# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:41:59 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: 7-(6-azanyl-5-methyl-pyridin-2-yl)-1-benzothiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(nc1N)c2cccc3cc(sc23)C(N)=N
#
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
 K8W  K8W  7-(6-azanyl-5-methyl-pyridin-2-yl)-1-benzothiophene-2-carboximidamide  ligand  34  20  .  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_K8W
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
 K8W  C10   C  CR16  0  -0.317  18.3478  21.8708   -4.9966
 K8W  C13   C  CR56  0   0.247  18.7516  19.1402   -4.7564
 K8W  C17   C  CR15  0  -0.243  19.0930  17.7529   -4.8089
 K8W  C02   C  CR6   0  -0.013  20.1709  23.5239   -9.3849
 K8W  C03   C  CR16  0  -0.195  19.6399  22.2710   -9.5973
 K8W  C04   C  CR16  0  -0.370  19.2311  21.4710   -8.5314
 K8W  C05   C  CR6   0   0.189  19.3847  21.9732   -7.2501
 K8W  C07   C  CR6   0   0.395  20.2684  23.9460   -8.0370
 K8W  C09   C  CR6   0   0.121  18.9611  21.2125   -6.0538
 K8W  C11   C  CR16  0  -0.239  17.9228  21.1941   -3.8506
 K8W  C12   C  CR16  0  -0.332  18.1167  19.8355   -3.7222
 K8W  C14   C  CR56  0  -0.303  19.1641  19.8336   -5.9105
 K8W  C16   C  CR5   0  -0.251  19.7492  17.4147   -5.9433
 K8W  C18   C  C     0   0.347  20.2409  16.0718   -6.3132
 K8W  N06   N  N     0  -0.474  19.8891  23.1861   -7.0184
 K8W  N08   N  NH2   0  -0.837  20.7236  25.1964   -7.7372
 K8W  N19   N  NH2   0  -0.811  21.3365  16.0703   -7.1269
 K8W  N20   N  N     0  -0.631  19.6811  14.9832   -5.9518
 K8W  S15   S  S2    0   0.225  19.9718  18.7661   -7.0166
 K8W  H101  H  HCR6  0   0.257  18.1889  22.9382   -5.0731
 K8W  H171  H  HCR5  0   0.280  18.8784  17.0558   -4.0104
 K8W  H011  H  HCH3  0   0.249  20.0340  25.3525  -10.5101
 K8W  H012  H  HCH3  0   0.247  21.6574  24.6855  -10.4324
 K8W  H013  H  HCH3  0   0.258  20.4510  23.9334  -11.4687
 K8W  H031  H  HCR6  0   0.260  19.5238  21.9085  -10.6117
 K8W  H041  H  HCR6  0   0.260  18.7716  20.5110   -8.7193
 K8W  H111  H  HCR6  0   0.263  17.4378  21.7474   -3.0576
 K8W  H121  H  HCR6  0   0.262  17.7913  19.3099   -2.8339
 K8W  H082  H  HNH2  0   0.383  20.9593  25.3581   -6.7716
 K8W  H081  H  HNH2  0   0.396  21.3400  25.6526   -8.3887
 K8W  H191  H  HNH2  0   0.390  21.7542  15.1668   -7.2892
 K8W  H1    H  HNH2  0   0.394  22.0132  16.8075   -7.0104
 K8W  H201  H  H     0   0.339  18.8193  15.1684   -5.4524
 K8W  C01   C  CH3   0  -0.745  20.6000  24.4178  -10.5052

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
 K8W  C01  C02   single    1.496  0.020  1.496
 K8W  C03  C02   aromatic  1.377  0.020  1.377
 K8W  C03  C04   aromatic  1.394  0.020  1.394
 K8W  C02  C07   aromatic  1.416  0.020  1.416
 K8W  C04  C05   aromatic  1.385  0.020  1.385
 K8W  C07  N08   single    1.364  0.020  1.364
 K8W  C07  N06   aromatic  1.326  0.020  1.326
 K8W  N19  C18   single    1.365  0.020  1.365
 K8W  C05  N06   aromatic  1.334  0.020  1.334
 K8W  C05  C09   single    1.480  0.020  1.480
 K8W  S15  C16   aromatic  1.740  0.020  1.740
 K8W  S15  C14   aromatic  1.737  0.020  1.737
 K8W  C18  C16   single    1.477  0.020  1.477
 K8W  C18  N20   double    1.276  0.020  1.276
 K8W  C09  C14   aromatic  1.401  0.020  1.401
