# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:08:47 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-phenyl-5-(piperidin-4-ylmethyl)thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1sc(CC2CCNCC2)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
 KDK  KDK  4-phenyl-5-(piperidin-4-ylmethyl)thiophene-2-carboximidamide  ligand  42  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 OK
;

data_comp_KDK
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
 KDK  C10   C  CR16  0  -0.305  21.2091  21.6311   9.7504
 KDK  C13   C  CR16  0  -0.240  20.2951  23.9061   8.4586
 KDK  C15   C  CH2   0  -0.513  22.9725  21.3716   5.8722
 KDK  C17   C  CH2   0  -0.431  25.1975  20.6061   6.8495
 KDK  C20   C  CH2   0  -0.317  26.1823  23.3260   6.8068
 KDK  C21   C  CH2   0  -0.429  24.9010  22.9602   6.0614
 KDK  C02   C  CR5   0  -0.231  22.1419  20.3002   6.5040
 KDK  C03   C  CR5   0   0.185  21.3296  20.3748   7.6098
 KDK  C04   C  CR15  0  -0.242  20.7958  19.1075   7.9728
 KDK  C05   C  CR5   0  -0.260  21.1879  18.0940   7.1483
 KDK  C06   C  C     0   0.340  20.8145  16.6721   7.2357
 KDK  C09   C  CR6   0   0.062  21.0384  21.6074   8.3656
 KDK  C11   C  CR16  0  -0.239  20.9293  22.7776  10.4800
 KDK  C12   C  CR16  0  -0.266  20.4750  23.9209   9.8356
 KDK  C14   C  CR16  0  -0.309  20.5702  22.7576   7.7302
 KDK  C16   C  CH1   0  -0.220  24.2069  21.7580   6.6986
 KDK  C18   C  CH2   0  -0.312  26.4707  21.0631   7.5617
 KDK  N07   N  NH2   0  -0.815  20.8831  15.9863   6.0553
 KDK  N08   N  N     0  -0.638  20.4949  16.0796   8.3214
 KDK  N19   N  NH1   0  -0.576  27.1118  22.2183   6.9557
 KDK  S01   S  S2    0   0.253  22.2343  18.6896   5.9179
 KDK  H101  H  HCR6  0   0.252  21.5751  20.7475  10.2591
 KDK  H131  H  HCR6  0   0.257  19.9285  24.7881   7.9499
 KDK  H151  H  HCH2  0   0.251  23.2941  21.0556   4.8757
 KDK  H152  H  HCH2  0   0.259  22.3610  22.2629   5.7207
 KDK  H172  H  HCH2  0   0.230  24.7480  19.7778   7.4037
 KDK  H171  H  HCH2  0   0.210  25.4578  20.2184   5.8566
 KDK  H201  H  HCH2  0   0.233  26.6923  24.1466   6.2973
 KDK  H202  H  HCH2  0   0.212  25.9257  23.6917   7.8075
 KDK  H211  H  HCH2  0   0.226  24.2241  23.8195   6.0400
 KDK  H212  H  HCH2  0   0.212  25.1455  22.7255   5.0185
 KDK  H041  H  HCR5  0   0.272  20.1088  18.9694   8.7978
 KDK  H111  H  HCR6  0   0.257  21.0695  22.7783  11.5533
 KDK  H121  H  HCR6  0   0.257  20.2561  24.8159  10.4034
 KDK  H141  H  HCR6  0   0.253  20.3963  22.7523   6.6615
 KDK  H161  H  HCH1  0   0.226  23.8648  22.0513   7.7001
 KDK  H181  H  HCH2  0   0.233  27.1913  20.2436   7.6039
 KDK  H182  H  HCH2  0   0.212  26.2295  21.3176   8.5999
 KDK  H1    H  HNH2  0   0.387  20.5346  15.0407   6.0869
 KDK  H071  H  HNH2  0   0.392  20.6300  16.4742   5.2108
 KDK  H082  H  H     0   0.336  20.6100  16.6981   9.1159
 KDK  H191  H  HNH1  0   0.337  27.4596  21.9588   6.0390

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
 KDK  C15  C02   single    1.496  0.020  1.496
 KDK  C15  C16   single    1.535  0.020  1.535
 KDK  S01  C02   aromatic  1.716  0.020  1.716
 KDK  S01  C05   aromatic  1.722  0.020  1.722
 KDK  C21  C20   single    1.527  0.020  1.527
 KDK  C21  C16   single    1.527  0.020  1.527
 KDK  N07  C06   single    1.367  0.020  1.367
 KDK  C02  C03   aromatic  1.374  0.020  1.374
 KDK  C20  N19   single    1.454  0.020  1.454
 KDK  C16  C17   single    1.527  0.020  1.527
 KDK  N19  C18   single    1.454  0.020  1.454
 KDK  C17  C18   single    1.529  0.020  1.529
