# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:31:16 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)[S](=O)(=O)NCc2ccc(cc2)C(=O)NCc3cccnc3
#
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
 5YD  5YD  4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide  ligand  46  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5YD
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
 5YD  C4   C  CR16  0  -0.042   6.5506  -0.8716  -0.6262
 5YD  C14  C  CR6   0   0.045  -0.4485   0.5469   0.2367
 5YD  C6   C  CR16  0  -0.101   8.1099  -2.1025   0.4791
 5YD  C11  C  CR6   0  -0.191   2.1854   1.2936  -0.3303
 5YD  C7   C  CH2   0  -0.282   5.9454   1.4942  -0.0208
 5YD  C9   C  C     0   0.564   3.5768   1.7128  -0.6757
 5YD  C12  C  CR16  0  -0.178   1.9076   0.0394   0.2112
 5YD  C13  C  CR16  0  -0.284   0.6027  -0.3309   0.4816
 5YD  C3   C  CR6   0  -0.103   6.7459   0.2389   0.1922
 5YD  C1   C  CR16  0  -0.206   8.3850  -1.0635   1.3517
 5YD  C2   C  CR16  0  -0.215   7.6879   0.1267   1.2031
 5YD  N5   N  N     0  -0.340   7.2090  -2.0129  -0.4949
 5YD  N8   N  NH1   0  -0.687   4.5337   1.2391   0.1480
 5YD  O10  O  O     0  -0.448   3.8076   2.4223  -1.6415
 5YD  C15  C  CR16  0  -0.226  -0.1700   1.7939  -0.3085
 5YD  C16  C  CR16  0  -0.162   1.1345   2.1605  -0.6048
 5YD  N18  N  NC1   0  -0.690  -2.2492  -0.8882  -0.4707
 5YD  S19  S  S     0   1.408  -3.5474  -1.8635  -0.1541
 5YD  O20  O  OS    0  -0.665  -3.7331  -2.6544  -1.3585
 5YD  O21  O  OS    0  -0.608  -3.2751  -2.5135   1.1171
 5YD  C22  C  CR6   0  -0.231  -4.9417  -0.8053   0.0569
 5YD  C23  C  CR16  0  -0.273  -5.3337  -0.4273   1.3351
 5YD  C24  C  CR16  0  -0.304  -6.3947   0.4465   1.4927
 5YD  C25  C  CR6   0   0.484  -7.0397   0.9244   0.3641
 5YD  C26  C  CR16  0  -0.312  -6.6627   0.5481  -0.9137
 5YD  C27  C  CR16  0  -0.224  -5.6032  -0.3258  -1.0688
 5YD  F28  F  F     0  -0.395  -8.0593   1.7651   0.5105
 5YD  H1   H  HCR6  0   0.254   5.8178  -0.8295  -1.4265
 5YD  H2   H  HCR6  0   0.226   8.6346  -3.0467   0.5693
 5YD  H3   H  HCH2  0   0.236   6.2806   2.2739   0.6680
 5YD  H4   H  HCH2  0   0.207   6.1002   1.8784  -1.0283
 5YD  H5   H  HCR6  0   0.265   2.7015  -0.6718   0.4008
 5YD  H6   H  HCR6  0   0.250   0.3997  -1.3167   0.8804
 5YD  H7   H  HCR6  0   0.269   9.1242  -1.1846   2.1306
 5YD  H8   H  HCR6  0   0.240   7.8779   0.9562   1.8731
 5YD  H9   H  HNH1  0   0.394   4.2495   0.8315   1.0235
 5YD  H10  H  HCR6  0   0.253  -0.9760   2.4868  -0.5159
 5YD  H11  H  HCR6  0   0.271   1.3337   3.1294  -1.0420
 5YD  H12  H  HCH2  0   0.245  -1.9127  -0.3409   1.5039
 5YD  H13  H  HCH2  0   0.262  -2.5374   0.9745   0.5141
 5YD  H14  H  HNC1  0   0.445  -2.2667  -0.5365  -1.4214
 5YD  H15  H  HCR6  0   0.294  -4.8266  -0.8079   2.2106
 5YD  H16  H  HCR6  0   0.306  -6.7156   0.7502   2.4790
 5YD  H17  H  HCR6  0   0.304  -7.1882   0.9300  -1.7749
 5YD  H18  H  HCR6  0   0.279  -5.3139  -0.6130  -2.0690
