# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:13:45 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 7-(6-azanylpyridin-2-yl)-1-benzothiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1sc2c(cccc2c3cccc(N)n3)c1
#
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
 K6B  K6B  7-(6-azanylpyridin-2-yl)-1-benzothiophene-2-carboximidamide  ligand  31  19  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K6B
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
 K6B  C10   C  CR16  0  -0.232  -19.1866  22.0678   4.6584
 K6B  C13   C  CR6   0   0.287  -19.8564  22.3504   8.3847
 K6B  C15   C  CR6   0   0.466  -20.3328  21.8365  10.5859
 K6B  C17   C  CR16  0  -0.140  -19.9408  24.1099   9.9860
 K6B  C02   C  CR56  0  -0.255  -19.7577  20.4045   6.7994
 K6B  C03   C  CR56  0   0.234  -19.5586  19.8648   5.5126
 K6B  C04   C  CR15  0  -0.239  -19.6893  18.4408   5.4902
 K6B  C05   C  CR5   0  -0.265  -19.9837  17.9309   6.7085
 K6B  C06   C  C     0   0.354  -20.2229  16.5162   7.0600
 K6B  C09   C  CR16  0  -0.330  -19.2726  20.7103   4.4371
 K6B  C11   C  CR16  0  -0.377  -19.3790  22.5922   5.9368
 K6B  C12   C  CR6   0   0.098  -19.6635  21.7878   7.0343
 K6B  C16   C  CR16  0  -0.393  -20.2365  23.1866  10.9637
 K6B  C18   C  CR16  0  -0.392  -19.7453  23.7063   8.6690
 K6B  N07   N  N     0  -0.639  -20.9897  16.1209   8.0038
 K6B  N08   N  NH2   0  -0.804  -19.5877  15.6212   6.2539
 K6B  N14   N  N     0  -0.527  -20.1411  21.4554   9.3281
 K6B  N19   N  NH2   0  -0.838  -20.6699  20.8712  11.4836
 K6B  S01   S  S2    0   0.235  -20.1019  19.1491   7.9491
 K6B  H101  H  HCR6  0   0.264  -18.9682  22.7391   3.8389
 K6B  H171  H  HCR6  0   0.270  -19.8588  25.1580  10.2436
 K6B  H041  H  HCR5  0   0.274  -19.5884  17.8519   4.5886
 K6B  H091  H  HCR6  0   0.262  -19.1214  20.2976   3.4479
 K6B  H111  H  HCR6  0   0.260  -19.3037  23.6636   6.0605
 K6B  H161  H  HCR6  0   0.270  -20.3928  23.4844  11.9921
 K6B  H181  H  HCR6  0   0.264  -19.5134  24.4378   7.9098
 K6B  H071  H  H     0   0.331  -21.4742  16.8974   8.4386
 K6B  H081  H  HNH2  0   0.387  -19.6367  14.6556   6.5390
 K6B  H1    H  HNH2  0   0.395  -18.7089  15.8877   5.8423
 K6B  H192  H  HNH2  0   0.386  -20.4791  19.9189  11.2201
 K6B  H191  H  HNH2  0   0.393  -20.5400  21.0693  12.4612

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
 K6B  C09  C10   aromatic  1.378  0.020  1.378
 K6B  C09  C03   aromatic  1.398  0.020  1.398
 K6B  C10  C11   aromatic  1.395  0.020  1.395
 K6B  C04  C03   aromatic  1.430  0.020  1.430
 K6B  C04  C05   aromatic  1.353  0.020  1.353
 K6B  C03  C02   aromatic  1.410  0.020  1.410
 K6B  N08  C06   single    1.362  0.020  1.362
 K6B  C11  C12   aromatic  1.390  0.020  1.390
 K6B  C05  C06   single    1.477  0.020  1.477
 K6B  C05  S01   aromatic  1.743  0.020  1.743
 K6B  C06  N07   double    1.279  0.020  1.279
 K6B  C02  C12   aromatic  1.406  0.020  1.406
 K6B  C02  S01   aromatic  1.737  0.020  1.737
 K6B  C12  C13   single    1.476  0.020  1.476
 K6B  C13  C18   aromatic  1.390  0.020  1.390
 K6B  C13  N14   aromatic  1.331  0.020  1.331
