# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:45:24 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: 5-[1-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCn1cnc(c1)c2sc(cc2c3ccccc3)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
 K7N  K7N  5-[1-(2-azanylethyl)imidazol-4-yl]-4-phenyl-thiophene-2-carboximidamide  ligand  39  22  .  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_K7N
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
 K7N  C13   C  CR15  0  -0.118  -18.3334  22.4102   5.4504
 K7N  C15   C  CR15  0   0.095  -18.0551  22.0415   3.3164
 K7N  C17   C  CH2   0  -0.314  -17.2787  24.2733   4.1424
 K7N  C01   C  CR16  0  -0.263  -19.9325  23.5144   9.7938
 K7N  C02   C  CR16  0  -0.240  -19.1207  22.4431  10.1406
 K7N  C03   C  CR16  0  -0.297  -19.0449  21.3294   9.3145
 K7N  C04   C  CR6   0   0.007  -19.7779  21.2752   8.1305
 K7N  C05   C  CR16  0  -0.295  -20.6007  22.3508   7.7965
 K7N  C06   C  CR16  0  -0.238  -20.6750  23.4639   8.6203
 K7N  C07   C  CR5   0   0.169  -19.7059  20.0858   7.2609
 K7N  C08   C  CR15  0  -0.232  -20.0806  18.7889   7.6993
 K7N  C09   C  CR5   0  -0.259  -19.9654  17.8321   6.7339
 K7N  C11   C  CR5   0  -0.305  -19.2892  20.0867   5.9496
 K7N  C12   C  CR5   0   0.151  -18.7601  21.1473   5.1186
 K7N  C18   C  CH2   0  -0.296  -15.8330  24.2817   4.6105
 K7N  N14   N  NR5   0  -0.402  -17.8947  22.9666   4.2869
 K7N  N16   N  N     0  -0.466  -18.5749  20.9362   3.7792
 K7N  N19   N  NH2   0  -0.798  -15.0254  23.3663   3.8251
 K7N  N21   N  N     0  -0.636  -21.1798  15.9285   7.6439
 K7N  N22   N  NH2   0  -0.813  -19.6229  15.5875   5.9843
 K7N  S10   S  S2    0   0.268  -19.3842  18.5102   5.2599
 K7N  H131  H  HCR5  0   0.293  -18.3003  22.9434   6.3851
 K7N  H151  H  HCR5  0   0.289  -17.7843  22.2336   2.2892
 K7N  H171  H  HCH2  0   0.267  -17.3328  24.5486   3.0897
 K7N  H172  H  HCH2  0   0.271  -17.8642  24.9979   4.7076
 K7N  H011  H  HCR6  0   0.258  -19.9894  24.3827  10.4374
 K7N  H021  H  HCR6  0   0.258  -18.5420  22.4738  11.0546
 K7N  H031  H  HCR6  0   0.252  -18.4027  20.5005   9.5864
 K7N  H051  H  HCR6  0   0.256  -21.1878  22.3129   6.8871
 K7N  H061  H  HCR6  0   0.258  -21.3192  24.2905   8.3496
 K7N  H081  H  HCR5  0   0.272  -20.4217  18.5845   8.7055
 K7N  H181  H  HCH2  0   0.211  -15.8032  24.0928   5.6923
 K7N  H182  H  HCH2  0   0.244  -15.4577  25.2960   4.4630
 K7N  H191  H  HNH2  0   0.357  -14.0476  23.5191   4.0337
 K7N  H192  H  HNH2  0   0.346  -15.2129  22.4119   4.1049
 K7N  H211  H  H     0   0.336  -21.6750  16.6724   8.1218
 K7N  H222  H  HNH2  0   0.387  -19.7753  14.5991   6.1138
 K7N  H221  H  HNH2  0   0.392  -18.6660  15.8186   5.7699
