# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:23:32 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N,N'-biphenyl-3,3'-diyldithiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C(Nc1cccc(c1)c2cccc(NC(=N)c3sccc3)c2)c4sccc4
#
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
 H38  H38  N,N'-biphenyl-3,3'-diyldithiophene-2-carboximidamide  ligand  46  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H38
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
 H38  N26  N  N     0  -0.632  -5.4491  -2.3153  -0.3225
 H38  C26  C  C     0   0.422  -5.2871  -1.0966   0.0142
 H38  C25  C  CR5   0  -0.296  -6.3762  -0.2303   0.5069
 H38  S21  S  S2    0   0.242  -6.1235   0.9642   1.7256
 H38  C22  C  CR15  0  -0.457  -7.7720   1.4154   1.7072
 H38  C23  C  CR15  0  -0.176  -8.4870   0.6804   0.8101
 H38  C24  C  CR15  0  -0.206  -7.6868  -0.2663   0.1227
 H38  N27  N  NH1   0  -0.759  -4.0732  -0.4637  -0.0532
 H38  C31  C  CR6   0   0.413  -2.8158  -0.9828  -0.3460
 H38  C36  C  CR16  0  -0.442  -1.7764  -0.0573  -0.4807
 H38  C32  C  CR16  0  -0.328  -2.5303  -2.3433  -0.4773
 H38  C33  C  CR16  0  -0.232  -1.2244  -2.7411  -0.7302
 H38  C34  C  CR16  0  -0.332  -0.1980  -1.8225  -0.8651
 H38  C35  C  CR6   0   0.107  -0.4718  -0.4590  -0.7405
 H38  C15  C  CR6   0   0.104   0.6031   0.5433  -0.8919
 H38  C14  C  CR16  0  -0.329   0.3604   1.7679  -1.5144
 H38  C13  C  CR16  0  -0.231   1.3827   2.6945  -1.6476
 H38  C12  C  CR16  0  -0.340   2.6598   2.4106  -1.1913
 H38  C16  C  CR16  0  -0.396   1.8814   0.2725  -0.4074
 H38  C11  C  CR6   0   0.378   2.9170   1.1906  -0.5691
 H38  N07  N  NH1   0  -0.765   4.1973   0.9311  -0.0694
 H38  C06  C  C     0   0.367   4.8838  -0.2592  -0.2271
 H38  N06  N  N     0  -0.620   4.5356  -1.2793  -0.9041
 H38  C05  C  CR5   0  -0.241   6.1575  -0.3063   0.5060
 H38  S01  S  S2    0   0.238   6.4373   0.6395   1.9212
 H38  C02  C  CR15  0  -0.459   8.0105  -0.0013   2.1073
 H38  C03  C  CR15  0  -0.176   8.3065  -0.9068   1.1320
 H38  C04  C  CR15  0  -0.199   7.2416  -1.0846   0.2148
 H38  H1   H  H     0   0.347  -6.4009  -2.6105  -0.1383
 H38  H2   H  HCR5  0   0.306  -8.1287   2.1939   2.3641
 H38  H3   H  HCR5  0   0.276  -9.5457   0.8120   0.6409
 H38  H4   H  HCR5  0   0.278  -8.0648  -0.9326  -0.6407
 H38  H5   H  HNH1  0   0.411  -4.1004   0.5426  -0.0011
 H38  H6   H  HCR6  0   0.266  -1.9935   0.9979  -0.3547
 H38  H7   H  HCR6  0   0.288  -3.3150  -3.0762  -0.3943
 H38  H8   H  HCR6  0   0.258  -1.0127  -3.7972  -0.8371
 H38  H9   H  HCR6  0   0.250   0.8040  -2.1617  -1.0946
 H38  H10  H  HCR6  0   0.256  -0.6206   1.9917  -1.9128
 H38  H11  H  HCR6  0   0.263   1.1889   3.6416  -2.1340
 H38  H12  H  HCR6  0   0.270   3.4573   3.1320  -1.3197
 H38  H13  H  HCR6  0   0.282   2.0592  -0.6466   0.1366
 H38  H14  H  HNH1  0   0.407   4.7697   1.7496   0.0779
 H38  H15  H  H     0   0.343   3.6815  -1.1194  -1.4297
 H38  H16  H  HCR5  0   0.303   8.6332   0.3199   2.9281
 H38  H17  H  HCR5  0   0.273   9.2515  -1.4265   1.0693
 H38  H18  H  HCR5  0   0.269   7.2733  -1.7510  -0.6347

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
