C6    C5   C4    113.04  3.000
 S1H  H62   C6   H61   106.00  3.000
 S1H  H62   C6   C7    109.14  3.000
 S1H  H61   C6   C7    109.34  3.000
 S1H  H62   C6   C5    109.21  3.000
 S1H  H61   C6   C5    109.32  3.000
 S1H  C7    C6   C5    113.55  3.000
 S1H  H72   C7   H71   106.03  3.000
 S1H  H72   C7   C8    109.43  3.000
 S1H  H71   C7   C8    109.30  3.000
 S1H  H72   C7   C6    109.46  3.000
 S1H  H71   C7   C6    109.25  3.000
 S1H  C8    C7   C6    113.12  3.000
 S1H  H82   C8   H81   105.98  3.000
 S1H  H82   C8   C9    109.12  3.000
 S1H  H81   C8   C9    109.35  3.000
 S1H  H82   C8   C7    109.20  3.000
 S1H  H81   C8   C7    109.33  3.000
 S1H  C9    C8   C7    113.59  3.000
 S1H  H92   C9   H91   106.00  3.000
 S1H  H92   C9   C10   109.37  3.000
 S1H  H91   C9   C10   109.33  3.000
 S1H  H92   C9   C8    109.48  3.000
 S1H  H91   C9   C8    109.23  3.000
 S1H  C10   C9   C8    113.18  3.000
 S1H  H102  C10  H101  106.01  3.000
 S1H  H102  C10  C11   109.05  3.000
 S1H  H101  C10  C11   110.14  3.000
 S1H  H102  C10  C9    109.21  3.000
 S1H  H101  C10  C9    109.00  3.000
 S1H  C11   C10  C9    113.18  3.000
 S1H  H112  C11  H111  105.88  3.000
 S1H  H112  C11  C12   109.30  3.000
 S1H  H111  C11  C12   108.93  3.000
 S1H  H112  C11  C10   109.45  3.000
 S1H  H111  C11  C10   108.63  3.000
 S1H  C12   C11  C10   114.31  3.000
 S1H  H122  C12  H121  105.92  3.000
 S1H  H122  C12  C13   108.61  3.000
 S1H  H121  C12  C13   109.31  3.000
 S1H  H122  C12  C11   108.92  3.000
 S1H  H121  C12  C11   109.33  3.000
 S1H  C13   C12  C11   114.40  3.000
 S1H  H132  C13  H131  106.04  3.000
 S1H  H132  C13  C14   109.00  3.000
 S1H  H131  C13  C14   109.38  3.000
 S1H  H132  C13  C12   110.16  3.000
 S1H  H131  C13  C12   109.09  3.000
 S1H  C14   C13  C12   112.93  3.000
 S1H  H142  C14  H141  105.96  3.000
 S1H  H142  C14  C15   109.30  3.000
 S1H  H141  C14  C15   109.27  3.000
 S1H  H142  C14  C13   109.38  3.000
 S1H  H141  C14  C13   109.29  3.000
 S1H  C15   C14  C13   113.38  3.000
 S1H  H152  C15  H151  106.03  3.000
 S1H  H152  C15  C16   109.55  3.000
 S1H  H151  C15  C16   109.64  3.000
 S1H  H152  C15  C14   109.25  3.000
 S1H  H151  C15  C14   109.19  3.000
 S1H  C16   C15  C14   112.94  3.000
 S1H  H163  C16  H162  107.48  3.000
 S1H  H163  C16  H161  107.62  3.000
 S1H  H162  C16  H161  107.59  3.000
 S1H  H163  C16  C15   111.19  3.000
 S1H  H162  C16  C15   111.08  3.000
 S1H  H161  C16  C15   111.69  3.000
 S1H  O2S   S1   O1S   117.68  3.000
 S1H  O2S   S1   C1    109.99  3.000
 S1H  O1S   S1   C1    110.33  3.000
 S1H  O2S   S1   OG    109.24  3.000
 S1H  O1S   S1   OG    109.52  3.000
 S1H  C1    S1   OG     98.34  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
 S1H  Var_01  C1    S1   OG   CB    173.96  30.0  3
 S1H  Var_02  C2    C1   S1   OG    -63.94  30.0  2
 S1H  Var_03  C4    C3   C2   C1   -179.66  30.0  3
 S1H  Var_04  C5    C4   C3   C2    179.73  30.0  3
 S1H  Var_05  S1    C1   C2   C3   -176.48  30.0  1
 S1H  Var_06  C6    C5   C4   C3    179.85  30.0  3
 S1H  Var_07  C7    C6   C5   C4    178.86  30.0  3
 S1H  Var_08  C8    C7   C6   C5   -179.80  30.0  3
 S1H  Var_09  C9    C8   C7   C6    178.26  30.0  3
 S1H  Var_10  C10   C9   C8   C7   -179.79  30.0  3
 S1H  Var_11  C11   C10  C9   C8    177.99  30.0  3
 S1H  Var_12  C12   C11  C10  C9   -177.13  30.0  3
 S1H  Var_13  C13   C12  C11  C10   -67.15  30.0  3
 S1H  Var_14  C14   C13  C12  C11  -177.90  30.0  3
 S1H  Var_15  C15   C14  C13  C12   178.88  30.0  3
 S1H  Var_16  C16   C15  C14  C13   179.40  30.0  3
 S1H  Var_17  H161  C16  C15  C14   179.97  30.0  3
 S1H  Var_18  HB2   CB   OG   S1     70.71  30.0  1

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
 S1H  chir_01  CA  N  C  CB  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
 S1H  plan-1  CA   0.020
 S1H  plan-1  C    0.020
 S1H  plan-1  O    0.020
 S1H  plan-1  OXT  0.020