 KDK  C05  C06   single    1.473  0.020  1.473
 KDK  C05  C04   aromatic  1.364  0.020  1.364
 KDK  C06  N08   double    1.277  0.020  1.277
 KDK  C03  C04   aromatic  1.422  0.020  1.422
 KDK  C03  C09   single    1.475  0.020  1.475
 KDK  C14  C09   aromatic  1.395  0.020  1.395
 KDK  C14  C13   aromatic  1.388  0.020  1.388
 KDK  C09  C10   aromatic  1.396  0.020  1.396
 KDK  C13  C12   aromatic  1.389  0.020  1.389
 KDK  C10  C11   aromatic  1.387  0.020  1.387
 KDK  C12  C11   aromatic  1.389  0.020  1.389
 KDK  C10  H101  single    0.930  0.020  1.080
 KDK  C13  H131  single    0.930  0.020  1.080
 KDK  C15  H151  single    0.970  0.020  1.090
 KDK  C15  H152  single    0.970  0.020  1.090
 KDK  C17  H172  single    0.970  0.020  1.090
 KDK  C17  H171  single    0.970  0.020  1.090
 KDK  C20  H201  single    0.970  0.020  1.090
 KDK  C20  H202  single    0.970  0.020  1.090
 KDK  C21  H211  single    0.970  0.020  1.090
 KDK  C21  H212  single    0.970  0.020  1.090
 KDK  C04  H041  single    0.930  0.020  1.080
 KDK  C11  H111  single    0.930  0.020  1.080
 KDK  C12  H121  single    0.930  0.020  1.080
 KDK  C14  H141  single    0.930  0.020  1.080
 KDK  C16  H161  single    0.970  0.020  1.090
 KDK  C18  H181  single    0.970  0.020  1.090
 KDK  C18  H182  single    0.970  0.020  1.090
 KDK  N07  H1    single    0.890  0.020  1.040
 KDK  N07  H071  single    0.890  0.020  1.040
 KDK  N08  H082  single    0.890  0.020  1.040
 KDK  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
 KDK  H101  C10  C11   119.68  3.000
 KDK  H101  C10  C09   119.57  3.000
 KDK  C11   C10  C09   120.74  3.000
 KDK  H131  C13  C14   119.67  3.000
 KDK  H131  C13  C12   120.08  3.000
 KDK  C14   C13  C12   120.25  3.000
 KDK  H152  C15  H151  105.91  3.000
 KDK  H152  C15  C16   108.65  3.000
 KDK  H151  C15  C16   109.07  3.000
 KDK  H152  C15  C02   109.42  3.000
 KDK  H151  C15  C02   109.95  3.000
 KDK  C16   C15  C02   113.55  3.000
 KDK  H171  C17  H172  106.77  3.000
 KDK  H171  C17  C18   109.25  3.000
 KDK  H172  C17  C18   109.43  3.000
 KDK  H171  C17  C16   109.34  3.000
 KDK  H172  C17  C16   110.79  3.000
 KDK  C18   C17  C16   111.15  3.000
 KDK  H202  C20  H201  106.54  3.000
 KDK  H202  C20  N19   108.08  3.000
 KDK  H201  C20  N19   108.76  3.000
 KDK  H202  C20  C21   109.23  3.000
 KDK  H201  C20  C21   110.13  3.000
 KDK  N19   C20  C21   113.83  3.000
 KDK  H212  C21  H211  106.70  3.000
 KDK  H212  C21  C16   109.25  3.000
 KDK  H211  C21  C16   110.19  3.000
 KDK  H212  C21  C20   109.18  3.000
 KDK  H211  C21  C20   109.91  3.000
 KDK  C16   C21  C20   111.49  3.000
 KDK  S01   C02  C03   110.95  3.000
 KDK  C03   C02  C15   129.00  3.000
 KDK  S01   C02  C15   119.87  3.000
 KDK  C09   C03  C04   122.67  3.000
 KDK  C09   C03  C02   125.06  3.000
 KDK  C04   C03  C02   112.26  3.000
 KDK  H041  C04  C05   123.26  3.000
 KDK  H041  C04  C03   123.12  3.000
 KDK  C05   C04  C03   113.57  3.000
 KDK  S01   C05  C06   122.05  3.000
 KDK  C06   C05  C04   127.49  3.000
 KDK  S01   C05  C04   110.47  3.000
 KDK  N08   C06  N07   120.92  3.000
 KDK  N08   C06  C05   124.17  3.000
 KDK  N07   C06  C05   114.86  3.000
 KDK  C14   C09  C03   121.46  3.000
 KDK  C14   C09  C10   118.62  3.000
 KDK  C03   C09  C10   119.90  3.000
 KDK  H111  C11  C12   120.13  3.000
 KDK  H111  C11  C10   119.72  3.000
 KDK  C12   C11  C10   120.15  3.000
 KDK  H121  C12  C11   120.23  3.000
 KDK  H121  C12  C13   120.19  3.000
 KDK  C11   C12  C13   119.58  3.000
 KDK  H141  C14  C09   119.97  3.000