 K7N  C20   C  C     0   0.335  -20.3000  16.4023   6.8480

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
 K7N  N19  C18   single    1.452  0.020  1.452
 K7N  C15  N16   aromatic  1.306  0.020  1.306
 K7N  C15  N14   aromatic  1.350  0.020  1.350
 K7N  C17  N14   single    1.452  0.020  1.452
 K7N  C17  C18   single    1.520  0.020  1.520
 K7N  N16  C12   aromatic  1.369  0.020  1.369
 K7N  N14  C13   aromatic  1.362  0.020  1.362
 K7N  C12  C13   aromatic  1.374  0.020  1.374
 K7N  C12  C11   single    1.448  0.020  1.448
 K7N  S10  C11   aromatic  1.723  0.020  1.723
 K7N  S10  C09   aromatic  1.723  0.020  1.723
 K7N  N22  C20   single    1.367  0.020  1.367
 K7N  C11  C07   aromatic  1.376  0.020  1.376
 K7N  C09  C20   single    1.473  0.020  1.473
 K7N  C09  C08   aromatic  1.364  0.020  1.364
 K7N  C20  N21   double    1.278  0.020  1.278
 K7N  C07  C08   aromatic  1.419  0.020  1.419
 K7N  C07  C04   single    1.475  0.020  1.475
 K7N  C05  C04   aromatic  1.395  0.020  1.395
 K7N  C05  C06   aromatic  1.387  0.020  1.387
 K7N  C04  C03   aromatic  1.394  0.020  1.394
 K7N  C06  C01   aromatic  1.390  0.020  1.390
 K7N  C03  C02   aromatic  1.389  0.020  1.389
 K7N  C01  C02   aromatic  1.388  0.020  1.388
 K7N  C13  H131  single    0.930  0.020  1.080
 K7N  C15  H151  single    0.930  0.020  1.080
 K7N  C17  H171  single    0.970  0.020  1.090
 K7N  C17  H172  single    0.970  0.020  1.090
 K7N  C01  H011  single    0.930  0.020  1.080
 K7N  C02  H021  single    0.930  0.020  1.080
 K7N  C03  H031  single    0.930  0.020  1.080
 K7N  C05  H051  single    0.930  0.020  1.080
 K7N  C06  H061  single    0.930  0.020  1.080
 K7N  C08  H081  single    0.930  0.020  1.080
 K7N  C18  H181  single    0.970  0.020  1.090
 K7N  C18  H182  single    0.970  0.020  1.090
 K7N  N19  H191  single    0.890  0.020  1.040
 K7N  N19  H192  single    0.890  0.020  1.040
 K7N  N21  H211  single    0.890  0.020  1.040
 K7N  N22  H222  single    0.890  0.020  1.040
 K7N  N22  H221  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
 K7N  H131  C13  N14   121.96  3.000
 K7N  H131  C13  C12   132.42  3.000
 K7N  N14   C13  C12   105.62  3.000
 K7N  H151  C15  N16   125.98  3.000
 K7N  H151  C15  N14   122.16  3.000
 K7N  N16   C15  N14   111.86  3.000
 K7N  H172  C17  H171  107.85  3.000
 K7N  H172  C17  N14   108.60  3.000
 K7N  H171  C17  N14   107.61  3.000
 K7N  H172  C17  C18   110.35  3.000
 K7N  H171  C17  C18   110.09  3.000
 K7N  N14   C17  C18   112.21  3.000
 K7N  H011  C01  C06   120.22  3.000
 K7N  H011  C01  C02   120.09  3.000
 K7N  C06   C01  C02   119.69  3.000
 K7N  H021  C02  C03   119.73  3.000
 K7N  H021  C02  C01   120.12  3.000
