# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 03:18:52 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-(imidazolidin-2-ylideneamino)-~{N}-[4-(imidazolidin-2-ylideneamino)phenyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(cc1)N=C2NCCN2)c3ccc(cc3)N=C4NCCN4
#
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
 6XV  6XV  4-(imidazolidin-2-ylideneamino)-~{N}-[4-(imidazolidin-2-ylideneamino)phenyl]benzamide  ligand  48  27  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6XV
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
 6XV  N10  N  NH1   0  -0.662  -6.6494  -0.5421  -0.8843
 6XV  C14  C  CR16  0  -0.320  -3.9409  -0.9138   0.7414
 6XV  C18  C  CR16  0  -0.306   3.5909   0.8578  -1.1264
 6XV  C19  C  CR6   0   0.243   4.5953  -0.0537  -0.7676
 6XV  C26  C  CR16  0  -0.338   4.1870  -1.2430  -0.1380
 6XV  C27  C  CR16  0  -0.255   2.8548  -1.4835   0.1388
 6XV  C02  C  C     0   0.523   0.4545  -0.9026   0.1338
 6XV  C04  C  CR6   0   0.354  -1.7956   0.1304   0.3970
 6XV  C05  C  CR16  0  -0.353  -2.4223   1.3702   0.5450
 6XV  C06  C  CR16  0  -0.301  -3.7806   1.4635   0.7832
 6XV  C07  C  CR6   0   0.206  -4.5811   0.3213   0.8800
 6XV  N08  N  N     0  -0.545  -5.9341   0.4464   1.1801
 6XV  C09  C  C     0   0.631  -6.8127  -0.0219   0.3685
 6XV  C11  C  CH2   0  -0.291  -7.8908  -1.1303  -1.3512
 6XV  C12  C  CH2   0  -0.293  -8.9120  -0.3280  -0.5481
 6XV  N13  N  NH1   0  -0.662  -8.1498  -0.0351   0.6512
 6XV  C15  C  CR16  0  -0.315  -2.5776  -1.0199   0.5000
 6XV  C16  C  CR6   0  -0.076   1.8664  -0.5552  -0.1879
 6XV  C17  C  CR16  0  -0.292   2.2618   0.6160  -0.8389
 6XV  C21  C  C     0   0.645   6.8831   0.0438  -0.3305
 6XV  N22  N  NH1   0  -0.660   8.1782   0.1292  -0.7469
 6XV  C23  C  CH2   0  -0.293   9.0718   0.2142   0.3927
 6XV  C24  C  CH2   0  -0.290   8.2397  -0.4825   1.4678
 6XV  N25  N  NH1   0  -0.662   6.8949  -0.1830   1.0128
 6XV  H1   H  HNH1  0   0.402  -5.7682  -0.9530  -1.1448
 6XV  H2   H  HCR6  0   0.257  -4.5152  -1.8274   0.8486
 6XV  H3   H  HCR6  0   0.250   3.8736   1.7649  -1.6452
 6XV  H4   H  HCR6  0   0.264   4.9181  -2.0051   0.1055
 6XV  H5   H  HCR6  0   0.259   2.5708  -2.4127   0.6152
 6XV  H6   H  HNH1  0   0.411  -0.0256   1.0643   0.0443
 6XV  H7   H  HCR6  0   0.262  -1.8368   2.2800   0.4693
 6XV  H8   H  HCR6  0   0.246  -4.2346   2.4398   0.9002
 6XV  H9   H  HCH2  0   0.253  -8.0167  -1.0095  -2.4257
 6XV  H10  H  HCH2  0   0.241  -7.9505  -2.1969  -1.1128
 6XV  H11  H  HCH2  0   0.239  -9.2048   0.5826  -1.0809
 6XV  H12  H  HCH2  0   0.252  -9.8111  -0.9009  -0.3278
 6XV  H13  H  HNH1  0   0.390  -8.4965   0.6413   1.3124
 6XV  H14  H  HCR6  0   0.284  -2.1371  -1.9987   0.4032
 6XV  H15  H  HCR6  0   0.245   1.5375   1.3548  -1.1614
 6XV  H16  H  HNH1  0   0.394   8.3702   0.6566  -1.5835
 6XV  H17  H  HCH2  0   0.255  10.0171  -0.2914   0.2044
 6XV  H18  H  HCH2  0   0.242   9.2828   1.2518   0.6699
 6XV  H19  H  HCH2  0   0.244   8.4308  -1.5598   1.4835
 6XV  H20  H  HCH2  0   0.256   8.4275  -0.0843   2.4631
 6XV  H21  H  HNH1  0   0.404   6.0972  -0.5840   1.4766
