# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:34:11 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: 5-(1~{H}-imidazol-5-yl)-4-phenyl-thiophene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1sc(c2[nH]cnc2)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
 KLB  KLB  5-(1~{H}-imidazol-5-yl)-4-phenyl-thiophene-2-carboximidamide  ligand  31  19  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KLB
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
 KLB  C12  C  CR16  0  -0.263  -16.2213  -21.8290  -3.1537
 KLB  C13  C  CR16  0  -0.240  -15.7195  -20.7895  -3.9267
 KLB  C14  C  CR16  0  -0.298  -16.5715  -20.0429  -4.7278
 KLB  C11  C  CR16  0  -0.243  -17.5798  -22.1127  -3.1819
 KLB  C10  C  CR16  0  -0.302  -18.4316  -21.3648  -3.9838
 KLB  C15  C  CR5   0   0.288  -19.5497  -21.2419  -7.3487
 KLB  C17  C  CR15  0   0.091  -19.5737  -22.7117  -8.9817
 KLB  C19  C  CR15  0  -0.252  -19.6537  -22.5240  -6.8642
 KLB  S01  S  S2    0   0.275  -20.4046  -18.6426  -7.4504
 KLB  C02  C  CR5   0  -0.325  -19.5211  -19.9367  -6.7212
 KLB  C03  C  CR5   0   0.201  -18.8270  -19.5075  -5.6134
 KLB  C04  C  CR15  0  -0.252  -19.0134  -18.1176  -5.3805
 KLB  C05  C  CR5   0  -0.184  -19.8358  -17.5168  -6.2865
 KLB  C06  C  C     0   0.347  -20.2778  -16.1193  -6.3929
 KLB  N07  N  NH2   0  -0.829  -19.8940  -15.3019  -5.3716
 KLB  N08  N  N     0  -0.659  -20.9322  -15.7907  -7.4406
 KLB  C09  C  CR6   0   0.045  -17.9361  -20.3293  -4.7725
 KLB  N16  N  NR15  0  -0.616  -19.5098  -21.3964  -8.7123
 KLB  N18  N  N     0  -0.433  -19.6645  -23.4231  -7.8858
 KLB  H1   H  HCR6  0   0.259  -15.5574  -22.4100  -2.5270
 KLB  H2   H  HCR6  0   0.259  -14.6623  -20.5589  -3.9074
 KLB  H3   H  HCR6  0   0.253  -16.1736  -19.2355  -5.3303
 KLB  H4   H  HCR6  0   0.259  -17.9814  -22.9134  -2.5745
 KLB  H5   H  HCR6  0   0.258  -19.4936  -21.5748  -3.9795
 KLB  H6   H  HCR5  0   0.284  -19.5479  -23.0947  -9.9901
 KLB  H7   H  HCR5  0   0.256  -19.7460  -22.8338  -5.8364
 KLB  H8   H  HCR5  0   0.269  -18.5314  -17.6013  -4.5612
 KLB  H9   H  HNH2  0   0.399  -19.7296  -15.7062  -4.4647
 KLB  H10  H  HNH2  0   0.396  -20.3210  -14.3903  -5.3296
 KLB  H11  H  H     0   0.333  -21.2167  -14.8157  -7.4153
 KLB  H12  H  HNR5  0   0.422  -19.3857  -20.6635  -9.3944

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
 KLB  C17  N16  aromatic  1.344  0.020  1.344
 KLB  C17  N18  aromatic  1.310  0.020  1.310
 KLB  N16  C15  aromatic  1.373  0.020  1.373
 KLB  N18  C19  aromatic  1.361  0.020  1.361
 KLB  N08  C06  double    1.278  0.020  1.278
 KLB  S01  C02  aromatic  1.728  0.020  1.728
 KLB  S01  C05  aromatic  1.716  0.020  1.716
 KLB  C15  C19  aromatic  1.375  0.020  1.375
 KLB  C15  C02  single    1.449  0.020  1.449
 KLB  C02  C03  aromatic  1.376  0.020  1.376
 KLB  C06  C05  single    1.470  0.020  1.470
 KLB  C06  N07  single    1.363  0.020  1.363
