# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:44:01 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: 3-[(4-cyclopropylphenyl)sulfonylamino]-4-methyl-~{N}-(pyridin-3-ylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1N[S](=O)(=O)c2ccc(cc2)C3CC3)C(=O)NCc4cccnc4
#
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
 S40  S40  3-[(4-cyclopropylphenyl)sulfonylamino]-4-methyl-~{N}-(pyridin-3-ylmethyl)benzamide  ligand  53  30  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S40
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
 S40  C1   C  CR16  0  -0.093  -12.3806  22.5048  18.9904
 S40  C10  C  CR6   0  -0.054  -16.5885  20.1634  16.9041
 S40  C11  C  CR16  0  -0.273  -17.7115  20.7182  16.3072
 S40  C12  C  CR6   0   0.220  -18.8623  19.9619  16.1087
 S40  C13  C  CR6   0   0.104  -18.9158  18.6227  16.5019
 S40  C14  C  CR16  0  -0.298  -17.7780  18.0814  17.1032
 S40  C15  C  CR16  0  -0.251  -16.6318  18.8274  17.2968
 S40  C18  C  CR6   0  -0.226  -21.7504  20.4543  17.4763
 S40  C19  C  CR16  0  -0.205  -22.8885  19.7853  17.0417
 S40  C2   C  CR6   0   0.031  -13.6971  22.9245  18.8497
 S40  C20  C  CR16  0  -0.342  -23.4946  18.8695  17.8792
 S40  C21  C  CR6   0   0.236  -22.9767  18.6017  19.1505
 S40  C22  C  CR16  0  -0.312  -21.8376  19.2938  19.5619
 S40  C23  C  CR16  0  -0.205  -21.2222  20.2210  18.7370
 S40  C3   C  CR16  0  -0.180  -14.4218  23.1577  20.0125
 S40  C35  C  CH3   0  -0.720  -20.1236  17.7636  16.2890
 S40  C4   C  CR16  0  -0.320  -13.8087  22.9675  21.2399
 S40  C44  C  CH1   0  -0.375  -23.5966  17.6155  20.0597
 S40  C45  C  CH2   0  -0.473  -25.0932  17.4422  20.1108
 S40  C46  C  CH2   0  -0.473  -24.2496  16.3704  19.5170
 S40  C5   C  CR16  0  -0.072  -12.4857  22.5486  21.2609
 S40  C7   C  CH2   0  -0.384  -14.3100  23.1139  17.4870
 S40  C9   C  C     0   0.542  -15.3264  20.9325  17.1136
 S40  N16  N  NC1   0  -0.811  -19.9947  20.5518  15.4726
 S40  N6   N  N     0  -0.403  -11.7799  22.3214  20.1601
 S40  N8   N  NH1   0  -0.641  -15.4567  22.2631  17.2592
 S40  O26  O  O     0  -0.475  -14.2394  20.3744  17.1499
 S40  O27  O  OS    0  -0.659  -21.9072  22.1341  15.4451
 S40  O28  O  OS    0  -0.640  -20.1411  22.4840  17.1895
 S40  S17  S  S     0   1.349  -20.9476  21.5764  16.3857
 S40  H1   H  HCR6  0   0.256  -11.7843  22.3079  18.1046
 S40  H2   H  HCR6  0   0.264  -17.7021  21.7406  15.9513
 S40  H3   H  HCR6  0   0.260  -17.7927  17.0435  17.4119
 S40  H4   H  HCR6  0   0.263  -15.7651  18.3709  17.7559
 S40  H5   H  HCR6  0   0.283  -23.2989  19.9687  16.0578
 S40  H6   H  HCR6  0   0.265  -24.3812  18.3560  17.5291
 S40  H7   H  HCR6  0   0.266  -21.4237  19.1071  20.5448
 S40  H8   H  HCR6  0   0.283  -20.3409  20.7458  19.0791