 K7N  C03   C02  C01   120.15  3.000
 K7N  H031  C03  C04   119.69  3.000
 K7N  H031  C03  C02   119.79  3.000
 K7N  C04   C03  C02   120.52  3.000
 K7N  C07   C04  C05   120.63  3.000
 K7N  C05   C04  C03   118.93  3.000
 K7N  C07   C04  C03   120.44  3.000
 K7N  H051  C05  C06   119.85  3.000
 K7N  H051  C05  C04   119.59  3.000
 K7N  C06   C05  C04   120.56  3.000
 K7N  H061  C06  C05   119.76  3.000
 K7N  H061  C06  C01   120.09  3.000
 K7N  C05   C06  C01   120.15  3.000
 K7N  C11   C07  C08   112.02  3.000
 K7N  C08   C07  C04   122.80  3.000
 K7N  C11   C07  C04   125.18  3.000
 K7N  H081  C08  C09   123.52  3.000
 K7N  H081  C08  C07   122.90  3.000
 K7N  C09   C08  C07   113.58  3.000
 K7N  S10   C09  C08   110.97  3.000
 K7N  C08   C09  C20   127.36  3.000
 K7N  S10   C09  C20   121.65  3.000
 K7N  S10   C11  C12   117.43  3.000
 K7N  S10   C11  C07   111.36  3.000
 K7N  C12   C11  C07   131.16  3.000
 K7N  N16   C12  C11   119.88  3.000
 K7N  C11   C12  C13   130.43  3.000
 K7N  N16   C12  C13   109.65  3.000
 K7N  H182  C18  H181  106.47  3.000
 K7N  H182  C18  N19   108.76  3.000
 K7N  H181  C18  N19   114.16  3.000
 K7N  H182  C18  C17   106.90  3.000
 K7N  H181  C18  C17   109.16  3.000
 K7N  N19   C18  C17   111.05  3.000
 K7N  C17   N14  C15   126.55  3.000
 K7N  C17   N14  C13   126.10  3.000
 K7N  C15   N14  C13   107.21  3.000
 K7N  C12   N16  C15   105.67  3.000
 K7N  H192  N19  H191  105.34  3.000
 K7N  H192  N19  C18   110.00  3.000
 K7N  H191  N19  C18   109.33  3.000
 K7N  H211  N21  C20   110.98  3.000
 K7N  H221  N22  H222  113.31  3.000
 K7N  H221  N22  C20   117.92  3.000
 K7N  H222  N22  C20   115.36  3.000
 K7N  C11   S10  C09    92.07  3.000
 K7N  N22   C20  N21   120.91  3.000
 K7N  N21   C20  C09   124.39  3.000
 K7N  N22   C20  C09   114.66  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
 K7N  CONST_01  N16   C15  N14  C13     0.00   0.0  0
 K7N  CONST_02  C15   N16  C12  C13     0.00   0.0  0
 K7N  CONST_03  S10   C11  C12  C13   180.00   0.0  0
 K7N  CONST_04  C07   C11  C12  C13     0.00   0.0  0
 K7N  CONST_05  C11   C12  N16  C15   180.00   0.0  0
 K7N  CONST_06  C12   C13  N14  C15     0.00   0.0  0
 K7N  CONST_07  C04   C05  C06  C01     0.00   0.0  0
 K7N  CONST_08  C04   C03  C02  C01     0.00   0.0  0
 K7N  CONST_09  C07   C04  C03  C02   180.00   0.0  0
 K7N  CONST_10  C05   C04  C03  C02     0.00   0.0  0
 K7N  CONST_11  C05   C06  C01  C02     0.00   0.0  0
 K7N  CONST_14  C06   C05  C04  C03     0.00   0.0  0
 K7N  CONST_15  C06   C01  C02  C03     0.00   0.0  0
 K7N  CONST_16  C12   C11  C07  C04     0.00   0.0  0
 K7N  CONST_17  S10   C11  C07  C04   180.00   0.0  0
 K7N  CONST_18  C09   C08  C07  C04   180.00   0.0  0
