# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:27:06 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-phenyl-5-(phenylmethyl)thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1sc(Cc2ccccc2)c(c1)c3ccccc3
#
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
 K6W  K6W  4-phenyl-5-(phenylmethyl)thiophene-2-carboximidamide  ligand  37  21  .  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_K6W
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
 K6W  C10   C  CR16  0  -0.311  20.1940  22.4573   -7.4609
 K6W  C13   C  CR16  0  -0.238  19.5781  22.3510  -10.1620
 K6W  C17   C  CR16  0  -0.280  16.2188  20.1960   -4.5999
 K6W  C20   C  CR16  0  -0.240  16.8815  19.7295   -1.9478
 K6W  C21   C  CR16  0  -0.299  17.8294  20.2450   -2.8237
 K6W  C02   C  CR5   0  -0.226  19.1537  19.9258   -5.9610
 K6W  C03   C  CR5   0   0.189  19.7048  20.0142   -7.2162
 K6W  C04   C  CR15  0  -0.239  20.1754  18.7526   -7.6812
 K6W  C05   C  CR5   0  -0.270  19.9852  17.7393   -6.7901
 K6W  C06   C  C     0   0.354  20.3371  16.3141   -6.9302
 K6W  C09   C  CR6   0   0.065  19.7942  21.2431   -8.0212
 K6W  C11   C  CR16  0  -0.241  20.2752  23.6042   -8.2381
 K6W  C12   C  CR16  0  -0.265  19.9666  23.5562   -9.5906
 K6W  C14   C  CR16  0  -0.312  19.4922  21.2061   -9.3845
 K6W  C16   C  CR6   0   0.084  17.5083  20.4822   -4.1564
 K6W  C18   C  CR16  0  -0.242  15.2697  19.6845   -3.7279
 K6W  C19   C  CR16  0  -0.266  15.5996  19.4483   -2.3979
 K6W  N07   N  NH2   0  -0.808  21.3498  16.0740   -7.8096
 K6W  N08   N  N     0  -0.643  19.7469  15.3485   -6.3345
 K6W  S01   S  S2    0   0.260  19.2170  18.3159   -5.3620
 K6W  H101  H  HCR6  0   0.258  20.4675  22.5074   -6.4149
 K6W  H131  H  HCR6  0   0.259  19.3371  22.3024  -11.2160
 K6W  H152  H  HCH2  0   0.285  19.3327  21.5140   -4.5509
 K6W  H151  H  HCH2  0   0.279  18.1043  21.7554   -5.7742
 K6W  H201  H  HCR6  0   0.256  17.1452  19.5510   -0.9133
 K6W  H211  H  HCR6  0   0.253  18.8282  20.4658   -2.4652
 K6W  H041  H  HCR5  0   0.272  20.6345  18.6147   -8.6512
 K6W  H111  H  HCR6  0   0.259  20.5897  24.5353   -7.7851
 K6W  H121  H  HCR6  0   0.258  20.0309  24.4500  -10.1973
 K6W  H141  H  HCR6  0   0.255  19.1733  20.2756   -9.8379
 K6W  H181  H  HCR6  0   0.257  14.2700  19.4707   -4.0838
 K6W  H191  H  HCR6  0   0.257  14.8583  19.0503   -1.7168
 K6W  H071  H  HNH2  0   0.387  21.6930  15.1271   -7.8398
 K6W  H1    H  HNH2  0   0.395  22.0610  16.7762   -7.9261
 K6W  H081  H  H     0   0.330  18.9416  15.6701   -5.8100
 K6W  C15   C  CH2   0  -0.582  18.5463  21.0048   -5.1147
 K6W  H171  H  HCR6  0   0.252  15.9571  20.3773   -5.6359

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
 K6W  C13  C12   aromatic  1.389  0.020  1.389
 K6W  C13  C14   aromatic  1.387  0.020  1.387
 K6W  C12  C11   aromatic  1.388  0.020  1.388
 K6W  C14  C09   aromatic  1.397  0.020  1.397
 K6W  C11  C10   aromatic  1.388  0.020  1.388
 K6W  C09  C10   aromatic  1.396  0.020  1.396
 K6W  C09  C03   single    1.472  0.020  1.472
 K6W  N07  C06   single    1.363  0.020  1.363
 K6W  C04  C03   aromatic  1.425  0.020  1.425
 K6W  C04  C05   aromatic  1.363  0.020  1.363
 K6W  C03  C02   aromatic  1.374  0.020  1.374
 K6W  C06  C05   single    1.475  0.020  1.475
 K6W  C06  N08   double    1.279  0.020  1.279
 K6W  C05  S01   aromatic  1.721  0.020  1.721
 K6W  C02  S01   aromatic  1.719  0.020  1.719
 K6W  C02  C15   single    1.500  0.020  1.500
