# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 05:21:12 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-(4-methoxybenzyl)thiophene-2,5-disulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CN[S](=O)(=O)c2sc(cc2)[S](N)(=O)=O)cc1
#
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
 AL9  AL9  N-(4-methoxybenzyl)thiophene-2,5-disulfonamide  ligand  36  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AL9
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
 AL9  C3    C  CR5   0  -0.422  -0.7331   0.7268  -0.9728
 AL9  C9    C  CH2   0  -0.402   2.2505  -2.0141   1.7513
 AL9  C10   C  CR6   0   0.084   0.9301  -1.4172   2.1654
 AL9  C11   C  CR16  0  -0.276  -0.2525  -1.7436   1.5071
 AL9  C12   C  CR16  0  -0.322  -1.4509  -1.1403   1.8411
 AL9  C13   C  CR6   0   0.381  -1.4966  -0.1879   2.8592
 AL9  C14   C  CR16  0  -0.369  -0.3262   0.1303   3.5458
 AL9  C15   C  CR16  0  -0.275   0.8662  -0.4876   3.1951
 AL9  O2A   O  OS    0  -0.652  -2.7284  -0.8065  -1.6614
 AL9  O1A   O  OS    0  -0.634  -3.1814   1.4999  -0.7924
 AL9  N21   N  NC2   0  -0.882  -2.1613   1.0942  -3.1442
 AL9  S1    S  S     0   1.369  -2.3679   0.5994  -1.5901
 AL9  C4    C  CR15  0  -0.126  -0.3121   1.5889  -0.0030
 AL9  C5    C  CR15  0  -0.127   1.0412   1.3697   0.3353
 AL9  C6    C  CR5   0  -0.427   1.5767   0.3438  -0.3856
 AL9  S2    S  S2    0   0.379   0.4792  -0.3616  -1.4895
 AL9  S7    S  S     0   1.397   3.1677  -0.3812  -0.1975
 AL9  O3B   O  OS    0  -0.642   4.1669   0.6683  -0.2318
 AL9  O4B   O  OS    0  -0.651   3.1850  -1.4652  -1.1640
 AL9  N8    N  NC1   0  -0.711   3.2370  -1.0293   1.2990
 AL9  O16   O  O2    0  -0.468  -2.6981   0.3653   3.1077
 AL9  C17   C  CH3   0  -0.436  -2.7833   1.3865   4.0802
 AL9  H91   H  HCH2  0   0.292   2.7209  -2.5364   2.5853
 AL9  H92   H  HCH2  0   0.281   2.1144  -2.7542   0.9629
 AL9  H11   H  HCR6  0   0.258  -0.2398  -2.4740   0.7075
 AL9  H12   H  HCR6  0   0.258  -2.3565  -1.3911   1.3032
 AL9  H14   H  HCR6  0   0.278  -0.3183   0.8563   4.3470
 AL9  H15   H  HCR6  0   0.254   1.7639  -0.2163   3.7406
 AL9  HNL1  H  HNC2  0   0.426  -2.9046   0.7613  -3.7512
 AL9  HNL2  H  HNC2  0   0.422  -2.0458   2.0987  -3.2321
 AL9  H4    H  HCR5  0   0.304  -0.9401   2.3365   0.4575
 AL9  H5    H  HCR5  0   0.306   1.5733   1.9270   1.0923
 AL9  HN8   H  HNC1  0   0.423   3.5336  -0.3607   2.0007
 AL9  H171  H  HCH3  0   0.259  -3.8203   1.7126   4.0972
 AL9  H172  H  HCH3  0   0.227  -2.5126   1.0296   5.0774
 AL9  H173  H  HCH3  0   0.226  -2.1511   2.2427   3.8297

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
 AL9  C3   S1    single    1.752  0.020  1.752
 AL9  C3   C4    aromatic  1.364  0.020  1.364
 AL9  C3   S2    aromatic  1.709  0.020  1.709
 AL9  C9   C10   single    1.507  0.020  1.507
 AL9  C9   N8    single    1.465  0.020  1.465
 AL9  C9   H91   single    0.970  0.020  1.090
 AL9  C9   H92   single    0.970  0.020  1.090
 AL9  C10  C11   aromatic  1.392  0.020  1.392