 KDK  H141  C14  C13   119.36  3.000
 KDK  C09   C14  C13   120.66  3.000
 KDK  H161  C16  C21   108.17  3.000
 KDK  H161  C16  C17   108.27  3.000
 KDK  C21   C16  C17   109.89  3.000
 KDK  H161  C16  C15   107.92  3.000
 KDK  C17   C16  C15   112.65  3.000
 KDK  C21   C16  C15   109.82  3.000
 KDK  H182  C18  H181  106.43  3.000
 KDK  H182  C18  N19   107.91  3.000
 KDK  H181  C18  N19   108.75  3.000
 KDK  H182  C18  C17   109.12  3.000
 KDK  H181  C18  C17   110.07  3.000
 KDK  N19   C18  C17   114.25  3.000
 KDK  H071  N07  H1    113.17  3.000
 KDK  H071  N07  C06   117.92  3.000
 KDK  H1    N07  C06   115.22  3.000
 KDK  H082  N08  C06   110.78  3.000
 KDK  H191  N19  C18   108.95  3.000
 KDK  H191  N19  C20   108.77  3.000
 KDK  C18   N19  C20   111.49  3.000
 KDK  C05   S01  C02    92.74  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
 KDK  CONST_03  C13   C14  C09  C10    0.00   0.0  0
 KDK  CONST_04  C13   C12  C11  C10    0.00   0.0  0
 KDK  CONST_05  C03   C09  C14  C13  180.00   0.0  0
 KDK  CONST_06  C04   C05  S01  C02    0.00   0.0  0
 KDK  CONST_07  C05   C04  C03  C02    0.00   0.0  0
 KDK  CONST_09  C05   S01  C02  C03    0.00   0.0  0
 KDK  CONST_10  S01   C05  C04  C03    0.00   0.0  0
 KDK  CONST_11  C11   C10  C09  C03  180.00   0.0  0
 KDK  CONST_12  S01   C02  C03  C04    0.00   0.0  0
 KDK  CONST_14  C09   C03  C04  C05  180.00   0.0  0
 KDK  CONST_15  S01   C02  C03  C09  180.00   0.0  0
 KDK  CONST_16  C12   C13  C14  C09    0.00   0.0  0
 KDK  CONST_17  C12   C11  C10  C09    0.00   0.0  0
 KDK  CONST_18  C14   C09  C10  C11    0.00   0.0  0
 KDK  CONST_19  C14   C13  C12  C11    0.00   0.0  0
 KDK  CONST_20  C05   S01  C02  C15  180.00   0.0  0
 KDK  CONST_21  C04   C03  C02  C15  180.00   0.0  0
 KDK  CONST_22  C09   C03  C02  C15    0.00   0.0  0
 KDK  CONST_23  C06   C05  S01  C02  180.00   0.0  0
 KDK  CONST_24  C06   C05  C04  C03  180.00   0.0  0
 KDK  CONST_25  H141  C14  C09  C10  180.00   0.0  0
 KDK  CONST_26  H121  C12  C11  C10  180.00   0.0  0
 KDK  CONST_27  H111  C11  C12  C13  180.00   0.0  0
 KDK  CONST_28  H041  C04  C03  C02  180.00   0.0  0
 KDK  CONST_29  H101  C10  C09  C03    0.00   0.0  0
 KDK  CONST_30  H131  C13  C14  C09  180.00   0.0  0
 KDK  CONST_31  H1    N07  C06  C05  180.00   0.0  0
 KDK  CONST_33  H082  N08  C06  C05    0.00   0.0  0
 KDK  Var_01    C20   N19  C18  C17   53.65  30.0  1
 KDK  Var_02    C18   N19  C20  C21  -53.61  30.0  1
 KDK  Var_03    N19   C20  C21  C16   54.04  30.0  1
 KDK  Var_04    N19   C18  C17  C16  -53.75  30.0  1
 KDK  Var_05    C16   C15  C02  C03   71.76  30.0  2
 KDK  Var_06    N07   C06  C05  C04  155.15  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KDK  chir_01  C16  C15  C21  C17  positiv

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
 KDK  plan-1  C15   0.020
 KDK  plan-1  C02   0.020
 KDK  plan-1  C03   0.020
 KDK  plan-1  C04   0.020
 KDK  plan-1  C05   0.020
 KDK  plan-1  C06   0.020
 KDK  plan-1  C09   0.020
 KDK  plan-1  S01   0.020
 KDK  plan-1  H041  0.020
 KDK  plan-2  C10   0.020
 KDK  plan-2  C13   0.020
 KDK  plan-2  C03   0.020
 KDK  plan-2  C09   0.020
 KDK  plan-2  C11   0.020
 KDK  plan-2  C12   0.020
 KDK  plan-2  C14   0.020
 KDK  plan-2  H101  0.020
 KDK  plan-2  H131  0.020
 KDK  plan-2  H111  0.020
 KDK  plan-2  H121  0.020
 KDK  plan-2  H141  0.020
 KDK  plan-3  C05   0.020
 KDK  plan-3  C06   0.020
 KDK  plan-3  N07   0.020
 KDK  plan-3  N08   0.020
 KDK  plan-3  H1    0.020
 KDK  plan-3  H071  0.020
 KDK  plan-3  H082  0.020