 K6B  C18  C17   aromatic  1.391  0.020  1.391
 K6B  N14  C15   aromatic  1.328  0.020  1.328
 K6B  C17  C16   aromatic  1.377  0.020  1.377
 K6B  C15  C16   aromatic  1.405  0.020  1.405
 K6B  C15  N19   single    1.361  0.020  1.361
 K6B  C10  H101  single    0.930  0.020  1.080
 K6B  C17  H171  single    0.930  0.020  1.080
 K6B  C04  H041  single    0.930  0.020  1.080
 K6B  C09  H091  single    0.930  0.020  1.080
 K6B  C11  H111  single    0.930  0.020  1.080
 K6B  C16  H161  single    0.930  0.020  1.080
 K6B  C18  H181  single    0.930  0.020  1.080
 K6B  N07  H071  single    0.890  0.020  1.040
 K6B  N08  H081  single    0.890  0.020  1.040
 K6B  N08  H1    single    0.890  0.020  1.040
 K6B  N19  H192  single    0.890  0.020  1.040
 K6B  N19  H191  single    0.890  0.020  1.040

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
 K6B  H101  C10  C11   119.26  3.000
 K6B  H101  C10  C09   120.15  3.000
 K6B  C11   C10  C09   120.59  3.000
 K6B  N14   C13  C18   121.87  3.000
 K6B  N14   C13  C12   114.85  3.000
 K6B  C18   C13  C12   123.28  3.000
 K6B  N19   C15  N14   117.20  3.000
 K6B  N19   C15  C16   121.41  3.000
 K6B  N14   C15  C16   121.36  3.000
 K6B  H171  C17  C18   119.71  3.000
 K6B  H171  C17  C16   119.78  3.000
 K6B  C18   C17  C16   120.51  3.000
 K6B  S01   C02  C12   127.86  3.000
 K6B  S01   C02  C03   110.83  3.000
 K6B  C12   C02  C03   121.31  3.000
 K6B  C09   C03  C04   127.52  3.000
 K6B  C04   C03  C02   112.50  3.000
 K6B  C09   C03  C02   119.98  3.000
 K6B  H041  C04  C05   124.45  3.000
 K6B  H041  C04  C03   123.14  3.000
 K6B  C05   C04  C03   112.39  3.000
 K6B  S01   C05  C06   119.28  3.000
 K6B  S01   C05  C04   113.10  3.000
 K6B  C06   C05  C04   127.61  3.000
 K6B  N08   C06  N07   120.89  3.000
 K6B  N07   C06  C05   124.67  3.000
 K6B  N08   C06  C05   114.40  3.000
 K6B  H091  C09  C03   120.07  3.000
 K6B  H091  C09  C10   120.91  3.000
 K6B  C03   C09  C10   119.02  3.000
 K6B  H111  C11  C12   119.83  3.000
 K6B  H111  C11  C10   117.89  3.000
 K6B  C12   C11  C10   122.28  3.000
 K6B  C11   C12  C02   116.81  3.000
 K6B  C02   C12  C13   121.27  3.000
 K6B  C11   C12  C13   121.91  3.000
 K6B  H161  C16  C17   121.42  3.000
 K6B  H161  C16  C15   120.66  3.000
 K6B  C17   C16  C15   117.91  3.000
 K6B  H181  C18  C17   119.95  3.000
 K6B  H181  C18  C13   122.30  3.000
 K6B  C17   C18  C13   117.74  3.000
 K6B  H071  N07  C06   111.50  3.000
 K6B  H1    N08  H081  114.33  3.000
 K6B  H1    N08  C06   118.38  3.000
 K6B  H081  N08  C06   116.07  3.000
 K6B  C15   N14  C13   120.60  3.000
 K6B  H191  N19  H192  114.61  3.000
 K6B  H191  N19  C15   118.00  3.000
 K6B  H192  N19  C15   116.85  3.000
 K6B  C05   S01  C02    91.18  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
 K6B  CONST_01  C04   C03  C09  C10  180.00   0.0  0
 K6B  CONST_02  C02   C03  C09  C10    0.00   0.0  0
 K6B  CONST_03  C02   C12  C11  C10    0.00   0.0  0
 K6B  CONST_04  C13   C12  C11  C10  180.00   0.0  0
 K6B  CONST_05  C03   C02  C12  C13  180.00   0.0  0
 K6B  CONST_06  S01   C02  C12  C13    0.00   0.0  0