 S40  H9   H  HCR6  0   0.269  -15.4540  23.4841  19.9622
 S40  H10  H  HCH3  0   0.253  -20.7093  18.0918  15.4337
 S40  H11  H  HCH3  0   0.255  -19.8299  16.7262  16.1341
 S40  H12  H  HCH3  0   0.256  -20.7782  17.7881  17.1619
 S40  H13  H  HCR6  0   0.271  -14.3406  23.1417  22.1651
 S40  H14  H  HCH1  0   0.269  -23.0793  17.5013  21.0052
 S40  H15  H  HCH2  0   0.258  -25.6940  18.0545  19.4498
 S40  H16  H  HCH2  0   0.267  -25.5341  17.2718  21.0842
 S40  H17  H  HCH2  0   0.258  -24.2623  16.2406  18.4418
 S40  H18  H  HCH2  0   0.267  -24.1066  15.4550  20.0761
 S40  H19  H  HCR6  0   0.263  -11.9781  22.3889  22.2058
 S40  H20  H  HCH2  0   0.267  -13.5597  22.9375  16.7148
 S40  H21  H  HCH2  0   0.283  -14.6487  24.1430  17.3690
 S40  H22  H  HNC1  0   0.420  -19.7960  20.9794  14.5715
 S40  H23  H  HNH1  0   0.409  -16.3712  22.6702  17.3606

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
 S40  N16  C12  single    1.427  0.020  1.427
 S40  N16  S17  single    1.671  0.020  1.671
 S40  C35  C13  single    1.497  0.020  1.497
 S40  O27  S17  double    1.455  0.020  1.455
 S40  C12  C13  aromatic  1.397  0.020  1.397
 S40  C12  C11  aromatic  1.391  0.020  1.391
 S40  C13  C14  aromatic  1.396  0.020  1.396
 S40  C11  C10  aromatic  1.388  0.020  1.388
 S40  C14  C15  aromatic  1.381  0.020  1.381
 S40  S17  O28  double    1.456  0.020  1.456
 S40  S17  C18  single    1.759  0.020  1.759
 S40  C10  C15  aromatic  1.393  0.020  1.393
 S40  C10  C9   single    1.493  0.020  1.493
 S40  C9   O26  double    1.222  0.020  1.222
 S40  C9   N8   single    1.345  0.020  1.345
 S40  N8   C7   single    1.446  0.020  1.446
 S40  C19  C18  aromatic  1.390  0.020  1.390
 S40  C19  C20  aromatic  1.381  0.020  1.381
 S40  C7   C2   single    1.506  0.020  1.506
 S40  C18  C23  aromatic  1.387  0.020  1.387
 S40  C20  C21  aromatic  1.399  0.020  1.399
 S40  C23  C22  aromatic  1.385  0.020  1.385
 S40  C2   C3   aromatic  1.390  0.020  1.390
 S40  C2   C1   aromatic  1.389  0.020  1.389
 S40  C21  C22  aromatic  1.395  0.020  1.395
 S40  C21  C44  single    1.478  0.020  1.478
 S40  C3   C4   aromatic  1.385  0.020  1.385
 S40  C1   N6   aromatic  1.328  0.020  1.328
 S40  C46  C44  single    1.507  0.020  1.507
 S40  C46  C45  single    1.488  0.020  1.488
 S40  C44  C45  single    1.508  0.020  1.508
 S40  C4   C5   aromatic  1.388  0.020  1.388
 S40  N6   C5   aromatic  1.327  0.020  1.327
 S40  C1   H1   single    0.930  0.020  1.080
 S40  C11  H2   single    0.930  0.020  1.080
 S40  C14  H3   single    0.930  0.020  1.080
 S40  C15  H4   single    0.930  0.020  1.080
 S40  C19  H5   single    0.930  0.020  1.080
 S40  C20  H6   single    0.930  0.020  1.080
 S40  C22  H7   single    0.930  0.020  1.080