 H38  C03  C02  aromatic  1.363  0.020  1.363
 H38  C03  C04  aromatic  1.417  0.020  1.417
 H38  C02  S01  aromatic  1.709  0.020  1.709
 H38  C04  C05  aromatic  1.366  0.020  1.366
 H38  S01  C05  aromatic  1.725  0.020  1.725
 H38  C05  C06  single    1.470  0.020  1.470
 H38  C06  N06  double    1.273  0.020  1.273
 H38  C06  N07  single    1.383  0.020  1.383
 H38  C12  C13  aromatic  1.386  0.020  1.386
 H38  C12  C11  aromatic  1.393  0.020  1.393
 H38  C13  C14  aromatic  1.386  0.020  1.386
 H38  C11  N07  single    1.399  0.020  1.399
 H38  C11  C16  aromatic  1.393  0.020  1.393
 H38  C14  C15  aromatic  1.395  0.020  1.395
 H38  C34  C33  aromatic  1.384  0.020  1.384
 H38  C34  C35  aromatic  1.396  0.020  1.396
 H38  C16  C15  aromatic  1.394  0.020  1.394
 H38  C15  C35  single    1.478  0.020  1.478
 H38  C33  C32  aromatic  1.388  0.020  1.388
 H38  C35  C36  aromatic  1.389  0.020  1.389
 H38  C32  C31  aromatic  1.396  0.020  1.396
 H38  C36  C31  aromatic  1.398  0.020  1.398
 H38  C31  N27  single    1.391  0.020  1.391
 H38  N27  C26  single    1.371  0.020  1.371
 H38  C26  C25  single    1.476  0.020  1.476
 H38  C26  N26  double    1.275  0.020  1.275
 H38  C25  C24  aromatic  1.366  0.020  1.366
 H38  C25  S21  aromatic  1.725  0.020  1.725
 H38  C24  C23  aromatic  1.417  0.020  1.417
 H38  S21  C22  aromatic  1.709  0.020  1.709
 H38  C23  C22  aromatic  1.362  0.020  1.362
 H38  N26  H1   single    0.890  0.020  1.040
 H38  C22  H2   single    0.930  0.020  1.080
 H38  C23  H3   single    0.930  0.020  1.080
 H38  C24  H4   single    0.930  0.020  1.080
 H38  N27  H5   single    0.860  0.020  1.020
 H38  C36  H6   single    0.930  0.020  1.080
 H38  C32  H7   single    0.930  0.020  1.080
 H38  C33  H8   single    0.930  0.020  1.080
 H38  C34  H9   single    0.930  0.020  1.080
 H38  C14  H10  single    0.930  0.020  1.080
 H38  C13  H11  single    0.930  0.020  1.080
 H38  C12  H12  single    0.930  0.020  1.080
 H38  C16  H13  single    0.930  0.020  1.080
 H38  N07  H14  single    0.890  0.020  1.040
 H38  N06  H15  single    0.890  0.020  1.040
 H38  C02  H16  single    0.930  0.020  1.080
 H38  C03  H17  single    0.930  0.020  1.080
 H38  C04  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
 H38  H1   N26  C26  110.48  3.000
 H38  N27  C26  C25  113.50  3.000
 H38  C25  C26  N26  123.74  3.000
 H38  N27  C26  N26  122.75  3.000
 H38  C24  C25  S21  110.94  3.000
 H38  S21  C25  C26  122.28  3.000
 H38  C24  C25  C26  126.75  3.000
 H38  C22  S21  C25   91.94  3.000
 H38  H2   C22  C23  128.05  3.000
 H38  H2   C22  S21  120.18  3.000
 H38  C23  C22  S21  111.77  3.000
 H38  H3   C23  C24  123.97  3.000
 H38  H3   C23  C22  123.49  3.000
 H38  C24  C23  C22  112.54  3.000
 H38  H4   C24  C23  123.81  3.000
 H38  H4   C24  C25  123.37  3.000
 H38  C23  C24  C25  112.81  3.000
 H38  H5   N27  C31  114.06  3.000
 H38  H5   N27  C26  115.75  3.000
 H38  C31  N27  C26  129.68  3.000
 H38  C32  C31  C36  118.94  3.000
 H38  C36  C31  N27  116.43  3.000
 H38  C32  C31  N27  124.61  3.000
 H38  H6   C36  C35  119.41  3.000
 H38  H6   C36  C31  118.94  3.000
 H38  C35  C36  C31  121.64  3.000
 H38  H7   C32  C33  120.30  3.000
