# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:54:48 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCc1sc(cc1c2ccccc2)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
 K5Z  K5Z  5-(3-azanylpropyl)-4-phenyl-thiophene-2-carboximidamide  ligand  35  18  .  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_K5Z
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
 K5Z  C10   C  CR16  0  -0.308  20.5910  -22.5667   -7.3730
 K5Z  C13   C  CR16  0  -0.241  21.8213  -22.5945   -9.8579
 K5Z  C17   C  CH2   0  -0.264  24.6508  -20.7301   -5.4752
 K5Z  C02   C  CR5   0  -0.224  21.6433  -20.0804   -5.7298
 K5Z  C03   C  CR5   0   0.172  21.2347  -20.1736   -7.0365
 K5Z  C04   C  CR15  0  -0.238  20.8221  -18.9165   -7.5653
 K5Z  C05   C  CR5   0  -0.266  20.9022  -17.8961   -6.6657
 K5Z  C06   C  C     0   0.352  20.5170  -16.4843   -6.8410
 K5Z  C09   C  CR6   0   0.059  21.2236  -21.4123   -7.8346
 K5Z  C11   C  CR16  0  -0.243  20.5823  -23.7237   -8.1394
 K5Z  C12   C  CR16  0  -0.264  21.1991  -23.7423   -9.3834
 K5Z  C14   C  CR16  0  -0.302  21.8327  -21.4393   -9.0899
 K5Z  C16   C  CH2   0  -0.444  23.6364  -20.8041   -4.3451
 K5Z  N08   N  NH2   0  -0.807  20.5322  -16.0587   -8.1364
 K5Z  N07   N  N     0  -0.642  20.1497  -15.6994   -5.9005
 K5Z  N18   N  NH2   0  -0.801  25.9791  -20.4387   -4.9551
 K5Z  S01   S  S2    0   0.237  21.5090  -18.4625   -5.1565
 K5Z  H101  H  HCR6  0   0.259  20.0843  -22.5556   -6.4158
 K5Z  H131  H  HCR6  0   0.258  22.3046  -22.5999  -10.8264
 K5Z  H151  H  HCH2  0   0.271  21.5673  -21.2790   -3.9720
 K5Z  H152  H  HCH2  0   0.254  22.2379  -22.0770   -5.3734
 K5Z  H172  H  HCH2  0   0.214  24.6850  -21.7000   -5.9796
 K5Z  H171  H  HCH2  0   0.197  24.3067  -20.0066   -6.2279
 K5Z  H041  H  HCR5  0   0.272  20.4449  -18.7971   -8.5723
 K5Z  H111  H  HCR6  0   0.258  20.0850  -24.6096   -7.7661
 K5Z  H121  H  HCR6  0   0.258  21.1936  -24.6442   -9.9816
 K5Z  H141  H  HCR6  0   0.253  22.3294  -20.5519   -9.4634
 K5Z  H161  H  HCH2  0   0.221  23.6317  -19.8612   -3.7873
 K5Z  H162  H  HCH2  0   0.238  23.9438  -21.5762   -3.6362
 K5Z  H082  H  HNH2  0   0.386  20.3854  -15.0709   -8.2735
 K5Z  H071  H  H     0   0.330  20.0757  -16.1874   -5.0155
 K5Z  H4    H  HNH2  0   0.347  26.6515  -20.4712   -5.7106
 K5Z  H3    H  HNH2  0   0.338  26.0014  -19.4855   -4.6136
 K5Z  H081  H  HNH2  0   0.394  21.2100  -16.4636   -8.7608
 K5Z  C15   C  CH2   0  -0.522  22.2226  -21.1282   -4.8337

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
 K5Z  C13  C12   aromatic  1.389  0.020  1.389
 K5Z  C13  C14   aromatic  1.387  0.020  1.387
 K5Z  C12  C11   aromatic  1.389  0.020  1.389
 K5Z  C14  C09   aromatic  1.395  0.020  1.395
 K5Z  N08  C06   single    1.364  0.020  1.364
 K5Z  C11  C10   aromatic  1.388  0.020  1.388
 K5Z  C09  C03   single    1.474  0.020  1.474
 K5Z  C09  C10   aromatic  1.395  0.020  1.395
 K5Z  C04  C03   aromatic  1.425  0.020  1.425
 K5Z  C04  C05   aromatic  1.363  0.020  1.363