 KLB  C05  C04  aromatic  1.363  0.020  1.363
 KLB  C03  C04  aromatic  1.422  0.020  1.422
 KLB  C03  C09  single    1.475  0.020  1.475
 KLB  C09  C14  aromatic  1.395  0.020  1.395
 KLB  C09  C10  aromatic  1.393  0.020  1.393
 KLB  C14  C13  aromatic  1.387  0.020  1.387
 KLB  C10  C11  aromatic  1.388  0.020  1.388
 KLB  C13  C12  aromatic  1.389  0.020  1.389
 KLB  C11  C12  aromatic  1.388  0.020  1.388
 KLB  C12  H1   single    0.930  0.020  1.080
 KLB  C13  H2   single    0.930  0.020  1.080
 KLB  C14  H3   single    0.930  0.020  1.080
 KLB  C11  H4   single    0.930  0.020  1.080
 KLB  C10  H5   single    0.930  0.020  1.080
 KLB  C17  H6   single    0.930  0.020  1.080
 KLB  C19  H7   single    0.930  0.020  1.080
 KLB  C04  H8   single    0.930  0.020  1.080
 KLB  N07  H9   single    0.890  0.020  1.040
 KLB  N07  H10  single    0.890  0.020  1.040
 KLB  N08  H11  single    0.890  0.020  1.040
 KLB  N16  H12  single    0.860  0.020  1.020

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
 KLB  H1   C12  C11  120.16  3.000
 KLB  H1   C12  C13  120.16  3.000
 KLB  C11  C12  C13  119.67  3.000
 KLB  H2   C13  C14  119.71  3.000
 KLB  H2   C13  C12  120.15  3.000
 KLB  C14  C13  C12  120.14  3.000
 KLB  H3   C14  C09  119.64  3.000
 KLB  H3   C14  C13  119.78  3.000
 KLB  C09  C14  C13  120.58  3.000
 KLB  H4   C11  C10  119.67  3.000
 KLB  H4   C11  C12  120.19  3.000
 KLB  C10  C11  C12  120.14  3.000
 KLB  H5   C10  C09  119.70  3.000
 KLB  H5   C10  C11  119.67  3.000
 KLB  C09  C10  C11  120.61  3.000
 KLB  N16  C15  C02  122.08  3.000
 KLB  C02  C15  C19  133.57  3.000
 KLB  N16  C15  C19  104.32  3.000
 KLB  H6   C17  N18  126.22  3.000
 KLB  H6   C17  N16  122.24  3.000
 KLB  N18  C17  N16  111.54  3.000
 KLB  H7   C19  N18  121.70  3.000
 KLB  H7   C19  C15  127.66  3.000
 KLB  N18  C19  C15  110.62  3.000
 KLB  C05  S01  C02   92.04  3.000
 KLB  C03  C02  S01  111.35  3.000
 KLB  C03  C02  C15  129.78  3.000
 KLB  S01  C02  C15  118.80  3.000
 KLB  C09  C03  C04  122.04  3.000
 KLB  C09  C03  C02  126.15  3.000
 KLB  C04  C03  C02  111.76  3.000
 KLB  H8   C04  C05  124.18  3.000
 KLB  H8   C04  C03  122.16  3.000
 KLB  C05  C04  C03  113.65  3.000
 KLB  C06  C05  C04  130.45  3.000
 KLB  C04  C05  S01  111.19  3.000
 KLB  C06  C05  S01  118.36  3.000
 KLB  N08  C06  N07  127.16  3.000
 KLB  N07  C06  C05  115.54  3.000
 KLB  N08  C06  C05  117.25  3.000
 KLB  H10  N07  H9   113.27  3.000
 KLB  H10  N07  C06  117.03  3.000
 KLB  H9   N07  C06  118.70  3.000
 KLB  H11  N08  C06  111.69  3.000
 KLB  C03  C09  C10  121.47  3.000
 KLB  C10  C09  C14  118.84  3.000
 KLB  C03  C09  C14  119.65  3.000
 KLB  H12  N16  C17  125.54  3.000
 KLB  H12  N16  C15  126.40  3.000
 KLB  C17  N16  C15  107.93  3.000
 KLB  C19  N18  C17  105.59  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
 KLB  CONST_01  C09  C14  C13  C12    0.00   0.0  0
