# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 01:10:41 2022
#   Inital geometry file: a 159 line input string
#   Ligand name: 3-{3-[(3R)-3,4-dihydroxybutyl]-1-(8-phenyloctyl)-1H-imidazol-3-ium-5-yl}-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[n+](CC[C@@H](O)CO)cn1CCCCCCCCc2ccccc2)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
 2SO  2SO  3-{3-[(3R)-3,4-dihydroxybutyl]-1-(8-phenyloctyl)-1H-imidazol-3-ium-5-yl}-L-alanine  L-peptide  68  31  .  2016-04-22  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_2SO
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
 2SO  C     C  C      0   0.421  10.5045  13.1710  14.2748
 2SO  CA    C  CH1    0  -0.218  10.6663  13.0255  12.7368
 2SO  CB    C  CH2    0  -0.518  12.1520  12.9946  12.3478
 2SO  C12   C  CR5    0   0.305  12.8586  14.2500  12.7173
 2SO  C13   C  CR15   0  -0.112  13.4151  14.6073  13.9052
 2SO  N14   N  NR5    1  -0.434  13.9050  15.8814  13.7749
 2SO  C15   C  CR15   0   0.258  13.6606  16.2975  12.5431
 2SO  N16   N  NR5    0  -0.461  13.0237  15.3370  11.8866
 2SO  C17   C  CH2    0  -0.329  12.6449  15.4288  10.4808
 2SO  C18   C  CH2    0  -0.430  13.7155  14.8691   9.5586
 2SO  C19   C  CH2    0  -0.419  13.2847  14.9512   8.1000
 2SO  C20   C  CH2    0  -0.419  14.3860  14.5200   7.1402
 2SO  C21   C  CH2    0  -0.418  13.9492  14.5699   5.6806
 2SO  C22   C  CH2    0  -0.419  15.0691  14.2954   4.6806
 2SO  C23   C  CH2    0  -0.429  15.6540  12.8916   4.7693
 2SO  C24   C  CH2    0  -0.506  16.7352  12.6149   3.7200
 2SO  C25   C  CR6    0   0.129  16.2211  12.6666   2.3069
 2SO  C26   C  CR16   0  -0.302  15.3527  11.6820   1.8349
 2SO  C27   C  CR16   0  -0.239  14.8548  11.7284   0.5408
 2SO  C28   C  CR16   0  -0.274  15.2184  12.7647  -0.3114
 2SO  C29   C  CR16   0  -0.239  16.0833  13.7495   0.1444
 2SO  C30   C  CR16   0  -0.312  16.5778  13.6983   1.4424
 2SO  N     N  NH2    0  -0.810   9.9775  14.0835  12.0210
 2SO  O     O  O      0  -0.588   9.6466  13.9774  14.6797
 2SO  CCA   C  CH2    0  -0.251  14.6209  16.6023  14.8271
 2SO  OXT   O  OC    -1  -0.602  11.2385  12.4412  14.9695
 2SO  HA    H  HCH1   0   0.227  10.2660  12.0312  12.4854
 2SO  HB2   H  HCH2   0   0.262  12.6422  12.1618  12.8489
 2SO  HB3   H  HCH2   0   0.259  12.2496  12.8091  11.2759
 2SO  H13   H  HCR5   0   0.316  13.4803  14.0597  14.8291
 2SO  H15   H  HCR5   0   0.352  13.9240  17.2541  12.1241
 2SO  H17   H  HCH2   0   0.285  11.6950  14.9101  10.3701
 2SO  H17A  H  HCH2   0   0.280  12.4637  16.4814  10.2633
 2SO  H18   H  HCH2   0   0.234  14.6445  15.4282   9.7037
 2SO  H18A  H  HCH2   0   0.238  13.9286  13.8294   9.8230
 2SO  H19   H  HCH2   0   0.221  12.3979  14.3277   7.9471
 2SO  H19A  H  HCH2   0   0.219  12.9814  15.9768   7.8649
 2SO  H20   H  HCH2   0   0.210  15.2576  15.1694   7.2780
 2SO  H20A  H  HCH2   0   0.218  14.7156  13.5100   7.4016
 2SO  H21   H  HCH2   0   0.209  13.1343  13.8559   5.5195
 2SO  H21A  H  HCH2   0   0.217  13.5298  15.5592   5.4715
 2SO  H22   H  HCH2   0   0.223  14.6834  14.4622   3.6708