 K7N  CONST_21  C07   C04  C05  C06   180.00   0.0  0
 K7N  CONST_22  N16   C12  C11  C07   180.00   0.0  0
 K7N  CONST_23  C09   S10  C11  C07     0.00   0.0  0
 K7N  CONST_24  S10   C09  C08  C07     0.00   0.0  0
 K7N  CONST_25  C11   S10  C09  C08     0.00   0.0  0
 K7N  CONST_26  C12   C11  C07  C08   180.00   0.0  0
 K7N  CONST_27  S10   C11  C07  C08     0.00   0.0  0
 K7N  CONST_28  C12   C11  S10  C09   180.00   0.0  0
 K7N  CONST_29  C11   C07  C08  C09     0.00   0.0  0
 K7N  CONST_30  N14   C13  C12  C11   180.00   0.0  0
 K7N  CONST_31  N14   C15  N16  C12     0.00   0.0  0
 K7N  CONST_32  N16   C12  C13  N14     0.00   0.0  0
 K7N  CONST_33  S10   C11  C12  N16     0.00   0.0  0
 K7N  CONST_34  N16   C15  N14  C17   180.00   0.0  0
 K7N  CONST_35  C12   C13  N14  C17   180.00   0.0  0
 K7N  CONST_36  C11   S10  C09  C20   180.00   0.0  0
 K7N  CONST_37  C07   C08  C09  C20   180.00   0.0  0
 K7N  CONST_38  H151  C15  N14  C13   180.00   0.0  0
 K7N  CONST_39  H131  C13  N14  C15   180.00   0.0  0
 K7N  CONST_40  H051  C05  C06  C01   180.00   0.0  0
 K7N  CONST_41  H031  C03  C02  C01   180.00   0.0  0
 K7N  CONST_42  H061  C06  C01  C02   180.00   0.0  0
 K7N  CONST_43  H011  C01  C02  C03   180.00   0.0  0
 K7N  CONST_44  H081  C08  C07  C04     0.00   0.0  0
 K7N  CONST_45  H021  C02  C03  C04   180.00   0.0  0
 K7N  CONST_46  H222  N22  C20  C09   180.00   0.0  0
 K7N  CONST_48  H211  N21  C20  C09     0.00   0.0  0
 K7N  Var_01    C18   C17  N14  C13    76.30  30.0  3
 K7N  Var_02    N22   C20  C09  C08  -154.88  30.0  2
 K7N  Var_03    N19   C18  C17  N14    61.41  30.0  3
 K7N  Var_04    H191  N19  C18  C17   169.25  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
 K7N  plan-1  C13   0.020
 K7N  plan-1  C15   0.020
 K7N  plan-1  C17   0.020
 K7N  plan-1  C11   0.020
 K7N  plan-1  C12   0.020
 K7N  plan-1  N14   0.020
 K7N  plan-1  N16   0.020
 K7N  plan-1  H131  0.020
 K7N  plan-1  H151  0.020
 K7N  plan-2  C04   0.020
 K7N  plan-2  C07   0.020
 K7N  plan-2  C08   0.020
 K7N  plan-2  C09   0.020
 K7N  plan-2  C11   0.020
 K7N  plan-2  C12   0.020
 K7N  plan-2  S10   0.020
 K7N  plan-2  H081  0.020
 K7N  plan-2  C20   0.020
 K7N  plan-3  C01   0.020
 K7N  plan-3  C02   0.020
 K7N  plan-3  C03   0.020
 K7N  plan-3  C04   0.020
 K7N  plan-3  C05   0.020
 K7N  plan-3  C06   0.020
 K7N  plan-3  C07   0.020
 K7N  plan-3  H011  0.020
 K7N  plan-3  H021  0.020
 K7N  plan-3  H031  0.020
 K7N  plan-3  H051  0.020
 K7N  plan-3  H061  0.020
 K7N  plan-4  C09   0.020
 K7N  plan-4  N21   0.020
 K7N  plan-4  N22   0.020
 K7N  plan-4  H211  0.020
 K7N  plan-4  H222  0.020
 K7N  plan-4  H221  0.020
 K7N  plan-4  C20   0.020

