# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:25:31 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(NCc2[nH]c(cn2)c3ccccc3)cc1OCc4cccnc4
#
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
 J08  J08  4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide  ligand  52  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J08
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
 J08  C10  C  CR5   0   0.397  -3.3885   1.3404  -0.6636
 J08  C13  C  CR15  0  -0.261  -5.0277   0.6264  -1.8238
 J08  C15  C  CR6   0   0.067  -6.2914  -0.6930  -0.0000
 J08  C17  C  CR16  0  -0.238  -7.1333  -2.2080   1.6867
 J08  C20  C  CR16  0  -0.327  -7.5206  -0.7848  -0.6591
 J08  C21  C  CR16  0  -0.498   1.3063   0.5349  -0.1829
 J08  C22  C  CR6   0   0.397   2.6270   0.8863   0.0402
 J08  C24  C  CH2   0  -0.272   3.3394  -1.3868  -0.1367
 J08  C26  C  CR16  0  -0.167   5.2923  -2.2032   1.2271
 J08  C28  C  CR16  0  -0.063   6.9821  -3.4901   0.1484
 J08  N01  N  NH2   0  -0.798   4.7266   3.8359  -0.0797
 J08  N03  N  N     0  -0.640   5.2206   2.0826   1.3045
 J08  C04  C  CR6   0  -0.151   2.9836   2.2309   0.2646
 J08  C05  C  CR16  0  -0.248   1.9605   3.1723   0.2474
 J08  C06  C  CR16  0  -0.376   0.6325   2.8377   0.0445
 J08  C07  C  CR6   0   0.419   0.2873   1.5020  -0.1835
 J08  N08  N  NH1   0  -0.694  -0.9970   1.1050  -0.4399
 J08  C09  C  CH2   0  -0.361  -2.1224   1.9889  -0.2229
 J08  N11  N  NR15  0  -0.655  -4.1667   0.6087   0.1624
 J08  C12  C  CR5   0   0.312  -5.2335   0.1402  -0.5552
 J08  N14  N  N     0  -0.432  -3.8856   1.3645  -1.8762
 J08  C16  C  CR16  0  -0.315  -6.1112  -1.4188   1.1793
 J08  C18  C  CR16  0  -0.268  -8.3487  -2.2956   1.0223
 J08  C19  C  CR16  0  -0.236  -8.5354  -1.5817  -0.1555
 J08  C25  C  CR6   0   0.008   4.6297  -2.1311   0.0065
 J08  C27  C  CR16  0  -0.320   6.4895  -2.8934   1.3015
 J08  N29  N  N     0  -0.401   6.3623  -3.4301  -1.0229
 J08  C30  C  CR16  0  -0.096   5.2164  -2.7617  -1.0828
 J08  H1   H  HCR5  0   0.260  -5.6412   0.4666  -2.6975
 J08  H2   H  HCR6  0   0.261  -6.9739  -2.7617   2.6026
 J08  H3   H  HCR6  0   0.254  -7.6892  -0.2200  -1.5673
 J08  H4   H  HCR6  0   0.289   1.0325  -0.4938  -0.3785
 J08  H5   H  HCH2  0   0.250   2.6221  -1.7188   0.6210
 J08  H6   H  HCH2  0   0.249   2.8990  -1.5762  -1.1210
 J08  H8   H  HCR6  0   0.268   7.9161  -4.0403   0.1758
 J08  H9   H  HNH2  0   0.387   4.3025   4.0438  -0.9683
 J08  H10  H  HNH2  0   0.378   5.6995   4.0925  -0.0196
 J08  H11  H  H     0   0.326   4.8006   1.2804   1.7552
 J08  H12  H  HCR6  0   0.261   2.2053   4.2115   0.4269
 J08  H13  H  HCR6  0   0.268  -0.1155   3.6170   0.0695
 J08  H14  H  HNH1  0   0.390  -1.1821   0.1256  -0.2904