 2SO  H22A  H  HCH2   0   0.207  15.8690  15.0306   4.8243
 2SO  H23   H  HCH2   0   0.229  16.0916  12.7283   5.7575
 2SO  H23A  H  HCH2   0   0.215  14.8517  12.1531   4.6666
 2SO  H24   H  HCH2   0   0.235  17.5476  13.3367   3.8403
 2SO  H24A  H  HCH2   0   0.244  17.1664  11.6288   3.9127
 2SO  H26   H  HCR6   0   0.244  15.0637  10.8664   2.4887
 2SO  H27   H  HCR6   0   0.249  14.1840  10.9522   0.1944
 2SO  H28   H  HCR6   0   0.249  14.8314  12.8016  -1.3216
 2SO  H29   H  HCR6   0   0.249  16.3746  14.5613  -0.5102
 2SO  H30   H  HCR6   0   0.244  17.2512  14.4736   1.7893
 2SO  H     H  HNH2   0   0.339   9.5589  13.7270  11.1731
 2SO  H2    H  HNH2   0   0.342   9.2306  14.4271  12.6110
 2SO  C32   C  CH2    0  -0.512  14.6421  18.1036  14.6015
 2SO  C33   C  CH1    0   0.019  15.2920  18.8317  15.7675
 2SO  C34   C  CH2    0  -0.160  15.2452  20.3339  15.5417
 2SO  O3    O  OH1    0  -0.671  15.8750  20.9557  16.6397
 2SO  O4    O  OH1    0  -0.670  16.6196  18.3729  15.8854
 2SO  HCA   H  HCH2   0   0.276  14.1165  16.3674  15.7643
 2SO  HCAA  H  HCH2   0   0.285  15.6303  16.1972  14.8792
 2SO  H32   H  HCH2   0   0.253  15.1866  18.3515  13.6857
 2SO  H33   H  HCH2   0   0.262  13.6193  18.4718  14.4873
 2SO  H34   H  HCH1   0   0.209  14.7207  18.6043  16.6818
 2SO  H35   H  HCH2   0   0.203  15.7518  20.5714  14.5976
 2SO  H36   H  HCH2   0   0.198  14.1989  20.6497  15.4396
 2SO  H37   H  HOH1   0   0.459  16.1055  21.8560  16.3950
 2SO  H38   H  HOH1   0   0.448  17.0592  18.9156  16.5489

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
 2SO  C    CA    single    1.525  0.021  1.525
 2SO  C    O     deloc     1.231  0.020  1.231
 2SO  C    OXT   deloc     1.247  0.020  1.247
 2SO  CA   CB    single    1.530  0.020  1.530
 2SO  CA   N     single    1.458  0.019  1.458
 2SO  CA   HA    single    0.970  0.020  0.970
 2SO  CB   C12   single    1.487  0.020  1.487
 2SO  CB   HB2   single    0.970  0.020  1.090
 2SO  CB   HB3   single    0.970  0.020  1.090
 2SO  C12  C13   aromatic  1.360  0.020  1.360
 2SO  C12  N16   aromatic  1.378  0.020  1.378
 2SO  C13  N14   aromatic  1.371  0.020  1.371
 2SO  C13  H13   single    0.930  0.020  1.080
 2SO  N14  C15   aromatic  1.323  0.020  1.323
 2SO  N14  CCA   single    1.463  0.020  1.463
 2SO  C15  N16   aromatic  1.326  0.020  1.326
 2SO  C15  H15   single    0.930  0.020  1.080
 2SO  N16  C17   single    1.459  0.020  1.459
 2SO  C17  C18   single    1.520  0.020  1.520
 2SO  C17  H17   single    0.970  0.020  1.090
 2SO  C17  H17A  single    0.970  0.020  1.090
 2SO  C18  C19   single    1.523  0.020  1.523
 2SO  C18  H18   single    0.970  0.020  1.090
 2SO  C18  H18A  single    0.970  0.020  1.090
 2SO  C19  C20   single    1.523  0.020  1.523
 2SO  C19  H19   single    0.970  0.020  1.090
 2SO  C19  H19A  single    0.970  0.020  1.090
 2SO  C20  C21   single    1.524  0.020  1.524
 2SO  C20  H20   single    0.970  0.020  1.090
 2SO  C20  H20A  single    0.970  0.020  1.090
 2SO  C21  C22   single    1.526  0.020  1.526