 K8W  C09  C10   aromatic  1.388  0.020  1.388
 K8W  C16  C17   aromatic  1.353  0.020  1.353
 K8W  C14  C13   aromatic  1.408  0.020  1.408
 K8W  C10  C11   aromatic  1.397  0.020  1.397
 K8W  C17  C13   aromatic  1.430  0.020  1.430
 K8W  C13  C12   aromatic  1.399  0.020  1.399
 K8W  C11  C12   aromatic  1.378  0.020  1.378
 K8W  C10  H101  single    0.930  0.020  1.080
 K8W  C17  H171  single    0.930  0.020  1.080
 K8W  C01  H011  single    0.970  0.020  1.090
 K8W  C01  H012  single    0.970  0.020  1.090
 K8W  C01  H013  single    0.970  0.020  1.090
 K8W  C03  H031  single    0.930  0.020  1.080
 K8W  C04  H041  single    0.930  0.020  1.080
 K8W  C11  H111  single    0.930  0.020  1.080
 K8W  C12  H121  single    0.930  0.020  1.080
 K8W  N08  H082  single    0.890  0.020  1.040
 K8W  N08  H081  single    0.890  0.020  1.040
 K8W  N19  H191  single    0.890  0.020  1.040
 K8W  N19  H1    single    0.890  0.020  1.040
 K8W  N20  H201  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
 K8W  H101  C10  C11   119.42  3.000
 K8W  H101  C10  C09   118.62  3.000
 K8W  C11   C10  C09   121.96  3.000
 K8W  C14   C13  C12   119.62  3.000
 K8W  C12   C13  C17   128.17  3.000
 K8W  C14   C13  C17   112.19  3.000
 K8W  H171  C17  C16   123.64  3.000
 K8W  H171  C17  C13   123.43  3.000
 K8W  C16   C17  C13   112.90  3.000
 K8W  C07   C02  C03   116.40  3.000
 K8W  C07   C02  C01   121.00  3.000
 K8W  C03   C02  C01   122.59  3.000
 K8W  H031  C03  C04   119.50  3.000
 K8W  H031  C03  C02   119.35  3.000
 K8W  C04   C03  C02   121.14  3.000
 K8W  H041  C04  C05   122.01  3.000
 K8W  H041  C04  C03   120.10  3.000
 K8W  C05   C04  C03   117.83  3.000
 K8W  N06   C05  C09   115.80  3.000
 K8W  C09   C05  C04   122.00  3.000
 K8W  N06   C05  C04   122.17  3.000
 K8W  N08   C07  N06   116.86  3.000
 K8W  N06   C07  C02   122.74  3.000
 K8W  N08   C07  C02   120.37  3.000
 K8W  C14   C09  C05   123.17  3.000
 K8W  C14   C09  C10   116.93  3.000
 K8W  C05   C09  C10   119.89  3.000
 K8W  H111  C11  C12   119.93  3.000
 K8W  H111  C11  C10   119.34  3.000
 K8W  C12   C11  C10   120.73  3.000
 K8W  H121  C12  C11   120.86  3.000
 K8W  H121  C12  C13   120.13  3.000
 K8W  C11   C12  C13   119.01  3.000
 K8W  S15   C14  C09   127.39  3.000
 K8W  C09   C14  C13   121.73  3.000
 K8W  S15   C14  C13   110.83  3.000
 K8W  S15   C16  C18   120.60  3.000
 K8W  C18   C16  C17   126.76  3.000
 K8W  S15   C16  C17   112.64  3.000
 K8W  N20   C18  N19   121.33  3.000
 K8W  N20   C18  C16   123.95  3.000
 K8W  N19   C18  C16   114.68  3.000
 K8W  C07   N06  C05   119.71  3.000
 K8W  H081  N08  H082  113.87  3.000
 K8W  H081  N08  C07   118.53  3.000
 K8W  H082  N08  C07   115.86  3.000
 K8W  H1    N19  H191  113.32  3.000
 K8W  H1    N19  C18   118.00  3.000
 K8W  H191  N19  C18   115.44  3.000
 K8W  H201  N20  C18   110.90  3.000
 K8W  C16   S15  C14    91.43  3.000
 K8W  H013  C01  H012  107.47  3.000
 K8W  H013  C01  H011  107.80  3.000
 K8W  H012  C01  H011  106.97  3.000
 K8W  H013  C01  C02   110.96  3.000
 K8W  H012  C01  C02   111.95  3.000
 K8W  H011  C01  C02   111.46  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
 K8W  CONST_03  S15   C14  C09  C10   180.00   0.0  0
 K8W  CONST_04  C13   C14  C09  C10     0.00   0.0  0
 K8W  CONST_05  C13   C12  C11  C10     0.00   0.0  0