 J08  H15  H  HCH2  0   0.267  -1.9916   2.8958  -0.8154
 J08  H16  H  HCH2  0   0.251  -2.2083   2.3015   0.8256
 J08  H17  H  HNR5  0   0.422  -4.0088   0.4797   1.1503
 J08  H19  H  HCR6  0   0.248  -5.1654  -1.3918   1.7067
 J08  H20  H  HCR6  0   0.259  -9.1433  -2.9143   1.4179
 J08  H21  H  HCR6  0   0.260  -9.4805  -1.6359  -0.6801
 J08  H22  H  HCR6  0   0.275   7.0327  -2.9758   2.2327
 J08  H23  H  HCR6  0   0.263   4.7296  -2.7230  -2.0528
 J08  O23  O  O2    0  -0.463   3.6324  -0.0085   0.0301
 J08  C02  C  C     0   0.325   4.3824   2.6604   0.5319
 J08  H7   H  HCR6  0   0.271   4.8760  -1.7314   2.1090

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
 J08  N03  C02  double    1.278  0.020  1.278
 J08  C02  N01  single    1.369  0.020  1.369
 J08  C02  C04  single    1.487  0.020  1.487
 J08  C05  C04  aromatic  1.390  0.020  1.390
 J08  C05  C06  aromatic  1.384  0.020  1.384
 J08  C04  C22  aromatic  1.409  0.020  1.409
 J08  C06  C07  aromatic  1.398  0.020  1.398
 J08  C22  O23  single    1.346  0.020  1.346
 J08  C22  C21  aromatic  1.385  0.020  1.385
 J08  C07  C21  aromatic  1.405  0.020  1.405
 J08  C07  N08  single    1.368  0.020  1.368
 J08  O23  C24  single    1.419  0.020  1.419
 J08  C30  N29  aromatic  1.328  0.020  1.328
 J08  C30  C25  aromatic  1.389  0.020  1.389
 J08  N08  C09  single    1.447  0.020  1.447
 J08  N29  C28  aromatic  1.327  0.020  1.327
 J08  C24  C25  single    1.496  0.020  1.496
 J08  C25  C26  aromatic  1.391  0.020  1.391
 J08  C28  C27  aromatic  1.389  0.020  1.389
 J08  C09  C10  single    1.489  0.020  1.489
 J08  C26  C27  aromatic  1.384  0.020  1.384
 J08  N14  C10  aromatic  1.311  0.020  1.311
 J08  N14  C13  aromatic  1.361  0.020  1.361
 J08  C10  N11  aromatic  1.350  0.020  1.350
 J08  C13  C12  aromatic  1.374  0.020  1.374
 J08  N11  C12  aromatic  1.368  0.020  1.368
 J08  C12  C15  single    1.457  0.020  1.457
 J08  C15  C20  aromatic  1.398  0.020  1.398
 J08  C15  C16  aromatic  1.396  0.020  1.396
 J08  C20  C19  aromatic  1.385  0.020  1.385
 J08  C16  C17  aromatic  1.387  0.020  1.387
 J08  C19  C18  aromatic  1.390  0.020  1.390
 J08  C17  C18  aromatic  1.388  0.020  1.388
 J08  C13  H1   single    0.930  0.020  1.080
 J08  C17  H2   single    0.930  0.020  1.080
 J08  C20  H3   single    0.930  0.020  1.080
 J08  C21  H4   single    0.930  0.020  1.080
 J08  C24  H5   single    0.970  0.020  1.090
 J08  C24  H6   single    0.970  0.020  1.090
 J08  C26  H7   single    0.930  0.020  1.080
 J08  C28  H8   single    0.930  0.020  1.080
 J08  N01  H9   single    0.890  0.020  1.040
 J08  N01  H10  single    0.890  0.020  1.040
 J08  N03  H11  single    0.890  0.020  1.040
 J08  C05  H12  single    0.930  0.020  1.080
 J08  C06  H13  single    0.930  0.020  1.080