 K6W  C15  C16   single    1.506  0.020  1.506
 K6W  C17  C16   aromatic  1.393  0.020  1.393
 K6W  C17  C18   aromatic  1.387  0.020  1.387
 K6W  C16  C21   aromatic  1.391  0.020  1.391
 K6W  C18  C19   aromatic  1.391  0.020  1.391
 K6W  C21  C20   aromatic  1.390  0.020  1.390
 K6W  C19  C20   aromatic  1.387  0.020  1.387
 K6W  C10  H101  single    0.930  0.020  1.080
 K6W  C13  H131  single    0.930  0.020  1.080
 K6W  C15  H152  single    0.970  0.020  1.090
 K6W  C15  H151  single    0.970  0.020  1.090
 K6W  C17  H171  single    0.930  0.020  1.080
 K6W  C20  H201  single    0.930  0.020  1.080
 K6W  C21  H211  single    0.930  0.020  1.080
 K6W  C04  H041  single    0.930  0.020  1.080
 K6W  C11  H111  single    0.930  0.020  1.080
 K6W  C12  H121  single    0.930  0.020  1.080
 K6W  C14  H141  single    0.930  0.020  1.080
 K6W  C18  H181  single    0.930  0.020  1.080
 K6W  C19  H191  single    0.930  0.020  1.080
 K6W  N07  H071  single    0.890  0.020  1.040
 K6W  N07  H1    single    0.890  0.020  1.040
 K6W  N08  H081  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
 K6W  H101  C10  C11   119.22  3.000
 K6W  H101  C10  C09   120.04  3.000
 K6W  C11   C10  C09   120.72  3.000
 K6W  H131  C13  C14   119.69  3.000
 K6W  H131  C13  C12   120.11  3.000
 K6W  C14   C13  C12   120.20  3.000
 K6W  H171  C17  C18   119.84  3.000
 K6W  H171  C17  C16   119.56  3.000
 K6W  C18   C17  C16   120.60  3.000
 K6W  H201  C20  C19   120.11  3.000
 K6W  H201  C20  C21   119.83  3.000
 K6W  C19   C20  C21   120.06  3.000
 K6W  H211  C21  C16   119.66  3.000
 K6W  H211  C21  C20   119.71  3.000
 K6W  C16   C21  C20   120.64  3.000
 K6W  S01   C02  C03   111.34  3.000
 K6W  S01   C02  C15   119.48  3.000
 K6W  C03   C02  C15   129.18  3.000
 K6W  C09   C03  C04   122.74  3.000
 K6W  C04   C03  C02   111.95  3.000
 K6W  C09   C03  C02   125.30  3.000
 K6W  H041  C04  C05   123.42  3.000
 K6W  H041  C04  C03   123.07  3.000
 K6W  C05   C04  C03   113.51  3.000
 K6W  S01   C05  C06   120.61  3.000
 K6W  S01   C05  C04   110.84  3.000
 K6W  C06   C05  C04   128.55  3.000
 K6W  N08   C06  N07   120.70  3.000
 K6W  N08   C06  C05   125.12  3.000
 K6W  N07   C06  C05   114.14  3.000
 K6W  C14   C09  C03   119.90  3.000
 K6W  C03   C09  C10   121.62  3.000
 K6W  C14   C09  C10   118.48  3.000
 K6W  H111  C11  C12   120.15  3.000
 K6W  H111  C11  C10   119.58  3.000
 K6W  C12   C11  C10   120.27  3.000
 K6W  H121  C12  C11   120.29  3.000
 K6W  H121  C12  C13   120.17  3.000
 K6W  C11   C12  C13   119.53  3.000
 K6W  H141  C14  C09   119.67  3.000
 K6W  H141  C14  C13   119.53  3.000
 K6W  C09   C14  C13   120.80  3.000
 K6W  C21   C16  C17   118.92  3.000
 K6W  C21   C16  C15   120.63  3.000
 K6W  C17   C16  C15   120.43  3.000
 K6W  H181  C18  C19   120.01  3.000
 K6W  H181  C18  C17   119.88  3.000
 K6W  C19   C18  C17   120.11  3.000
 K6W  H191  C19  C18   120.12  3.000
 K6W  H191  C19  C20   120.21  3.000
 K6W  C18   C19  C20   119.68  3.000
 K6W  H1    N07  H071  114.31  3.000
 K6W  H1    N07  C06   118.50  3.000
 K6W  H071  N07  C06   115.98  3.000
 K6W  H081  N08  C06   111.61  3.000
 K6W  C05   S01  C02    92.35  3.000
 K6W  H151  C15  H152  106.40  3.000
 K6W  H151  C15  C16   110.09  3.000
 K6W  H152  C15  C16   109.21  3.000
 K6W  H151  C15  C02   108.51  3.000
 K6W  H152  C15  C02   109.56  3.000
 K6W  C16   C15  C02   112.86  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