 K8W  CONST_06  C16   S15  C14  C13     0.00   0.0  0
 K8W  CONST_07  C05   C09  C14  C13   180.00   0.0  0
 K8W  CONST_08  S15   C16  C17  C13     0.00   0.0  0
 K8W  CONST_09  C14   S15  C16  C17     0.00   0.0  0
 K8W  CONST_10  S15   C14  C13  C17     0.00   0.0  0
 K8W  CONST_11  C09   C14  C13  C17   180.00   0.0  0
 K8W  CONST_12  C11   C12  C13  C17   180.00   0.0  0
 K8W  CONST_13  C05   C04  C03  C02     0.00   0.0  0
 K8W  CONST_14  C05   N06  C07  C02     0.00   0.0  0
 K8W  CONST_15  N06   C07  C02  C03     0.00   0.0  0
 K8W  CONST_16  N06   C05  C04  C03     0.00   0.0  0
 K8W  CONST_17  C09   C05  C04  C03   180.00   0.0  0
 K8W  CONST_18  C07   C02  C03  C04     0.00   0.0  0
 K8W  CONST_19  C07   N06  C05  C04     0.00   0.0  0
 K8W  CONST_21  S15   C14  C09  C05     0.00   0.0  0
 K8W  CONST_22  C11   C10  C09  C05   180.00   0.0  0
 K8W  CONST_23  C09   C05  N06  C07   180.00   0.0  0
 K8W  CONST_24  C16   S15  C14  C09   180.00   0.0  0
 K8W  CONST_25  C12   C13  C14  C09     0.00   0.0  0
 K8W  CONST_26  C12   C11  C10  C09     0.00   0.0  0
 K8W  CONST_27  C14   C09  C10  C11     0.00   0.0  0
 K8W  CONST_28  C14   C13  C12  C11     0.00   0.0  0
 K8W  CONST_29  S15   C14  C13  C12   180.00   0.0  0
 K8W  CONST_30  C16   C17  C13  C12   180.00   0.0  0
 K8W  CONST_32  C16   C17  C13  C14     0.00   0.0  0
 K8W  CONST_33  C18   C16  C17  C13   180.00   0.0  0
 K8W  CONST_34  C04   C03  C02  C01   180.00   0.0  0
 K8W  CONST_35  N06   C07  C02  C01   180.00   0.0  0
 K8W  CONST_36  N08   C07  C02  C03   180.00   0.0  0
 K8W  CONST_37  N08   C07  N06  C05   180.00   0.0  0
 K8W  CONST_38  C18   C16  S15  C14   180.00   0.0  0
 K8W  CONST_39  H121  C12  C11  C10   180.00   0.0  0
 K8W  CONST_40  H111  C11  C12  C13   180.00   0.0  0
 K8W  CONST_41  H041  C04  C03  C02   180.00   0.0  0
 K8W  CONST_42  H031  C03  C04  C05   180.00   0.0  0
 K8W  CONST_43  H101  C10  C09  C05     0.00   0.0  0
 K8W  CONST_44  H171  C17  C13  C12     0.00   0.0  0
 K8W  CONST_45  H082  N08  C07  C02   180.00   0.0  0
 K8W  CONST_47  H191  N19  C18  C16   180.00   0.0  0
 K8W  CONST_49  H201  N20  C18  C16     0.00   0.0  0
 K8W  Var_01    N19   C18  C16  C17  -151.43  30.0  3
 K8W  Var_02    H011  C01  C02  C03   119.04  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
 K8W  plan-1  C02   0.020
 K8W  plan-1  C03   0.020
 K8W  plan-1  C04   0.020
 K8W  plan-1  C05   0.020
 K8W  plan-1  C07   0.020
 K8W  plan-1  C09   0.020
 K8W  plan-1  N06   0.020
 K8W  plan-1  N08   0.020
 K8W  plan-1  H031  0.020
 K8W  plan-1  H041  0.020
 K8W  plan-1  C01   0.020
 K8W  plan-2  C10   0.020
 K8W  plan-2  C13   0.020
 K8W  plan-2  C17   0.020
 K8W  plan-2  C05   0.020
 K8W  plan-2  C09   0.020
 K8W  plan-2  C11   0.020
 K8W  plan-2  C12   0.020
 K8W  plan-2  C14   0.020
 K8W  plan-2  C16   0.020
 K8W  plan-2  C18   0.020
 K8W  plan-2  S15   0.020
 K8W  plan-2  H101  0.020
 K8W  plan-2  H171  0.020
 K8W  plan-2  H111  0.020
 K8W  plan-2  H121  0.020
 K8W  plan-3  C07   0.020
 K8W  plan-3  N08   0.020
 K8W  plan-3  H082  0.020
 K8W  plan-3  H081  0.020
 K8W  plan-4  C16   0.020
 K8W  plan-4  C18   0.020
 K8W  plan-4  N19   0.020
 K8W  plan-4  N20   0.020
 K8W  plan-4  H191  0.020
 K8W  plan-4  H1    0.020
 K8W  plan-4  H201  0.020