 J08  N08  H14  single    0.890  0.020  1.040
 J08  C09  H15  single    0.970  0.020  1.090
 J08  C09  H16  single    0.970  0.020  1.090
 J08  N11  H17  single    0.860  0.020  1.020
 J08  C16  H19  single    0.930  0.020  1.080
 J08  C18  H20  single    0.930  0.020  1.080
 J08  C19  H21  single    0.930  0.020  1.080
 J08  C27  H22  single    0.930  0.020  1.080
 J08  C30  H23  single    0.930  0.020  1.080

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
 J08  N14  C10  N11  110.94  3.000
 J08  N11  C10  C09  123.02  3.000
 J08  N14  C10  C09  126.03  3.000
 J08  H1   C13  N14  121.74  3.000
 J08  H1   C13  C12  127.57  3.000
 J08  N14  C13  C12  110.68  3.000
 J08  C16  C15  C12  121.70  3.000
 J08  C16  C15  C20  118.52  3.000
 J08  C12  C15  C20  119.77  3.000
 J08  H2   C17  C18  120.12  3.000
 J08  H2   C17  C16  119.48  3.000
 J08  C18  C17  C16  120.40  3.000
 J08  H3   C20  C19  119.40  3.000
 J08  H3   C20  C15  119.88  3.000
 J08  C19  C20  C15  120.71  3.000
 J08  H4   C21  C07  118.08  3.000
 J08  H4   C21  C22  120.77  3.000
 J08  C07  C21  C22  121.14  3.000
 J08  O23  C22  C04  116.52  3.000
 J08  O23  C22  C21  122.86  3.000
 J08  C04  C22  C21  120.61  3.000
 J08  H6   C24  H5   107.83  3.000
 J08  H6   C24  C25  110.29  3.000
 J08  H5   C24  C25  110.36  3.000
 J08  H6   C24  O23  110.90  3.000
 J08  H5   C24  O23  110.39  3.000
 J08  C25  C24  O23  107.09  3.000
 J08  H7   C26  C27  120.38  3.000
 J08  H7   C26  C25  120.59  3.000
 J08  C27  C26  C25  119.03  3.000
 J08  H8   C28  N29  116.60  3.000
 J08  H8   C28  C27  120.17  3.000
 J08  N29  C28  C27  123.23  3.000
 J08  H10  N01  H9   114.01  3.000
 J08  H10  N01  C02  115.76  3.000
 J08  H9   N01  C02  117.77  3.000
 J08  H11  N03  C02  110.83  3.000
 J08  C05  C04  C02  119.91  3.000
 J08  C05  C04  C22  117.25  3.000
 J08  C02  C04  C22  122.83  3.000
 J08  H12  C05  C06  118.24  3.000
 J08  H12  C05  C04  118.78  3.000
 J08  C06  C05  C04  122.95  3.000
 J08  H13  C06  C07  121.46  3.000
 J08  H13  C06  C05  119.10  3.000
 J08  C07  C06  C05  119.44  3.000
 J08  N08  C07  C06  122.64  3.000
 J08  N08  C07  C21  118.76  3.000
 J08  C06  C07  C21  118.59  3.000
 J08  H14  N08  C09  115.36  3.000
 J08  H14  N08  C07  115.24  3.000
 J08  C09  N08  C07  121.63  3.000
 J08  H16  C09  H15  106.94  3.000
 J08  H16  C09  N08  112.22  3.000
 J08  H15  C09  N08  109.45  3.000
 J08  H16  C09  C10  109.89  3.000
 J08  H15  C09  C10  107.65  3.000
 J08  N08  C09  C10  110.53  3.000
 J08  H17  N11  C12  126.29  3.000
 J08  H17  N11  C10  125.32  3.000
 J08  C12  N11  C10  108.30  3.000
 J08  N11  C12  C15  124.20  3.000
 J08  C15  C12  C13  131.54  3.000
 J08  N11  C12  C13  104.26  3.000
 J08  C13  N14  C10  105.83  3.000