 K5Z  C03  C02   aromatic  1.372  0.020  1.372
 K5Z  C06  C05   single    1.474  0.020  1.474
 K5Z  C06  N07   double    1.279  0.020  1.279
 K5Z  C05  S01   aromatic  1.722  0.020  1.722
 K5Z  C02  S01   aromatic  1.722  0.020  1.722
 K5Z  C02  C15   single    1.495  0.020  1.495
 K5Z  C15  C16   single    1.531  0.020  1.531
 K5Z  C17  C16   single    1.520  0.020  1.520
 K5Z  C17  N18   single    1.456  0.020  1.456
 K5Z  C10  H101  single    0.930  0.020  1.080
 K5Z  C13  H131  single    0.930  0.020  1.080
 K5Z  C15  H151  single    0.970  0.020  1.090
 K5Z  C15  H152  single    0.970  0.020  1.090
 K5Z  C17  H172  single    0.970  0.020  1.090
 K5Z  C17  H171  single    0.970  0.020  1.090
 K5Z  C04  H041  single    0.930  0.020  1.080
 K5Z  C11  H111  single    0.930  0.020  1.080
 K5Z  C12  H121  single    0.930  0.020  1.080
 K5Z  C14  H141  single    0.930  0.020  1.080
 K5Z  C16  H161  single    0.970  0.020  1.090
 K5Z  C16  H162  single    0.970  0.020  1.090
 K5Z  N08  H082  single    0.890  0.020  1.040
 K5Z  N07  H071  single    0.890  0.020  1.040
 K5Z  N18  H4    single    0.890  0.020  1.040
 K5Z  N18  H3    single    0.890  0.020  1.040
 K5Z  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
 K5Z  H101  C10  C11   119.58  3.000
 K5Z  H101  C10  C09   119.74  3.000
 K5Z  C11   C10  C09   120.67  3.000
 K5Z  H131  C13  C14   119.72  3.000
 K5Z  H131  C13  C12   120.11  3.000
 K5Z  C14   C13  C12   120.17  3.000
 K5Z  H171  C17  H172  106.12  3.000
 K5Z  H171  C17  N18   113.48  3.000
 K5Z  H172  C17  N18   108.28  3.000
 K5Z  H171  C17  C16   109.40  3.000
 K5Z  H172  C17  C16   108.69  3.000
 K5Z  N18   C17  C16   110.66  3.000
 K5Z  S01   C02  C03   110.96  3.000
 K5Z  S01   C02  C15   119.28  3.000
 K5Z  C03   C02  C15   129.67  3.000
 K5Z  C09   C03  C04   122.58  3.000
 K5Z  C04   C03  C02   112.32  3.000
 K5Z  C09   C03  C02   125.10  3.000
 K5Z  H041  C04  C05   123.53  3.000
 K5Z  H041  C04  C03   122.94  3.000
 K5Z  C05   C04  C03   113.49  3.000
 K5Z  S01   C05  C06   120.75  3.000
 K5Z  S01   C05  C04   110.67  3.000
 K5Z  C06   C05  C04   128.57  3.000
 K5Z  N07   C06  N08   120.69  3.000
 K5Z  N07   C06  C05   125.14  3.000
 K5Z  N08   C06  C05   114.14  3.000
 K5Z  C14   C09  C03   120.01  3.000
 K5Z  C03   C09  C10   121.32  3.000
 K5Z  C14   C09  C10   118.66  3.000
 K5Z  H111  C11  C12   120.14  3.000
 K5Z  H111  C11  C10   119.65  3.000
 K5Z  C12   C11  C10   120.20  3.000
 K5Z  H121  C12  C11   120.27  3.000
 K5Z  H121  C12  C13   120.13  3.000
 K5Z  C11   C12  C13   119.60  3.000
 K5Z  H141  C14  C09   119.63  3.000
 K5Z  H141  C14  C13   119.67  3.000
 K5Z  C09   C14  C13   120.70  3.000
 K5Z  H162  C16  H161  106.21  3.000
 K5Z  H162  C16  C17   109.21  3.000
 K5Z  H161  C16  C17   109.84  3.000
 K5Z  H162  C16  C15   108.50  3.000
 K5Z  H161  C16  C15   109.92  3.000
 K5Z  C17   C16  C15   112.91  3.000
 K5Z  H081  N08  H082  114.07  3.000
 K5Z  H081  N08  C06   118.12  3.000
 K5Z  H082  N08  C06   115.68  3.000