 KLB  CONST_02  C09  C10  C11  C12    0.00   0.0  0
 KLB  CONST_03  C03  C09  C14  C13  180.00   0.0  0
 KLB  CONST_04  C10  C09  C14  C13    0.00   0.0  0
 KLB  CONST_05  C10  C11  C12  C13    0.00   0.0  0
 KLB  CONST_08  C11  C10  C09  C14    0.00   0.0  0
 KLB  CONST_09  C11  C12  C13  C14    0.00   0.0  0
 KLB  CONST_10  C03  C09  C10  C11  180.00   0.0  0
 KLB  CONST_13  N18  C17  N16  C15    0.00   0.0  0
 KLB  CONST_14  C17  N18  C19  C15    0.00   0.0  0
 KLB  CONST_15  C05  S01  C02  C15  180.00   0.0  0
 KLB  CONST_16  C04  C03  C02  C15  180.00   0.0  0
 KLB  CONST_17  C09  C03  C02  C15    0.00   0.0  0
 KLB  CONST_18  C19  C15  N16  C17    0.00   0.0  0
 KLB  CONST_19  C02  C15  N16  C17  180.00   0.0  0
 KLB  CONST_20  N16  C17  N18  C19    0.00   0.0  0
 KLB  CONST_24  C04  C03  C02  S01    0.00   0.0  0
 KLB  CONST_25  C09  C03  C02  S01  180.00   0.0  0
 KLB  CONST_26  C03  C04  C05  S01    0.00   0.0  0
 KLB  CONST_27  C04  C05  S01  C02    0.00   0.0  0
 KLB  CONST_28  N18  C19  C15  C02  180.00   0.0  0
 KLB  CONST_29  C05  C04  C03  C02    0.00   0.0  0
 KLB  CONST_30  C05  S01  C02  C03    0.00   0.0  0
 KLB  CONST_32  C09  C03  C04  C05  180.00   0.0  0
 KLB  CONST_33  N18  C19  C15  N16    0.00   0.0  0
 KLB  CONST_34  C06  C05  S01  C02  180.00   0.0  0
 KLB  CONST_35  C06  C05  C04  C03  180.00   0.0  0
 KLB  CONST_36  H3   C14  C13  C12  180.00   0.0  0
 KLB  CONST_37  H5   C10  C11  C12  180.00   0.0  0
 KLB  CONST_38  H4   C11  C12  C13  180.00   0.0  0
 KLB  CONST_39  H1   C12  C13  C14  180.00   0.0  0
 KLB  CONST_40  H2   C13  C12  C11  180.00   0.0  0
 KLB  CONST_41  H6   C17  N16  C15  180.00   0.0  0
 KLB  CONST_42  H7   C19  N18  C17  180.00   0.0  0
 KLB  CONST_43  H12  N16  C15  C19  180.00   0.0  0
 KLB  CONST_44  H8   C04  C05  S01  180.00   0.0  0
 KLB  CONST_45  H11  N08  C06  C05  180.00   0.0  0
 KLB  CONST_47  H10  N07  C06  C05  180.00   0.0  0
 KLB  Var_01    N08  C06  C05  S01   -8.21  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
 KLB  plan-1  C15  0.020
 KLB  plan-1  C17  0.020
 KLB  plan-1  C19  0.020
 KLB  plan-1  C02  0.020
 KLB  plan-1  N16  0.020
 KLB  plan-1  N18  0.020
 KLB  plan-1  H6   0.020
 KLB  plan-1  H7   0.020
 KLB  plan-1  H12  0.020
 KLB  plan-2  C15  0.020
 KLB  plan-2  S01  0.020
 KLB  plan-2  C02  0.020
 KLB  plan-2  C03  0.020
 KLB  plan-2  C04  0.020
 KLB  plan-2  C05  0.020
 KLB  plan-2  C06  0.020
 KLB  plan-2  C09  0.020
 KLB  plan-2  H8   0.020
 KLB  plan-3  C12  0.020
 KLB  plan-3  C13  0.020
 KLB  plan-3  C14  0.020
 KLB  plan-3  C11  0.020
 KLB  plan-3  C10  0.020
 KLB  plan-3  C03  0.020
 KLB  plan-3  C09  0.020
 KLB  plan-3  H1   0.020
 KLB  plan-3  H2   0.020
 KLB  plan-3  H3   0.020
 KLB  plan-3  H4   0.020
 KLB  plan-3  H5   0.020
 KLB  plan-4  C05  0.020
 KLB  plan-4  C06  0.020
 KLB  plan-4  N07  0.020
 KLB  plan-4  N08  0.020
 KLB  plan-4  H9   0.020
 KLB  plan-4  H10  0.020
 KLB  plan-4  H11  0.020