 S40  C23  H8   single    0.930  0.020  1.080
 S40  C3   H9   single    0.930  0.020  1.080
 S40  C35  H10  single    0.970  0.020  1.090
 S40  C35  H11  single    0.970  0.020  1.090
 S40  C35  H12  single    0.970  0.020  1.090
 S40  C4   H13  single    0.930  0.020  1.080
 S40  C44  H14  single    0.970  0.020  1.090
 S40  C45  H15  single    0.970  0.020  1.090
 S40  C45  H16  single    0.970  0.020  1.090
 S40  C46  H17  single    0.970  0.020  1.090
 S40  C46  H18  single    0.970  0.020  1.090
 S40  C5   H19  single    0.930  0.020  1.080
 S40  C7   H20  single    0.970  0.020  1.090
 S40  C7   H21  single    0.970  0.020  1.090
 S40  N16  H22  single    0.890  0.020  1.040
 S40  N8   H23  single    0.860  0.020  1.020

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
 S40  H1   C1   N6   116.43  3.000
 S40  H1   C1   C2   119.52  3.000
 S40  N6   C1   C2   124.05  3.000
 S40  C9   C10  C15  118.74  3.000
 S40  C9   C10  C11  122.59  3.000
 S40  C15  C10  C11  118.65  3.000
 S40  H2   C11  C12  118.28  3.000
 S40  H2   C11  C10  120.79  3.000
 S40  C12  C11  C10  120.89  3.000
 S40  N16  C12  C13  119.44  3.000
 S40  C13  C12  C11  120.85  3.000
 S40  N16  C12  C11  119.70  3.000
 S40  C35  C13  C14  119.74  3.000
 S40  C14  C13  C12  117.50  3.000
 S40  C35  C13  C12  122.75  3.000
 S40  H3   C14  C15  119.27  3.000
 S40  H3   C14  C13  118.90  3.000
 S40  C15  C14  C13  121.82  3.000
 S40  H4   C15  C14  119.76  3.000
 S40  H4   C15  C10  119.96  3.000
 S40  C14  C15  C10  120.28  3.000
 S40  S17  C18  C23  119.82  3.000
 S40  C23  C18  C19  121.01  3.000
 S40  S17  C18  C19  119.14  3.000
 S40  H5   C19  C20  119.84  3.000
 S40  H5   C19  C18  120.89  3.000
 S40  C20  C19  C18  119.26  3.000
 S40  C7   C2   C3   121.58  3.000
 S40  C3   C2   C1   117.40  3.000
 S40  C7   C2   C1   121.02  3.000
 S40  H6   C20  C21  120.41  3.000
 S40  H6   C20  C19  118.54  3.000
 S40  C21  C20  C19  121.05  3.000
 S40  C44  C21  C22  119.49  3.000
 S40  C44  C21  C20  122.12  3.000
 S40  C22  C21  C20  118.39  3.000
 S40  H7   C22  C23  119.09  3.000
 S40  H7   C22  C21  119.63  3.000
 S40  C23  C22  C21  121.28  3.000
 S40  H8   C23  C22  119.91  3.000
 S40  H8   C23  C18  121.09  3.000
 S40  C22  C23  C18  119.00  3.000
 S40  H9   C3   C4   120.27  3.000
 S40  H9   C3   C2   120.55  3.000
 S40  C4   C3   C2   119.18  3.000
 S40  H12  C35  H11  107.27  3.000
 S40  H12  C35  H10  107.41  3.000
 S40  H11  C35  H10  108.71  3.000
 S40  H12  C35  C13  110.93  3.000
 S40  H11  C35  C13  110.44  3.000
 S40  H10  C35  C13  111.90  3.000
 S40  H13  C4   C5   120.30  3.000
 S40  H13  C4   C3   121.22  3.000
 S40  C5   C4   C3   118.48  3.000
 S40  H14  C44  C46  115.72  3.000
 S40  H14  C44  C45  115.60  3.000
 S40  C46  C44  C45   59.14  3.000