 K6B  CONST_07  C16   C17  C18  C13    0.00   0.0  0
 K6B  CONST_08  C16   C15  N14  C13    0.00   0.0  0
 K6B  CONST_09  C12   C13  N14  C15  180.00   0.0  0
 K6B  CONST_10  C18   C13  N14  C15    0.00   0.0  0
 K6B  CONST_11  C18   C17  C16  C15    0.00   0.0  0
 K6B  CONST_12  C12   C13  C18  C17  180.00   0.0  0
 K6B  CONST_13  N14   C13  C18  C17    0.00   0.0  0
 K6B  CONST_14  N14   C15  C16  C17    0.00   0.0  0
 K6B  CONST_15  C05   C04  C03  C02    0.00   0.0  0
 K6B  CONST_16  C18   C13  C12  C02  180.00   0.0  0
 K6B  CONST_17  N14   C13  C12  C02    0.00   0.0  0
 K6B  CONST_18  C04   C05  S01  C02    0.00   0.0  0
 K6B  CONST_19  C11   C10  C09  C03    0.00   0.0  0
 K6B  CONST_20  S01   C05  C04  C03    0.00   0.0  0
 K6B  CONST_21  C11   C12  C02  C03    0.00   0.0  0
 K6B  CONST_22  C05   S01  C02  C03    0.00   0.0  0
 K6B  CONST_23  C12   C02  C03  C04  180.00   0.0  0
 K6B  CONST_24  S01   C02  C03  C04    0.00   0.0  0
 K6B  CONST_25  C09   C03  C04  C05  180.00   0.0  0
 K6B  CONST_26  C12   C02  S01  C05  180.00   0.0  0
 K6B  CONST_27  C12   C11  C10  C09    0.00   0.0  0
 K6B  CONST_28  C12   C02  C03  C09    0.00   0.0  0
 K6B  CONST_29  S01   C02  C03  C09  180.00   0.0  0
 K6B  CONST_30  S01   C02  C12  C11  180.00   0.0  0
 K6B  CONST_31  C18   C13  C12  C11    0.00   0.0  0
 K6B  CONST_32  N14   C13  C12  C11  180.00   0.0  0
 K6B  CONST_33  N19   C15  N14  C13  180.00   0.0  0
 K6B  CONST_34  N19   C15  C16  C17  180.00   0.0  0
 K6B  CONST_35  C06   C05  S01  C02  180.00   0.0  0
 K6B  CONST_36  C06   C05  C04  C03  180.00   0.0  0
 K6B  CONST_37  H111  C11  C12  C13    0.00   0.0  0
 K6B  CONST_38  H171  C17  C18  C13  180.00   0.0  0
 K6B  CONST_39  H091  C09  C03  C02  180.00   0.0  0
 K6B  CONST_40  H041  C04  C03  C02  180.00   0.0  0
 K6B  CONST_41  H101  C10  C09  C03  180.00   0.0  0
 K6B  CONST_42  H181  C18  C13  C12    0.00   0.0  0
 K6B  CONST_43  H161  C16  C17  C18  180.00   0.0  0
 K6B  CONST_46  H081  N08  C06  C05  180.00   0.0  0
 K6B  CONST_48  H071  N07  C06  C05    0.00   0.0  0
 K6B  Var_01    N08   C06  C05  C04   27.67  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
 K6B  plan-1  C13   0.020
 K6B  plan-1  C15   0.020
 K6B  plan-1  C17   0.020
 K6B  plan-1  C12   0.020
 K6B  plan-1  C16   0.020
 K6B  plan-1  C18   0.020
 K6B  plan-1  N14   0.020
 K6B  plan-1  N19   0.020
 K6B  plan-1  H171  0.020
 K6B  plan-1  H161  0.020
 K6B  plan-1  H181  0.020
 K6B  plan-2  C10   0.020
 K6B  plan-2  C13   0.020
 K6B  plan-2  C02   0.020
 K6B  plan-2  C03   0.020
 K6B  plan-2  C04   0.020
 K6B  plan-2  C05   0.020
 K6B  plan-2  C06   0.020
 K6B  plan-2  C09   0.020
 K6B  plan-2  C11   0.020
 K6B  plan-2  C12   0.020
 K6B  plan-2  S01   0.020
 K6B  plan-2  H101  0.020
 K6B  plan-2  H041  0.020
 K6B  plan-2  H091  0.020
 K6B  plan-2  H111  0.020
 K6B  plan-3  C15   0.020
 K6B  plan-3  N19   0.020
 K6B  plan-3  H192  0.020
 K6B  plan-3  H191  0.020
 K6B  plan-4  C05   0.020
 K6B  plan-4  C06   0.020
 K6B  plan-4  N07   0.020
 K6B  plan-4  N08   0.020
 K6B  plan-4  H071  0.020
 K6B  plan-4  H081  0.020
 K6B  plan-4  H1    0.020