 5YD  C17  C  CH2   0  -0.334  -1.8611   0.1139   0.5143

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
 5YD  C13  C12  aromatic  1.383  0.020  1.383
 5YD  C13  C14  aromatic  1.391  0.020  1.391
 5YD  C12  C11  aromatic  1.394  0.020  1.394
 5YD  O10  C9   double    1.221  0.020  1.221
 5YD  O21  S19  double    1.453  0.020  1.453
 5YD  C24  C23  aromatic  1.383  0.020  1.383
 5YD  C24  C25  aromatic  1.385  0.020  1.385
 5YD  C23  C22  aromatic  1.389  0.020  1.389
 5YD  C17  C14  single    1.503  0.020  1.503
 5YD  C17  N18  single    1.458  0.020  1.458
 5YD  C14  C15  aromatic  1.389  0.020  1.389
 5YD  C11  C9   single    1.494  0.020  1.494
 5YD  C11  C16  aromatic  1.390  0.020  1.390
 5YD  C9   N8   single    1.349  0.020  1.349
 5YD  F28  C25  single    1.330  0.020  1.330
 5YD  N18  S19  single    1.654  0.020  1.654
 5YD  C25  C26  aromatic  1.384  0.020  1.384
 5YD  C22  S19  single    1.763  0.020  1.763
 5YD  C22  C27  aromatic  1.391  0.020  1.391
 5YD  S19  O20  double    1.453  0.020  1.453
 5YD  C15  C16  aromatic  1.387  0.020  1.387
 5YD  N8   C7   single    1.444  0.020  1.444
 5YD  C7   C3   single    1.504  0.020  1.504
 5YD  C3   C4   aromatic  1.393  0.020  1.393
 5YD  C3   C2   aromatic  1.386  0.020  1.386
 5YD  C26  C27  aromatic  1.382  0.020  1.382
 5YD  C4   N5   aromatic  1.324  0.020  1.324
 5YD  C2   C1   aromatic  1.387  0.020  1.387
 5YD  N5   C6   aromatic  1.330  0.020  1.330
 5YD  C1   C6   aromatic  1.384  0.020  1.384
 5YD  C4   H1   single    0.930  0.020  1.080
 5YD  C6   H2   single    0.930  0.020  1.080
 5YD  C7   H3   single    0.970  0.020  1.090
 5YD  C7   H4   single    0.970  0.020  1.090
 5YD  C12  H5   single    0.930  0.020  1.080
 5YD  C13  H6   single    0.930  0.020  1.080
 5YD  C1   H7   single    0.930  0.020  1.080
 5YD  C2   H8   single    0.930  0.020  1.080
 5YD  N8   H9   single    0.860  0.020  1.020
 5YD  C15  H10  single    0.930  0.020  1.080
 5YD  C16  H11  single    0.930  0.020  1.080
 5YD  C17  H12  single    0.970  0.020  1.090
 5YD  C17  H13  single    0.970  0.020  1.090
 5YD  N18  H14  single    0.890  0.020  1.040
 5YD  C23  H15  single    0.930  0.020  1.080
 5YD  C24  H16  single    0.930  0.020  1.080
 5YD  C26  H17  single    0.930  0.020  1.080
 5YD  C27  H18  single    0.930  0.020  1.080

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
 5YD  H1   C4   N5   116.24  3.000
 5YD  H1   C4   C3   119.77  3.000
 5YD  N5   C4   C3   123.99  3.000
 5YD  C17  C14  C15  121.29  3.000
 5YD  C15  C14  C13  118.94  3.000
 5YD  C17  C14  C13  119.72  3.000
 5YD  H2   C6   N5   116.60  3.000
 5YD  H2   C6   C1   120.33  3.000
 5YD  N5   C6   C1   123.07  3.000
 5YD  C16  C11  C12  119.16  3.000
 5YD  C16  C11  C9   118.93  3.000
 5YD  C12  C11  C9   121.86  3.000
 5YD  H4   C7   H3   106.72  3.000
 5YD  H4   C7   N8   108.02  3.000
 5YD  H3   C7   N8   110.61  3.000
 5YD  H4   C7   C3   110.47  3.000
 5YD  H3   C7   C3   110.06  3.000
 5YD  N8   C7   C3   110.86  3.000