 S40  H14  C44  C21  114.01  3.000
 S40  C45  C44  C21  120.94  3.000
 S40  C46  C44  C21  120.77  3.000
 S40  H16  C45  H15  114.34  3.000
 S40  H16  C45  C46  118.47  3.000
 S40  H15  C45  C46  118.57  3.000
 S40  H16  C45  C44  116.94  3.000
 S40  H15  C45  C44  117.71  3.000
 S40  C46  C45  C44   60.42  3.000
 S40  H18  C46  H17  114.39  3.000
 S40  H18  C46  C45  118.57  3.000
 S40  H17  C46  C45  118.42  3.000
 S40  H18  C46  C44  117.11  3.000
 S40  H17  C46  C44  117.49  3.000
 S40  C45  C46  C44   60.45  3.000
 S40  H19  C5   N6   116.65  3.000
 S40  H19  C5   C4   120.25  3.000
 S40  N6   C5   C4   123.10  3.000
 S40  H21  C7   H20  106.85  3.000
 S40  H21  C7   N8   106.98  3.000
 S40  H20  C7   N8   109.80  3.000
 S40  H21  C7   C2   110.06  3.000
 S40  H20  C7   C2   109.89  3.000
 S40  N8   C7   C2   113.03  3.000
 S40  O26  C9   N8   122.32  3.000
 S40  N8   C9   C10  116.30  3.000
 S40  O26  C9   C10  121.38  3.000
 S40  H22  N16  S17  109.74  3.000
 S40  H22  N16  C12  114.45  3.000
 S40  S17  N16  C12  117.56  3.000
 S40  C5   N6   C1   117.80  3.000
 S40  H23  N8   C9   119.95  3.000
 S40  H23  N8   C7   117.83  3.000
 S40  C9   N8   C7   121.49  3.000
 S40  O28  S17  O27  118.90  3.000
 S40  O28  S17  N16  111.59  3.000
 S40  O27  S17  N16  104.95  3.000
 S40  O28  S17  C18  107.95  3.000
 S40  O27  S17  C18  110.15  3.000
 S40  N16  S17  C18  102.01  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
 S40  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 S40  CONST_02  C4   C5   N6   C1      0.00   0.0  0
 S40  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 S40  CONST_04  C13  C14  C15  C10     0.00   0.0  0
 S40  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 S40  CONST_06  C14  C15  C10  C11     0.00   0.0  0
 S40  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 S40  CONST_08  C15  C10  C11  C12     0.00   0.0  0
 S40  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 S40  CONST_10  C21  C22  C23  C18     0.00   0.0  0
 S40  CONST_11  C22  C23  C18  C19     0.00   0.0  0
 S40  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 S40  CONST_13  C5   C4   C3   C2      0.00   0.0  0
 S40  CONST_14  C5   N6   C1   C2      0.00   0.0  0
 S40  CONST_15  C23  C18  C19  C20     0.00   0.0  0
 S40  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 S40  CONST_17  N6   C1   C2   C3      0.00   0.0  0
 S40  CONST_18  N6   C5   C4   C3      0.00   0.0  0
 S40  CONST_19  C44  C21  C20  C19   180.00   0.0  0
 S40  CONST_20  C44  C21  C22  C23   180.00   0.0  0
 S40  CONST_21  N16  C12  C11  C10   180.00   0.0  0
 S40  CONST_22  C35  C13  C12  C11   180.00   0.0  0
 S40  CONST_23  C9   C10  C11  C12   180.00   0.0  0
 S40  CONST_24  N16  C12  C13  C14   180.00   0.0  0