 AL9  C10  C15   aromatic  1.389  0.020  1.389
 AL9  C11  C12   aromatic  1.383  0.020  1.383
 AL9  C11  H11   single    0.930  0.020  1.080
 AL9  C12  C13   aromatic  1.395  0.020  1.395
 AL9  C12  H12   single    0.930  0.020  1.080
 AL9  C13  C14   aromatic  1.394  0.020  1.394
 AL9  C13  O16   single    1.346  0.020  1.346
 AL9  C14  C15   aromatic  1.388  0.020  1.388
 AL9  C14  H14   single    0.930  0.020  1.080
 AL9  C15  H15   single    0.930  0.020  1.080
 AL9  O2A  S1    double    1.453  0.020  1.453
 AL9  O1A  S1    double    1.452  0.020  1.452
 AL9  N21  S1    single    1.644  0.020  1.644
 AL9  N21  HNL1  single    0.890  0.020  1.040
 AL9  N21  HNL2  single    0.890  0.020  1.040
 AL9  C4   C5    aromatic  1.412  0.020  1.412
 AL9  C4   H4    single    0.930  0.020  1.080
 AL9  C5   C6    aromatic  1.363  0.020  1.363
 AL9  C5   H5    single    0.930  0.020  1.080
 AL9  C6   S2    aromatic  1.709  0.020  1.709
 AL9  C6   S7    single    1.758  0.020  1.758
 AL9  S7   O3B   double    1.449  0.020  1.449
 AL9  S7   O4B   double    1.452  0.020  1.452
 AL9  S7   N8    single    1.632  0.020  1.632
 AL9  N8   HN8   single    0.890  0.020  1.040
 AL9  O16  C17   single    1.413  0.020  1.413
 AL9  C17  H171  single    0.970  0.020  1.090
 AL9  C17  H172  single    0.970  0.020  1.090
 AL9  C17  H173  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
 AL9  S2    C3   C4    113.48  3.000
 AL9  S2    C3   S1    120.59  3.000
 AL9  C4    C3   S1    125.76  3.000
 AL9  H92   C9   H91   106.36  3.000
 AL9  H92   C9   N8    108.49  3.000
 AL9  H91   C9   N8    105.52  3.000
 AL9  H92   C9   C10   111.00  3.000
 AL9  H91   C9   C10   110.95  3.000
 AL9  N8    C9   C10   114.11  3.000
 AL9  C15   C10  C11   117.93  3.000
 AL9  C15   C10  C9    120.61  3.000
 AL9  C11   C10  C9    121.43  3.000
 AL9  H11   C11  C12   118.86  3.000
 AL9  H11   C11  C10   119.82  3.000
 AL9  C12   C11  C10   121.31  3.000
 AL9  H12   C12  C13   119.56  3.000
 AL9  H12   C12  C11   120.26  3.000
 AL9  C13   C12  C11   120.18  3.000
 AL9  O16   C13  C14   124.39  3.000
 AL9  O16   C13  C12   116.40  3.000
 AL9  C14   C13  C12   119.20  3.000
 AL9  H14   C14  C15   118.68  3.000
 AL9  H14   C14  C13   121.63  3.000
 AL9  C15   C14  C13   119.69  3.000
 AL9  H15   C15  C14   118.19  3.000
 AL9  H15   C15  C10   120.15  3.000
 AL9  C14   C15  C10   121.66  3.000
 AL9  HNL2  N21  HNL1  110.85  3.000
 AL9  HNL2  N21  S1    113.21  3.000
 AL9  HNL1  N21  S1    111.98  3.000
 AL9  N21   S1   O1A   113.77  3.000
 AL9  N21   S1   O2A   106.02  3.000
 AL9  O1A   S1   O2A   119.21  3.000
 AL9  N21   S1   C3    101.18  3.000
 AL9  O1A   S1   C3    106.50  3.000
 AL9  O2A   S1   C3    108.61  3.000
 AL9  H4    C4   C5    124.26  3.000
 AL9  H4    C4   C3    124.14  3.000
 AL9  C5    C4   C3    111.59  3.000
 AL9  H5    C5   C6    124.42  3.000
 AL9  H5    C5   C4    124.05  3.000
 AL9  C6    C5   C4    111.50  3.000
 AL9  S7    C6   S2    118.68  3.000
 AL9  S7    C6   C5    127.52  3.000