 H38  H7   C32  C31  120.45  3.000
 H38  C33  C32  C31  119.25  3.000
 H38  H8   C33  C34  119.53  3.000
 H38  H8   C33  C32  118.79  3.000
 H38  C34  C33  C32  121.68  3.000
 H38  H9   C34  C35  120.43  3.000
 H38  H9   C34  C33  119.94  3.000
 H38  C35  C34  C33  119.60  3.000
 H38  C15  C35  C34  120.70  3.000
 H38  C15  C35  C36  120.40  3.000
 H38  C34  C35  C36  118.89  3.000
 H38  C16  C15  C14  119.04  3.000
 H38  C16  C15  C35  120.00  3.000
 H38  C14  C15  C35  120.97  3.000
 H38  H10  C14  C13  119.66  3.000
 H38  H10  C14  C15  120.24  3.000
 H38  C13  C14  C15  120.09  3.000
 H38  H11  C13  C12  119.50  3.000
 H38  H11  C13  C14  119.74  3.000
 H38  C12  C13  C14  120.74  3.000
 H38  H12  C12  C11  120.02  3.000
 H38  H12  C12  C13  120.21  3.000
 H38  C11  C12  C13  119.78  3.000
 H38  H13  C16  C11  119.71  3.000
 H38  H13  C16  C15  119.36  3.000
 H38  C11  C16  C15  120.89  3.000
 H38  N07  C11  C16  121.10  3.000
 H38  C16  C11  C12  119.44  3.000
 H38  N07  C11  C12  119.40  3.000
 H38  H14  N07  C06  115.65  3.000
 H38  H14  N07  C11  114.88  3.000
 H38  C06  N07  C11  124.98  3.000
 H38  C05  C06  N06  118.45  3.000
 H38  N06  C06  N07  127.92  3.000
 H38  C05  C06  N07  113.62  3.000
 H38  H15  N06  C06  112.28  3.000
 H38  C04  C05  S01  111.02  3.000
 H38  S01  C05  C06  122.14  3.000
 H38  C04  C05  C06  126.83  3.000
 H38  C02  S01  C05   91.89  3.000
 H38  H16  C02  C03  128.06  3.000
 H38  H16  C02  S01  120.16  3.000
 H38  C03  C02  S01  111.78  3.000
 H38  H17  C03  C04  124.03  3.000
 H38  H17  C03  C02  123.43  3.000
 H38  C04  C03  C02  112.54  3.000
 H38  H18  C04  C03  124.37  3.000
 H38  H18  C04  C05  122.85  3.000
 H38  C03  C04  C05  112.77  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
 H38  CONST_01  C22  C23  C24  C25     0.00   0.0  0
 H38  CONST_02  C23  C22  S21  C25     0.00   0.0  0
 H38  CONST_03  C23  C24  C25  S21     0.00   0.0  0
 H38  CONST_04  C24  C23  C22  S21     0.00   0.0  0
 H38  CONST_05  C24  C25  S21  C22     0.00   0.0  0
 H38  CONST_06  C34  C33  C32  C31     0.00   0.0  0
 H38  CONST_07  C34  C35  C36  C31     0.00   0.0  0
 H38  CONST_08  C15  C35  C36  C31   180.00   0.0  0
 H38  CONST_09  C33  C34  C35  C36     0.00   0.0  0
 H38  CONST_12  C33  C32  C31  C36     0.00   0.0  0
 H38  CONST_13  C35  C34  C33  C32     0.00   0.0  0
 H38  CONST_14  C35  C36  C31  C32     0.00   0.0  0
 H38  CONST_15  C15  C35  C34  C33   180.00   0.0  0
 H38  CONST_18  C13  C14  C15  C35   180.00   0.0  0
 H38  CONST_19  C11  C16  C15  C35   180.00   0.0  0
 H38  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 H38  CONST_21  C12  C11  C16  C15     0.00   0.0  0
 H38  CONST_22  C11  C12  C13  C14     0.00   0.0  0
 H38  CONST_23  C11  C16  C15  C14     0.00   0.0  0
 H38  CONST_24  C16  C11  C12  C13     0.00   0.0  0
 H38  CONST_25  C16  C15  C14  C13     0.00   0.0  0
 H38  CONST_26  C02  C03  C04  C05     0.00   0.0  0
 H38  CONST_27  C03  C02  S01  C05     0.00   0.0  0
 H38  CONST_28  C04  C03  C02  S01     0.00   0.0  0
 H38  CONST_29  C03  C04  C05  S01     0.00   0.0  0
 H38  CONST_30  C04  C05  S01  C02     0.00   0.0  0