 2SO  C21  H21   single    0.970  0.020  1.090
 2SO  C21  H21A  single    0.970  0.020  1.090
 2SO  C22  C23   single    1.523  0.020  1.523
 2SO  C22  H22   single    0.970  0.020  1.090
 2SO  C22  H22A  single    0.970  0.020  1.090
 2SO  C23  C24   single    1.532  0.020  1.532
 2SO  C23  H23   single    0.970  0.020  1.090
 2SO  C23  H23A  single    0.970  0.020  1.090
 2SO  C24  C25   single    1.505  0.020  1.505
 2SO  C24  H24   single    0.970  0.020  1.090
 2SO  C24  H24A  single    0.970  0.020  1.090
 2SO  C25  C26   aromatic  1.395  0.020  1.395
 2SO  C25  C30   aromatic  1.392  0.020  1.392
 2SO  C26  C27   aromatic  1.387  0.020  1.387
 2SO  C26  H26   single    0.930  0.020  1.080
 2SO  C27  C28   aromatic  1.390  0.020  1.390
 2SO  C27  H27   single    0.930  0.020  1.080
 2SO  C28  C29   aromatic  1.388  0.020  1.388
 2SO  C28  H28   single    0.930  0.020  1.080
 2SO  C29  C30   aromatic  1.390  0.020  1.390
 2SO  C29  H29   single    0.930  0.020  1.080
 2SO  C30  H30   single    0.930  0.020  1.080
 2SO  N    H     single    0.860  0.020  0.860
 2SO  N    H2    single    0.890  0.020  1.040
 2SO  CCA  C32   single    1.518  0.020  1.518
 2SO  C32  C33   single    1.520  0.020  1.520
 2SO  C33  C34   single    1.520  0.020  1.520
 2SO  C34  O3    single    1.410  0.020  1.410
 2SO  C33  O4    single    1.410  0.020  1.410
 2SO  CCA  HCA   single    0.970  0.020  1.090
 2SO  CCA  HCAA  single    0.970  0.020  1.090
 2SO  C32  H32   single    0.970  0.020  1.090
 2SO  C32  H33   single    0.970  0.020  1.090
 2SO  C33  H34   single    0.970  0.020  1.090
 2SO  C34  H35   single    0.970  0.020  1.090
 2SO  C34  H36   single    0.970  0.020  1.090
 2SO  O3   H37   single    0.850  0.020  0.980
 2SO  O4   H38   single    0.850  0.020  0.980

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
 2SO  OXT   C    O    127.13  3.000
 2SO  OXT   C    CA   115.82  3.000
 2SO  O     C    CA   120.80  1.700
 2SO  HA    CA   N    110.00  3.000
 2SO  HA    CA   CB   109.00  3.000
 2SO  N     CA   CB   110.50  1.700
 2SO  HA    CA   C    109.00  3.000
 2SO  N     CA   C    111.00  2.800
 2SO  CB    CA   C    110.10  1.900
 2SO  HB3   CB   HB2  106.35  3.000
 2SO  HB3   CB   C12  110.17  3.000
 2SO  HB2   CB   C12  108.51  3.000
 2SO  HB3   CB   CA   109.78  3.000
 2SO  HB2   CB   CA   109.53  3.000
 2SO  C12   CB   CA   112.31  3.000
 2SO  N16   C12  C13  105.69  3.000
 2SO  N16   C12  CB   124.96  3.000
 2SO  C13   C12  CB   129.30  3.000
 2SO  H13   C13  N14  122.20  3.000
 2SO  H13   C13  C12  129.89  3.000
 2SO  N14   C13  C12  107.90  3.000
 2SO  CCA   N14  C15  127.24  3.000
 2SO  CCA   N14  C13  124.36  3.000
 2SO  C15   N14  C13  108.35  3.000
 2SO  H15   C15  N16  124.61  3.000
 2SO  H15   C15  N14  126.62  3.000
 2SO  N16   C15  N14  108.77  3.000
 2SO  C17   N16  C15  123.78  3.000
 2SO  C17   N16  C12  126.84  3.000
 2SO  C15   N16  C12  109.29  3.000
 2SO  H17A  C17  H17  107.16  3.000
 2SO  H17A  C17  C18  110.59  3.000
 2SO  H17   C17  C18  112.19  3.000
 2SO  H17A  C17  N16  107.23  3.000
 2SO  H17   C17  N16  107.14  3.000