 K5Z  H071  N07  C06   111.57  3.000
 K5Z  H3    N18  H4    105.51  3.000
 K5Z  H3    N18  C17   109.20  3.000
 K5Z  H4    N18  C17   109.45  3.000
 K5Z  C05   S01  C02    92.56  3.000
 K5Z  H152  C15  H151  106.16  3.000
 K5Z  H152  C15  C16   109.21  3.000
 K5Z  H151  C15  C16   109.35  3.000
 K5Z  H152  C15  C02   108.54  3.000
 K5Z  H151  C15  C02   109.68  3.000
 K5Z  C16   C15  C02   113.62  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
 K5Z  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 K5Z  CONST_02  C13   C14  C09  C10     0.00   0.0  0
 K5Z  CONST_05  C03   C09  C14  C13   180.00   0.0  0
 K5Z  CONST_07  C05   C04  C03  C02     0.00   0.0  0
 K5Z  CONST_08  C04   C05  S01  C02     0.00   0.0  0
 K5Z  CONST_09  C11   C10  C09  C03   180.00   0.0  0
 K5Z  CONST_10  S01   C05  C04  C03     0.00   0.0  0
 K5Z  CONST_11  C05   S01  C02  C03     0.00   0.0  0
 K5Z  CONST_13  S01   C02  C03  C04     0.00   0.0  0
 K5Z  CONST_14  C09   C03  C04  C05   180.00   0.0  0
 K5Z  CONST_15  C12   C13  C14  C09     0.00   0.0  0
 K5Z  CONST_16  S01   C02  C03  C09   180.00   0.0  0
 K5Z  CONST_17  C12   C11  C10  C09     0.00   0.0  0
 K5Z  CONST_18  C14   C13  C12  C11     0.00   0.0  0
 K5Z  CONST_19  C14   C09  C10  C11     0.00   0.0  0
 K5Z  CONST_20  C09   C03  C02  C15     0.00   0.0  0
 K5Z  CONST_21  C04   C03  C02  C15   180.00   0.0  0
 K5Z  CONST_22  C05   S01  C02  C15   180.00   0.0  0
 K5Z  CONST_23  C06   C05  S01  C02   180.00   0.0  0
 K5Z  CONST_24  C06   C05  C04  C03   180.00   0.0  0
 K5Z  CONST_25  H121  C12  C11  C10   180.00   0.0  0
 K5Z  CONST_26  H141  C14  C09  C10   180.00   0.0  0
 K5Z  CONST_27  H111  C11  C12  C13   180.00   0.0  0
 K5Z  CONST_28  H041  C04  C03  C02   180.00   0.0  0
 K5Z  CONST_29  H101  C10  C09  C03     0.00   0.0  0
 K5Z  CONST_30  H131  C13  C14  C09   180.00   0.0  0
 K5Z  CONST_31  H082  N08  C06  C05   180.00   0.0  0
 K5Z  CONST_33  H071  N07  C06  C05     0.00   0.0  0
 K5Z  Var_01    C16   C15  C02  C03   118.60  30.0  2
 K5Z  Var_02    N08   C06  C05  C04   -24.78  30.0  2
 K5Z  Var_03    C02   C15  C16  C17   -63.46  30.0  2
 K5Z  Var_04    N18   C17  C16  C15  -179.19  30.0  1
 K5Z  Var_05    H4    N18  C17  C16   175.23  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
 K5Z  plan-1  C02   0.020
 K5Z  plan-1  C03   0.020
 K5Z  plan-1  C04   0.020
 K5Z  plan-1  C05   0.020
 K5Z  plan-1  C06   0.020
 K5Z  plan-1  C09   0.020
 K5Z  plan-1  S01   0.020
 K5Z  plan-1  H041  0.020
 K5Z  plan-1  C15   0.020
 K5Z  plan-2  C10   0.020
 K5Z  plan-2  C13   0.020
 K5Z  plan-2  C03   0.020
 K5Z  plan-2  C09   0.020
 K5Z  plan-2  C11   0.020
 K5Z  plan-2  C12   0.020
 K5Z  plan-2  C14   0.020
 K5Z  plan-2  H101  0.020
 K5Z  plan-2  H131  0.020
 K5Z  plan-2  H111  0.020
 K5Z  plan-2  H121  0.020
 K5Z  plan-2  H141  0.020
 K5Z  plan-3  C05   0.020
 K5Z  plan-3  C06   0.020
 K5Z  plan-3  N08   0.020
 K5Z  plan-3  N07   0.020
 K5Z  plan-3  H082  0.020
 K5Z  plan-3  H071  0.020
 K5Z  plan-3  H081  0.020