 J08  H19  C16  C17  118.64  3.000
 J08  H19  C16  C15  120.72  3.000
 J08  C17  C16  C15  120.63  3.000
 J08  H20  C18  C19  120.33  3.000
 J08  H20  C18  C17  120.28  3.000
 J08  C19  C18  C17  119.40  3.000
 J08  H21  C19  C18  120.15  3.000
 J08  H21  C19  C20  119.50  3.000
 J08  C18  C19  C20  120.34  3.000
 J08  C30  C25  C26  117.62  3.000
 J08  C26  C25  C24  121.37  3.000
 J08  C30  C25  C24  121.01  3.000
 J08  H22  C27  C28  120.27  3.000
 J08  H22  C27  C26  121.27  3.000
 J08  C28  C27  C26  118.46  3.000
 J08  C30  N29  C28  117.76  3.000
 J08  H23  C30  N29  116.43  3.000
 J08  H23  C30  C25  119.67  3.000
 J08  N29  C30  C25  123.90  3.000
 J08  C24  O23  C22  119.50  3.000
 J08  C04  C02  N03  126.50  3.000
 J08  C04  C02  N01  113.83  3.000
 J08  N03  C02  N01  119.56  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
 J08  CONST_01  C12  C13  N14  C10     0.00   0.0  0
 J08  CONST_02  C13  C12  N11  C10     0.00   0.0  0
 J08  CONST_03  C15  C12  N11  C10   180.00   0.0  0
 J08  CONST_04  N11  C10  N14  C13     0.00   0.0  0
 J08  CONST_07  N14  C13  C12  C15   180.00   0.0  0
 J08  CONST_08  C18  C19  C20  C15     0.00   0.0  0
 J08  CONST_09  C18  C17  C16  C15     0.00   0.0  0
 J08  CONST_10  C12  C15  C16  C17   180.00   0.0  0
 J08  CONST_11  C20  C15  C16  C17     0.00   0.0  0
 J08  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 J08  CONST_14  C05  C04  C22  C21     0.00   0.0  0
 J08  CONST_15  C05  C06  C07  C21     0.00   0.0  0
 J08  CONST_16  C06  C05  C04  C22     0.00   0.0  0
 J08  CONST_17  C06  C07  C21  C22     0.00   0.0  0
 J08  CONST_18  N29  C30  C25  C26     0.00   0.0  0
 J08  CONST_19  N29  C28  C27  C26     0.00   0.0  0
 J08  CONST_20  C25  C30  N29  C28     0.00   0.0  0
 J08  CONST_21  C25  C26  C27  C28     0.00   0.0  0
 J08  CONST_22  C07  C06  C05  C04     0.00   0.0  0
 J08  CONST_23  C07  C21  C22  C04     0.00   0.0  0
 J08  CONST_24  N14  C13  C12  N11     0.00   0.0  0
 J08  CONST_26  N14  C10  N11  C12     0.00   0.0  0
 J08  CONST_27  C19  C20  C15  C12   180.00   0.0  0
 J08  CONST_28  C19  C20  C15  C16     0.00   0.0  0
 J08  CONST_29  C19  C18  C17  C16     0.00   0.0  0
 J08  CONST_30  C30  N29  C28  C27     0.00   0.0  0
 J08  CONST_31  C30  C25  C26  C27     0.00   0.0  0
 J08  CONST_32  C09  C10  N14  C13   180.00   0.0  0
 J08  CONST_33  C02  C04  C22  C21   180.00   0.0  0
 J08  CONST_34  N08  C07  C21  C22   180.00   0.0  0
 J08  CONST_35  N29  C30  C25  C24   180.00   0.0  0
 J08  CONST_36  C27  C26  C25  C24   180.00   0.0  0
 J08  CONST_37  C06  C05  C04  C02   180.00   0.0  0
 J08  CONST_38  O23  C22  C04  C05   180.00   0.0  0
 J08  CONST_39  N08  C07  C06  C05   180.00   0.0  0
 J08  CONST_40  O23  C22  C21  C07   180.00   0.0  0