 2SO  C18   C17  N16  112.25  3.000
 2SO  H18A  C18  H18  106.76  3.000
 2SO  H18A  C18  C19  109.74  3.000
 2SO  H18   C18  C19  109.86  3.000
 2SO  H18A  C18  C17  109.92  3.000
 2SO  H18   C18  C17  109.24  3.000
 2SO  C19   C18  C17  111.22  3.000
 2SO  H19A  C19  H19  106.20  3.000
 2SO  H19A  C19  C20  109.28  3.000
 2SO  H19   C19  C20  109.66  3.000
 2SO  H19A  C19  C18  109.53  3.000
 2SO  H19   C19  C18  109.40  3.000
 2SO  C20   C19  C18  112.56  3.000
 2SO  H20A  C20  H20  106.11  3.000
 2SO  H20A  C20  C21  110.20  3.000
 2SO  H20   C20  C21  109.21  3.000
 2SO  H20A  C20  C19  109.18  3.000
 2SO  H20   C20  C19  109.16  3.000
 2SO  C21   C20  C19  112.76  3.000
 2SO  H21A  C21  H21  106.02  3.000
 2SO  H21A  C21  C22  108.57  3.000
 2SO  H21   C21  C22  109.41  3.000
 2SO  H21A  C21  C20  108.80  3.000
 2SO  H21   C21  C20  109.43  3.000
 2SO  C22   C21  C20  114.28  3.000
 2SO  H22A  C22  H22  106.03  3.000
 2SO  H22A  C22  C23  109.29  3.000
 2SO  H22   C22  C23  109.25  3.000
 2SO  H22A  C22  C21  109.21  3.000
 2SO  H22   C22  C21  108.58  3.000
 2SO  C23   C22  C21  114.16  3.000
 2SO  H23A  C23  H23  106.10  3.000
 2SO  H23A  C23  C24  109.33  3.000
 2SO  H23   C23  C24  108.04  3.000
 2SO  H23A  C23  C22  109.55  3.000
 2SO  H23   C23  C22  110.12  3.000
 2SO  C24   C23  C22  113.43  3.000
 2SO  H24A  C24  H24  106.43  3.000
 2SO  H24A  C24  C25  109.34  3.000
 2SO  H24   C24  C25  109.55  3.000
 2SO  H24A  C24  C23  108.70  3.000
 2SO  H24   C24  C23  109.26  3.000
 2SO  C25   C24  C23  113.33  3.000
 2SO  C30   C25  C26  118.18  3.000
 2SO  C30   C25  C24  121.40  3.000
 2SO  C26   C25  C24  120.41  3.000
 2SO  H26   C26  C27  119.47  3.000
 2SO  H26   C26  C25  119.51  3.000
 2SO  C27   C26  C25  121.02  3.000
 2SO  H27   C27  C28  120.03  3.000
 2SO  H27   C27  C26  119.78  3.000
 2SO  C28   C27  C26  120.19  3.000
 2SO  H28   C28  C29  120.34  3.000
 2SO  H28   C28  C27  120.27  3.000
 2SO  C29   C28  C27  119.39  3.000
 2SO  H29   C29  C30  119.77  3.000
 2SO  H29   C29  C28  120.08  3.000
 2SO  C30   C29  C28  120.15  3.000
 2SO  H30   C30  C29  119.57  3.000
 2SO  H30   C30  C25  119.37  3.000
 2SO  C29   C30  C25  121.06  3.000
 2SO  H2    N    H    107.65  3.000
 2SO  H2    N    CA   108.08  3.000
 2SO  H     N    CA   114.00  3.000
 2SO  HCAA  CCA  HCA  107.92  3.000
 2SO  HCAA  CCA  C32  111.22  3.000
 2SO  HCA   CCA  C32  110.32  3.000
 2SO  HCAA  CCA  N14  107.75  3.000
 2SO  HCA   CCA  N14  106.61  3.000
 2SO  C32   CCA  N14  112.79  3.000
 2SO  H33   C32  H32  107.57  3.000
 2SO  H33   C32  C33  108.59  3.000
 2SO  H32   C32  C33  108.71  3.000
 2SO  H33   C32  CCA  109.60  3.000
 2SO  H32   C32  CCA  110.82  3.000
 2SO  C33   C32  CCA  111.44  3.000
 2SO  H34   C33  O4   110.60  3.000
 2SO  H34   C33  C34  108.14  3.000
 2SO  O4    C33  C34  111.29  3.000
 2SO  H34   C33  C32  108.42  3.000
 2SO  O4    C33  C32  108.11  3.000
 2SO  C34   C33  C32  110.26  3.000
 2SO  H36   C34  H35  107.32  3.000
 2SO  H36   C34  O3   111.79  3.000
 2SO  H35   C34  O3   111.61  3.000