 H38  CONST_31  C23  C24  C25  C26   180.00   0.0  0
 H38  CONST_32  C22  S21  C25  C26   180.00   0.0  0
 H38  CONST_33  C33  C32  C31  N27   180.00   0.0  0
 H38  CONST_34  C35  C36  C31  N27   180.00   0.0  0
 H38  CONST_35  N07  C11  C16  C15   180.00   0.0  0
 H38  CONST_36  N07  C11  C12  C13   180.00   0.0  0
 H38  CONST_37  C03  C04  C05  C06   180.00   0.0  0
 H38  CONST_38  C02  S01  C05  C06   180.00   0.0  0
 H38  CONST_39  H3   C23  C24  C25   180.00   0.0  0
 H38  CONST_40  H2   C22  S21  C25   180.00   0.0  0
 H38  CONST_41  H4   C24  C25  S21   180.00   0.0  0
 H38  CONST_42  H8   C33  C32  C31   180.00   0.0  0
 H38  CONST_43  H9   C34  C35  C36   180.00   0.0  0
 H38  CONST_44  H7   C32  C31  C36   180.00   0.0  0
 H38  CONST_45  H6   C36  C31  C32   180.00   0.0  0
 H38  CONST_46  H10  C14  C15  C35     0.00   0.0  0
 H38  CONST_47  H13  C16  C15  C35     0.00   0.0  0
 H38  CONST_48  H11  C13  C14  C15   180.00   0.0  0
 H38  CONST_49  H12  C12  C13  C14   180.00   0.0  0
 H38  CONST_50  H17  C03  C04  C05   180.00   0.0  0
 H38  CONST_51  H16  C02  S01  C05   180.00   0.0  0
 H38  CONST_52  H18  C04  C05  S01   180.00   0.0  0
 H38  CONST_53  C32  C31  N27  C26     0.00   0.0  0
 H38  CONST_54  C36  C31  N27  C26   180.00   0.0  0
 H38  CONST_55  C31  N27  C26  C25   180.00   0.0  0
 H38  CONST_58  C05  C06  N07  C11   180.00   0.0  0
 H38  CONST_59  H5   N27  C31  C36     0.00   0.0  0
 H38  CONST_61  C31  N27  C26  N26     0.00   0.0  0
 H38  CONST_62  N06  C06  N07  C11     0.00   0.0  0
 H38  CONST_63  H1   N26  C26  C25     0.00   0.0  0
 H38  CONST_64  H15  N06  C06  C05   180.00   0.0  0
 H38  Var_01    C24  C25  C26  N26   -33.78  30.0  2
 H38  Var_02    C04  C05  C06  N07  -155.70  30.0  2

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
 H38  plan-1  C26  0.020
 H38  plan-1  C25  0.020
 H38  plan-1  S21  0.020
 H38  plan-1  C22  0.020
 H38  plan-1  C23  0.020
 H38  plan-1  C24  0.020
 H38  plan-1  H2   0.020
 H38  plan-1  H3   0.020
 H38  plan-1  H4   0.020
 H38  plan-2  C06  0.020
 H38  plan-2  C05  0.020
 H38  plan-2  S01  0.020
 H38  plan-2  C02  0.020
 H38  plan-2  C03  0.020
 H38  plan-2  C04  0.020
 H38  plan-2  H16  0.020
 H38  plan-2  H17  0.020
 H38  plan-2  H18  0.020
 H38  plan-3  N27  0.020
 H38  plan-3  C31  0.020
 H38  plan-3  C36  0.020
 H38  plan-3  C32  0.020
 H38  plan-3  C33  0.020
 H38  plan-3  C34  0.020
 H38  plan-3  C35  0.020
 H38  plan-3  C15  0.020
 H38  plan-3  H6   0.020
 H38  plan-3  H7   0.020
 H38  plan-3  H8   0.020
 H38  plan-3  H9   0.020
 H38  plan-4  C35  0.020
 H38  plan-4  C15  0.020
 H38  plan-4  C14  0.020
 H38  plan-4  C13  0.020
 H38  plan-4  C12  0.020
 H38  plan-4  C16  0.020
 H38  plan-4  C11  0.020
 H38  plan-4  N07  0.020
 H38  plan-4  H10  0.020
 H38  plan-4  H11  0.020
 H38  plan-4  H12  0.020
 H38  plan-4  H13  0.020
 H38  plan-5  N26  0.020
 H38  plan-5  C26  0.020
 H38  plan-5  C25  0.020
 H38  plan-5  N27  0.020
 H38  plan-5  C31  0.020
 H38  plan-5  H1   0.020
 H38  plan-5  H5   0.020
 H38  plan-6  C11  0.020
 H38  plan-6  N07  0.020
 H38  plan-6  C06  0.020
 H38  plan-6  N06  0.020
 H38  plan-6  C05  0.020
 H38  plan-6  H14  0.020
 H38  plan-6  H15  0.020