 5YD  O10  C9   N8   123.60  3.000
 5YD  N8   C9   C11  114.91  3.000
 5YD  O10  C9   C11  121.49  3.000
 5YD  H5   C12  C13  118.80  3.000
 5YD  H5   C12  C11  120.86  3.000
 5YD  C13  C12  C11  120.32  3.000
 5YD  H6   C13  C12  119.52  3.000
 5YD  H6   C13  C14  119.84  3.000
 5YD  C12  C13  C14  120.63  3.000
 5YD  C2   C3   C7   122.17  3.000
 5YD  C2   C3   C4   117.33  3.000
 5YD  C7   C3   C4   120.50  3.000
 5YD  H7   C1   C2   121.13  3.000
 5YD  H7   C1   C6   120.41  3.000
 5YD  C2   C1   C6   118.46  3.000
 5YD  H8   C2   C1   120.17  3.000
 5YD  H8   C2   C3   120.56  3.000
 5YD  C1   C2   C3   119.27  3.000
 5YD  C6   N5   C4   117.88  3.000
 5YD  H9   N8   C9   118.24  3.000
 5YD  H9   N8   C7   116.69  3.000
 5YD  C9   N8   C7   124.06  3.000
 5YD  H10  C15  C16  119.34  3.000
 5YD  H10  C15  C14  120.02  3.000
 5YD  C16  C15  C14  120.64  3.000
 5YD  H11  C16  C15  119.76  3.000
 5YD  H11  C16  C11  119.96  3.000
 5YD  C15  C16  C11  120.27  3.000
 5YD  H14  N18  S19  111.74  3.000
 5YD  H14  N18  C17  113.56  3.000
 5YD  S19  N18  C17  119.01  3.000
 5YD  C22  S19  O21  108.18  3.000
 5YD  C22  S19  O20  108.96  3.000
 5YD  O21  S19  O20  120.37  3.000
 5YD  O20  S19  N18  105.22  3.000
 5YD  C22  S19  N18  106.84  3.000
 5YD  O21  S19  N18  106.50  3.000
 5YD  C27  C22  C23  121.10  3.000
 5YD  C27  C22  S19  119.09  3.000
 5YD  C23  C22  S19  119.77  3.000
 5YD  H15  C23  C24  119.33  3.000
 5YD  H15  C23  C22  121.13  3.000
 5YD  C24  C23  C22  119.54  3.000
 5YD  H16  C24  C25  120.56  3.000
 5YD  H16  C24  C23  120.61  3.000
 5YD  C25  C24  C23  118.83  3.000
 5YD  F28  C25  C26  118.84  3.000
 5YD  C26  C25  C24  122.11  3.000
 5YD  F28  C25  C24  119.05  3.000
 5YD  H17  C26  C27  120.51  3.000
 5YD  H17  C26  C25  120.53  3.000
 5YD  C27  C26  C25  118.96  3.000
 5YD  H18  C27  C26  118.52  3.000
 5YD  H18  C27  C22  122.03  3.000
 5YD  C26  C27  C22  119.45  3.000
 5YD  H13  C17  H12  107.39  3.000
 5YD  H13  C17  N18  112.07  3.000
 5YD  H12  C17  N18  108.29  3.000
 5YD  H13  C17  C14  110.74  3.000
 5YD  H12  C17  C14  109.41  3.000
 5YD  N18  C17  C14  108.87  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
 5YD  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 5YD  CONST_02  C1   C6   N5   C4      0.00   0.0  0
 5YD  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 5YD  CONST_04  C11  C16  C15  C14     0.00   0.0  0
 5YD  CONST_05  C3   C4   N5   C6      0.00   0.0  0
 5YD  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 5YD  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 5YD  CONST_08  C15  C16  C11  C12     0.00   0.0  0
 5YD  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 5YD  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 5YD  CONST_11  N5   C4   C3   C2      0.00   0.0  0
 5YD  CONST_12  N5   C6   C1   C2      0.00   0.0  0
 5YD  CONST_13  C25  C24  C23  C22     0.00   0.0  0
 5YD  CONST_14  C25  C26  C27  C22     0.00   0.0  0