 2SO  H36   C34  C33  109.12  3.000
 2SO  H35   C34  C33  109.12  3.000
 2SO  O3    C34  C33  107.84  3.000
 2SO  H37   O3   C34  108.78  3.000
 2SO  H38   O4   C33  107.70  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
 2SO  CONST_01  C15  N14  C13  C12     0.00   0.0  0
 2SO  CONST_02  N14  C15  N16  C12     0.00   0.0  0
 2SO  CONST_03  C15  N16  C12  C13     0.00   0.0  0
 2SO  CONST_04  N16  C15  N14  C13     0.00   0.0  0
 2SO  CONST_05  N16  C12  C13  N14     0.00   0.0  0
 2SO  CONST_06  C28  C27  C26  C25     0.00   0.0  0
 2SO  CONST_07  C28  C29  C30  C25     0.00   0.0  0
 2SO  CONST_08  C29  C30  C25  C26     0.00   0.0  0
 2SO  CONST_09  C29  C28  C27  C26     0.00   0.0  0
 2SO  CONST_10  C30  C25  C26  C27     0.00   0.0  0
 2SO  CONST_11  C30  C29  C28  C27     0.00   0.0  0
 2SO  CONST_12  N14  C13  C12  CB    180.00   0.0  0
 2SO  CONST_13  C15  N16  C12  CB    180.00   0.0  0
 2SO  CONST_14  CCA  N14  C13  C12   180.00   0.0  0
 2SO  CONST_15  C17  N16  C12  C13   180.00   0.0  0
 2SO  CONST_16  C17  N16  C15  N14   180.00   0.0  0
 2SO  CONST_17  CCA  N14  C15  N16   180.00   0.0  0
 2SO  CONST_18  C27  C26  C25  C24   180.00   0.0  0
 2SO  CONST_19  C29  C30  C25  C24   180.00   0.0  0
 2SO  CONST_20  H15  C15  N16  C12   180.00   0.0  0
 2SO  CONST_21  H13  C13  N14  C15   180.00   0.0  0
 2SO  CONST_22  H27  C27  C26  C25   180.00   0.0  0
 2SO  CONST_23  H29  C29  C30  C25   180.00   0.0  0
 2SO  CONST_24  H30  C30  C25  C26   180.00   0.0  0
 2SO  CONST_25  H28  C28  C27  C26   180.00   0.0  0
 2SO  CONST_26  H26  C26  C27  C28   180.00   0.0  0
 2SO  Var_01    C13  C12  CB   CA     84.30  30.0  2
 2SO  Var_02    C18  C17  N16  C12   -84.79  30.0  2
 2SO  Var_03    C32  CCA  N14  C13  -160.93  30.0  2
 2SO  Var_04    C26  C25  C24  C23   -69.25  30.0  2
 2SO  Var_05    C33  C32  CCA  N14   175.31  30.0  3
 2SO  Var_06    C19  C18  C17  N16   178.87  30.0  3
 2SO  Var_07    C25  C24  C23  C22   -63.58  30.0  3
 2SO  Var_08    C20  C19  C18  C17   174.61  30.0  3
 2SO  Var_09    C21  C20  C19  C18   178.68  30.0  3
 2SO  Var_10    C22  C21  C20  C19   173.53  30.0  3
 2SO  Var_11    C23  C22  C21  C20    64.03  30.0  3
 2SO  Var_12    C24  C23  C22  C21   177.57  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
 2SO  chir_01  CA   C    CB   N   positiv
 2SO  chir_02  C33  C32  C34  O4  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
 2SO  plan-1  CB   0.020
 2SO  plan-1  C12  0.020
 2SO  plan-1  C13  0.020
 2SO  plan-1  N14  0.020
 2SO  plan-1  C15  0.020
 2SO  plan-1  N16  0.020
 2SO  plan-1  C17  0.020
 2SO  plan-1  CCA  0.020
 2SO  plan-1  H13  0.020
 2SO  plan-1  H15  0.020
 2SO  plan-2  C24  0.020
 2SO  plan-2  C25  0.020
 2SO  plan-2  C26  0.020
 2SO  plan-2  C27  0.020
 2SO  plan-2  C28  0.020
 2SO  plan-2  C29  0.020
 2SO  plan-2  C30  0.020
 2SO  plan-2  H26  0.020
 2SO  plan-2  H27  0.020
 2SO  plan-2  H28  0.020
 2SO  plan-2  H29  0.020
 2SO  plan-2  H30  0.020
 2SO  plan-3  C    0.020
 2SO  plan-3  CA   0.020
 2SO  plan-3  O    0.020
 2SO  plan-3  OXT  0.020