 K6W  CONST_01  C13   C12  C11  C10    0.00   0.0  0
 K6W  CONST_02  C13   C14  C09  C10    0.00   0.0  0
 K6W  CONST_05  C03   C09  C14  C13  180.00   0.0  0
 K6W  CONST_06  C20   C21  C16  C17    0.00   0.0  0
 K6W  CONST_07  C20   C19  C18  C17    0.00   0.0  0
 K6W  CONST_08  C18   C17  C16  C21    0.00   0.0  0
 K6W  CONST_09  C18   C19  C20  C21    0.00   0.0  0
 K6W  CONST_11  C05   C04  C03  C02    0.00   0.0  0
 K6W  CONST_12  C04   C05  S01  C02    0.00   0.0  0
 K6W  CONST_13  C11   C10  C09  C03  180.00   0.0  0
 K6W  CONST_14  S01   C05  C04  C03    0.00   0.0  0
 K6W  CONST_15  C05   S01  C02  C03    0.00   0.0  0
 K6W  CONST_17  S01   C02  C03  C04    0.00   0.0  0
 K6W  CONST_18  C09   C03  C04  C05  180.00   0.0  0
 K6W  CONST_19  C12   C13  C14  C09    0.00   0.0  0
 K6W  CONST_20  C12   C11  C10  C09    0.00   0.0  0
 K6W  CONST_21  S01   C02  C03  C09  180.00   0.0  0
 K6W  CONST_22  C14   C13  C12  C11    0.00   0.0  0
 K6W  CONST_23  C14   C09  C10  C11    0.00   0.0  0
 K6W  CONST_24  C19   C18  C17  C16    0.00   0.0  0
 K6W  CONST_25  C19   C20  C21  C16    0.00   0.0  0
 K6W  CONST_26  C09   C03  C02  C15    0.00   0.0  0
 K6W  CONST_27  C04   C03  C02  C15  180.00   0.0  0
 K6W  CONST_28  C05   S01  C02  C15  180.00   0.0  0
 K6W  CONST_29  C18   C17  C16  C15  180.00   0.0  0
 K6W  CONST_30  C20   C21  C16  C15  180.00   0.0  0
 K6W  CONST_31  C06   C05  S01  C02  180.00   0.0  0
 K6W  CONST_32  C06   C05  C04  C03  180.00   0.0  0
 K6W  CONST_33  H121  C12  C11  C10  180.00   0.0  0
 K6W  CONST_34  H141  C14  C09  C10  180.00   0.0  0
 K6W  CONST_35  H111  C11  C12  C13  180.00   0.0  0
 K6W  CONST_36  H211  C21  C16  C17  180.00   0.0  0
 K6W  CONST_37  H191  C19  C18  C17  180.00   0.0  0
 K6W  CONST_38  H181  C18  C19  C20  180.00   0.0  0
 K6W  CONST_39  H171  C17  C16  C21  180.00   0.0  0
 K6W  CONST_40  H041  C04  C03  C02  180.00   0.0  0
 K6W  CONST_41  H101  C10  C09  C03    0.00   0.0  0
 K6W  CONST_42  H131  C13  C14  C09  180.00   0.0  0
 K6W  CONST_43  H201  C20  C21  C16  180.00   0.0  0
 K6W  CONST_44  H071  N07  C06  C05  180.00   0.0  0
 K6W  CONST_46  H081  N08  C06  C05    0.00   0.0  0
 K6W  Var_01    C02   C15  C16  C17  -79.16  30.0  2
 K6W  Var_02    C16   C15  C02  C03  152.70  30.0  2
 K6W  Var_03    N07   C06  C05  C04   24.45  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
 K6W  plan-1  C02   0.020
 K6W  plan-1  C03   0.020
 K6W  plan-1  C04   0.020
 K6W  plan-1  C05   0.020
 K6W  plan-1  C06   0.020
 K6W  plan-1  C09   0.020
 K6W  plan-1  S01   0.020
 K6W  plan-1  H041  0.020
 K6W  plan-1  C15   0.020
 K6W  plan-2  C10   0.020
 K6W  plan-2  C13   0.020
 K6W  plan-2  C03   0.020
 K6W  plan-2  C09   0.020
 K6W  plan-2  C11   0.020
 K6W  plan-2  C12   0.020
 K6W  plan-2  C14   0.020
 K6W  plan-2  H101  0.020
 K6W  plan-2  H131  0.020
 K6W  plan-2  H111  0.020
 K6W  plan-2  H121  0.020
 K6W  plan-2  H141  0.020
 K6W  plan-3  C17   0.020
 K6W  plan-3  C20   0.020
 K6W  plan-3  C21   0.020
 K6W  plan-3  C16   0.020
 K6W  plan-3  C18   0.020
 K6W  plan-3  C19   0.020
 K6W  plan-3  H201  0.020
 K6W  plan-3  H211  0.020
 K6W  plan-3  H181  0.020
 K6W  plan-3  H191  0.020
 K6W  plan-3  C15   0.020
 K6W  plan-3  H171  0.020
 K6W  plan-4  C05   0.020
 K6W  plan-4  C06   0.020
 K6W  plan-4  N07   0.020
 K6W  plan-4  N08   0.020
 K6W  plan-4  H071  0.020
 K6W  plan-4  H1    0.020
 K6W  plan-4  H081  0.020