 J08  CONST_41  C12  N11  C10  C09   180.00   0.0  0
 J08  CONST_42  H1   C13  N14  C10   180.00   0.0  0
 J08  CONST_43  H17  N11  C12  C13   180.00   0.0  0
 J08  CONST_44  H21  C19  C20  C15   180.00   0.0  0
 J08  CONST_45  H2   C17  C16  C15   180.00   0.0  0
 J08  CONST_46  H19  C16  C15  C20   180.00   0.0  0
 J08  CONST_47  H20  C18  C19  C20   180.00   0.0  0
 J08  CONST_48  H13  C06  C07  C21   180.00   0.0  0
 J08  CONST_49  H12  C05  C04  C22   180.00   0.0  0
 J08  CONST_50  H23  C30  C25  C26   180.00   0.0  0
 J08  CONST_51  H8   C28  C27  C26   180.00   0.0  0
 J08  CONST_52  H7   C26  C27  C28   180.00   0.0  0
 J08  CONST_53  H4   C21  C22  C04   180.00   0.0  0
 J08  CONST_54  H3   C20  C15  C12     0.00   0.0  0
 J08  CONST_55  H22  C27  C26  C25   180.00   0.0  0
 J08  CONST_56  C09  N08  C07  C21   180.00   0.0  0
 J08  CONST_57  C09  N08  C07  C06     0.00   0.0  0
 J08  CONST_59  H11  N03  C02  C04     0.00   0.0  0
 J08  CONST_61  H10  N01  C02  C04   180.00   0.0  0
 J08  Var_01    C07  N08  C09  C10   176.31  30.0  1
 J08  Var_02    N03  C02  C04  C22   -43.29  30.0  2
 J08  Var_03    C25  C24  O23  C22  -175.46  30.0  3
 J08  Var_04    C04  C22  O23  C24   177.48  30.0  1
 J08  Var_05    O23  C24  C25  C26    68.12  30.0  2
 J08  Var_06    N14  C10  C09  N08   -87.06  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
 J08  plan-1  C10  0.020
 J08  plan-1  C13  0.020
 J08  plan-1  C15  0.020
 J08  plan-1  C09  0.020
 J08  plan-1  N11  0.020
 J08  plan-1  C12  0.020
 J08  plan-1  N14  0.020
 J08  plan-1  H1   0.020
 J08  plan-1  H17  0.020
 J08  plan-2  C15  0.020
 J08  plan-2  C17  0.020
 J08  plan-2  C20  0.020
 J08  plan-2  C12  0.020
 J08  plan-2  C16  0.020
 J08  plan-2  C18  0.020
 J08  plan-2  C19  0.020
 J08  plan-2  H2   0.020
 J08  plan-2  H3   0.020
 J08  plan-2  H19  0.020
 J08  plan-2  H20  0.020
 J08  plan-2  H21  0.020
 J08  plan-3  C21  0.020
 J08  plan-3  C22  0.020
 J08  plan-3  C04  0.020
 J08  plan-3  C05  0.020
 J08  plan-3  C06  0.020
 J08  plan-3  C07  0.020
 J08  plan-3  N08  0.020
 J08  plan-3  H4   0.020
 J08  plan-3  H12  0.020
 J08  plan-3  H13  0.020
 J08  plan-3  O23  0.020
 J08  plan-3  C02  0.020
 J08  plan-4  C24  0.020
 J08  plan-4  C26  0.020
 J08  plan-4  C28  0.020
 J08  plan-4  C25  0.020
 J08  plan-4  C27  0.020
 J08  plan-4  N29  0.020
 J08  plan-4  C30  0.020
 J08  plan-4  H8   0.020
 J08  plan-4  H22  0.020
 J08  plan-4  H23  0.020
 J08  plan-4  H7   0.020
 J08  plan-5  C07  0.020
 J08  plan-5  N08  0.020
 J08  plan-5  C09  0.020
 J08  plan-5  H14  0.020
 J08  plan-6  N01  0.020
 J08  plan-6  N03  0.020
 J08  plan-6  C04  0.020
 J08  plan-6  H9   0.020
 J08  plan-6  H10  0.020
 J08  plan-6  H11  0.020
 J08  plan-6  C02  0.020