 AL9  S2    C6   C5    113.57  3.000
 AL9  C6    S2   C3     89.85  3.000
 AL9  N8    S7   O4B   108.25  3.000
 AL9  N8    S7   O3B   106.25  3.000
 AL9  O4B   S7   O3B   121.09  3.000
 AL9  N8    S7   C6    107.47  3.000
 AL9  O4B   S7   C6    104.32  3.000
 AL9  O3B   S7   C6    108.83  3.000
 AL9  HN8   N8   S7    112.66  3.000
 AL9  HN8   N8   C9    115.25  3.000
 AL9  S7    N8   C9    121.41  3.000
 AL9  C17   O16  C13   118.56  3.000
 AL9  H173  C17  H172  108.76  3.000
 AL9  H173  C17  H171  108.67  3.000
 AL9  H172  C17  H171  108.65  3.000
 AL9  H173  C17  O16   111.93  3.000
 AL9  H172  C17  O16   112.15  3.000
 AL9  H171  C17  O16   106.56  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
 AL9  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 AL9  CONST_02  C5    C6   S2   C3      0.00   0.0  0
 AL9  CONST_03  C13   C12  C11  C10     0.00   0.0  0
 AL9  CONST_04  C13   C14  C15  C10     0.00   0.0  0
 AL9  CONST_05  C14   C15  C10  C11     0.00   0.0  0
 AL9  CONST_06  C14   C13  C12  C11     0.00   0.0  0
 AL9  CONST_07  C15   C10  C11  C12     0.00   0.0  0
 AL9  CONST_08  C15   C14  C13  C12     0.00   0.0  0
 AL9  CONST_09  C6    S2   C3   C4      0.00   0.0  0
 AL9  CONST_10  S2    C6   C5   C4      0.00   0.0  0
 AL9  CONST_11  S2    C3   C4   C5      0.00   0.0  0
 AL9  CONST_12  S7    C6   S2   C3    180.00   0.0  0
 AL9  CONST_13  C12   C11  C10  C9    180.00   0.0  0
 AL9  CONST_14  C14   C15  C10  C9    180.00   0.0  0
 AL9  CONST_15  O16   C13  C12  C11   180.00   0.0  0
 AL9  CONST_16  O16   C13  C14  C15   180.00   0.0  0
 AL9  CONST_17  C5    C4   C3   S1    180.00   0.0  0
 AL9  CONST_18  C6    S2   C3   S1    180.00   0.0  0
 AL9  CONST_19  S7    C6   C5   C4    180.00   0.0  0
 AL9  CONST_20  H5    C5   C4   C3    180.00   0.0  0
 AL9  CONST_21  H12   C12  C11  C10   180.00   0.0  0
 AL9  CONST_22  H14   C14  C15  C10   180.00   0.0  0
 AL9  CONST_23  H15   C15  C10  C11   180.00   0.0  0
 AL9  CONST_24  H11   C11  C12  C13   180.00   0.0  0
 AL9  CONST_25  H4    C4   C5   C6    180.00   0.0  0
 AL9  Var_01    N8    C9   C10  C11   118.39  30.0  2
 AL9  Var_02    C4    C3   S1   O2A  -134.22  30.0  1
 AL9  Var_03    O3B   S7   C6   C5    -52.40  30.0  2
 AL9  Var_04    C6    S7   N8   C9     55.99  30.0  2
 AL9  Var_05    S7    N8   C9   C10   -78.49  30.0  3
 AL9  Var_06    HNL1  N21  S1   C3    158.19  30.0  3
 AL9  Var_07    H171  C17  O16  C13   178.05  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
 AL9  plan-1  C3   0.020
 AL9  plan-1  S1   0.020
 AL9  plan-1  C4   0.020
 AL9  plan-1  C5   0.020
 AL9  plan-1  C6   0.020
 AL9  plan-1  S2   0.020
 AL9  plan-1  S7   0.020
 AL9  plan-1  H4   0.020
 AL9  plan-1  H5   0.020
 AL9  plan-2  C9   0.020
 AL9  plan-2  C10  0.020
 AL9  plan-2  C11  0.020
 AL9  plan-2  C12  0.020
 AL9  plan-2  C13  0.020
 AL9  plan-2  C14  0.020
 AL9  plan-2  C15  0.020
 AL9  plan-2  O16  0.020
 AL9  plan-2  H11  0.020
 AL9  plan-2  H12  0.020
 AL9  plan-2  H14  0.020
 AL9  plan-2  H15  0.020