 5YD  CONST_15  C26  C25  C24  C23     0.00   0.0  0
 5YD  CONST_16  C26  C27  C22  C23     0.00   0.0  0
 5YD  CONST_17  C27  C22  C23  C24     0.00   0.0  0
 5YD  CONST_18  C27  C26  C25  C24     0.00   0.0  0
 5YD  CONST_19  N5   C4   C3   C7    180.00   0.0  0
 5YD  CONST_20  C1   C2   C3   C7    180.00   0.0  0
 5YD  CONST_21  C13  C12  C11  C9    180.00   0.0  0
 5YD  CONST_22  C15  C16  C11  C9    180.00   0.0  0
 5YD  CONST_23  C17  C14  C13  C12   180.00   0.0  0
 5YD  CONST_24  C17  C14  C15  C16   180.00   0.0  0
 5YD  CONST_25  C24  C23  C22  S19   180.00   0.0  0
 5YD  CONST_26  C26  C27  C22  S19   180.00   0.0  0
 5YD  CONST_27  F28  C25  C24  C23   180.00   0.0  0
 5YD  CONST_28  F28  C25  C26  C27   180.00   0.0  0
 5YD  CONST_29  H8   C2   C3   C4    180.00   0.0  0
 5YD  CONST_30  H2   C6   N5   C4    180.00   0.0  0
 5YD  CONST_31  H5   C12  C13  C14   180.00   0.0  0
 5YD  CONST_32  H11  C16  C15  C14   180.00   0.0  0
 5YD  CONST_33  H1   C4   N5   C6    180.00   0.0  0
 5YD  CONST_34  H6   C13  C12  C11   180.00   0.0  0
 5YD  CONST_35  H10  C15  C16  C11   180.00   0.0  0
 5YD  CONST_36  H7   C1   C2   C3    180.00   0.0  0
 5YD  CONST_37  H16  C24  C23  C22   180.00   0.0  0
 5YD  CONST_38  H17  C26  C27  C22   180.00   0.0  0
 5YD  CONST_39  H18  C27  C22  C23   180.00   0.0  0
 5YD  CONST_40  H15  C23  C24  C25   180.00   0.0  0
 5YD  CONST_41  C7   N8   C9   C11   180.00   0.0  0
 5YD  CONST_42  H9   N8   C9   C11     0.00   0.0  0
 5YD  CONST_43  O10  C9   N8   C7      0.00   0.0  0
 5YD  Var_01    N8   C7   C3   C4     61.04  30.0  2
 5YD  Var_02    O10  C9   C11  C12   144.88  30.0  2
 5YD  Var_03    N18  C17  C14  C13   -70.52  30.0  1
 5YD  Var_04    C23  C22  S19  N18   -96.44  30.0  2
 5YD  Var_05    S19  N18  C17  C14   161.70  30.0  3
 5YD  Var_06    C3   C7   N8   C9   -136.11  30.0  3
 5YD  Var_07    C22  S19  N18  C17    59.62  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
 5YD  plan-1  C14  0.020
 5YD  plan-1  C11  0.020
 5YD  plan-1  C9   0.020
 5YD  plan-1  C12  0.020
 5YD  plan-1  C13  0.020
 5YD  plan-1  C15  0.020
 5YD  plan-1  C16  0.020
 5YD  plan-1  H5   0.020
 5YD  plan-1  H6   0.020
 5YD  plan-1  H10  0.020
 5YD  plan-1  H11  0.020
 5YD  plan-1  C17  0.020
 5YD  plan-2  C4   0.020
 5YD  plan-2  C6   0.020
 5YD  plan-2  C7   0.020
 5YD  plan-2  C3   0.020
 5YD  plan-2  C1   0.020
 5YD  plan-2  C2   0.020
 5YD  plan-2  N5   0.020
 5YD  plan-2  H1   0.020
 5YD  plan-2  H2   0.020
 5YD  plan-2  H7   0.020
 5YD  plan-2  H8   0.020
 5YD  plan-3  S19  0.020
 5YD  plan-3  C22  0.020
 5YD  plan-3  C23  0.020
 5YD  plan-3  C24  0.020
 5YD  plan-3  C25  0.020
 5YD  plan-3  C26  0.020
 5YD  plan-3  C27  0.020
 5YD  plan-3  F28  0.020
 5YD  plan-3  H15  0.020
 5YD  plan-3  H16  0.020
 5YD  plan-3  H17  0.020
 5YD  plan-3  H18  0.020
 5YD  plan-4  C11  0.020
 5YD  plan-4  C7   0.020
 5YD  plan-4  C9   0.020
 5YD  plan-4  N8   0.020
 5YD  plan-4  O10  0.020
 5YD  plan-4  H9   0.020