 S40  CONST_25  C9   C10  C15  C14   180.00   0.0  0
 S40  CONST_26  C35  C13  C14  C15   180.00   0.0  0
 S40  CONST_27  S17  C18  C19  C20   180.00   0.0  0
 S40  CONST_28  S17  C18  C23  C22   180.00   0.0  0
 S40  CONST_29  C7   C2   C3   C4    180.00   0.0  0
 S40  CONST_30  N6   C1   C2   C7    180.00   0.0  0
 S40  CONST_31  H9   C3   C2   C1    180.00   0.0  0
 S40  CONST_32  H19  C5   N6   C1    180.00   0.0  0
 S40  CONST_33  H3   C14  C15  C10   180.00   0.0  0
 S40  CONST_34  H4   C15  C10  C11   180.00   0.0  0
 S40  CONST_35  H2   C11  C12  C13   180.00   0.0  0
 S40  CONST_36  H6   C20  C19  C18   180.00   0.0  0
 S40  CONST_37  H7   C22  C23  C18   180.00   0.0  0
 S40  CONST_38  H8   C23  C18  C19   180.00   0.0  0
 S40  CONST_39  H13  C4   C3   C2    180.00   0.0  0
 S40  CONST_40  H5   C19  C20  C21   180.00   0.0  0
 S40  CONST_41  H1   C1   C2   C3    180.00   0.0  0
 S40  CONST_45  C7   N8   C9   C10   180.00   0.0  0
 S40  CONST_46  H23  N8   C9   C10     0.00   0.0  0
 S40  CONST_47  O26  C9   N8   C7      0.00   0.0  0
 S40  Var_01    C46  C44  C21  C20    34.24  30.0  2
 S40  Var_02    C45  C46  C44  C21  -109.95  30.0  1
 S40  Var_03    N8   C7   C2   C1    119.49  30.0  2
 S40  Var_04    O26  C9   C10  C11  -151.90  30.0  2
 S40  Var_05    C18  S17  N16  C12   -71.57  30.0  3
 S40  Var_06    N16  S17  C18  C19   -83.25  30.0  2
 S40  Var_07    H10  C35  C13  C12    27.51  30.0  2
 S40  Var_08    C9   N8   C7   C2    -69.86  30.0  2

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
 S40  chir_01  C44  C21  C46  C45  both

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
 S40  plan-1  C10  0.020
 S40  plan-1  C11  0.020
 S40  plan-1  C12  0.020
 S40  plan-1  C13  0.020
 S40  plan-1  C14  0.020
 S40  plan-1  C15  0.020
 S40  plan-1  C35  0.020
 S40  plan-1  C9   0.020
 S40  plan-1  N16  0.020
 S40  plan-1  H2   0.020
 S40  plan-1  H3   0.020
 S40  plan-1  H4   0.020
 S40  plan-2  C18  0.020
 S40  plan-2  C19  0.020
 S40  plan-2  C20  0.020
 S40  plan-2  C21  0.020
 S40  plan-2  C22  0.020
 S40  plan-2  C23  0.020
 S40  plan-2  C44  0.020
 S40  plan-2  S17  0.020
 S40  plan-2  H5   0.020
 S40  plan-2  H6   0.020
 S40  plan-2  H7   0.020
 S40  plan-2  H8   0.020
 S40  plan-3  C1   0.020
 S40  plan-3  C2   0.020
 S40  plan-3  C3   0.020
 S40  plan-3  C4   0.020
 S40  plan-3  C5   0.020
 S40  plan-3  C7   0.020
 S40  plan-3  N6   0.020
 S40  plan-3  H1   0.020
 S40  plan-3  H9   0.020
 S40  plan-3  H13  0.020
 S40  plan-3  H19  0.020
 S40  plan-4  C12  0.020
 S40  plan-4  N16  0.020
 S40  plan-4  S17  0.020
 S40  plan-4  H22  0.020
 S40  plan-5  C10  0.020
 S40  plan-5  C7   0.020
 S40  plan-5  C9   0.020
 S40  plan-5  N8   0.020
 S40  plan-5  O26  0.020
 S40  plan-5  H23  0.020