 6XV  N03  N  NH1   0  -0.771  -0.4176   0.1421   0.1452
 6XV  N20  N  N     0  -0.525   5.8912   0.2189  -1.1331
 6XV  O01  O  O     0  -0.442   0.1254  -2.0502   0.3789

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
 6XV  C24  C23  single    1.528  0.020  1.528
 6XV  C24  N25  single    1.451  0.020  1.451
 6XV  C23  N22  single    1.451  0.020  1.451
 6XV  N22  C21  single    1.363  0.020  1.363
 6XV  N25  C21  single    1.362  0.020  1.362
 6XV  C21  N20  double    1.288  0.020  1.288
 6XV  N20  C19  single    1.374  0.020  1.374
 6XV  C18  C19  aromatic  1.403  0.020  1.403
 6XV  C18  C17  aromatic  1.381  0.020  1.381
 6XV  C19  C26  aromatic  1.406  0.020  1.406
 6XV  C17  C16  aromatic  1.397  0.020  1.397
 6XV  C26  C27  aromatic  1.382  0.020  1.382
 6XV  O01  C02  double    1.219  0.020  1.219
 6XV  C16  C27  aromatic  1.395  0.020  1.395
 6XV  C16  C02  single    1.489  0.020  1.489
 6XV  C02  N03  single    1.361  0.020  1.361
 6XV  C05  C06  aromatic  1.382  0.020  1.382
 6XV  C05  C04  aromatic  1.397  0.020  1.397
 6XV  N03  C04  single    1.401  0.020  1.401
 6XV  C06  C07  aromatic  1.398  0.020  1.398
 6XV  C04  C15  aromatic  1.395  0.020  1.395
 6XV  C07  N08  single    1.391  0.020  1.391
 6XV  C07  C14  aromatic  1.398  0.020  1.398
 6XV  C15  C14  aromatic  1.389  0.020  1.389
 6XV  N08  C09  double    1.284  0.020  1.284
 6XV  C09  N13  single    1.367  0.020  1.367
 6XV  C09  N10  single    1.366  0.020  1.366
 6XV  N13  C12  single    1.451  0.020  1.451
 6XV  N10  C11  single    1.451  0.020  1.451
 6XV  C12  C11  single    1.527  0.020  1.527
 6XV  N10  H1   single    0.890  0.020  1.040
 6XV  C14  H2   single    0.930  0.020  1.080
 6XV  C18  H3   single    0.930  0.020  1.080
 6XV  C26  H4   single    0.930  0.020  1.080
 6XV  C27  H5   single    0.930  0.020  1.080
 6XV  N03  H6   single    0.860  0.020  1.020
 6XV  C05  H7   single    0.930  0.020  1.080
 6XV  C06  H8   single    0.930  0.020  1.080
 6XV  C11  H9   single    0.970  0.020  1.090
 6XV  C11  H10  single    0.970  0.020  1.090
 6XV  C12  H11  single    0.970  0.020  1.090
 6XV  C12  H12  single    0.970  0.020  1.090
 6XV  N13  H13  single    0.890  0.020  1.040
 6XV  C15  H14  single    0.930  0.020  1.080
 6XV  C17  H15  single    0.930  0.020  1.080
 6XV  N22  H16  single    0.890  0.020  1.040
 6XV  C23  H17  single    0.970  0.020  1.090
 6XV  C23  H18  single    0.970  0.020  1.090
 6XV  C24  H19  single    0.970  0.020  1.090
 6XV  C24  H20  single    0.970  0.020  1.090
 6XV  N25  H21  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
 6XV  H1   N10  C11  120.02  3.000
 6XV  H1   N10  C09  119.82  3.000
 6XV  C11  N10  C09  110.32  3.000
 6XV  H2   C14  C15  118.22  3.000
 6XV  H2   C14  C07  119.47  3.000
 6XV  C15  C14  C07  122.30  3.000
 6XV  H3   C18  C17  119.85  3.000
 6XV  H3   C18  C19  118.69  3.000
 6XV  C17  C18  C19  121.46  3.000
 6XV  N20  C19  C26  124.11  3.000
 6XV  C26  C19  C18  117.13  3.000
 6XV  N20  C19  C18  118.58  3.000
 6XV  H4   C26  C27  118.88  3.000
 6XV  H4   C26  C19  119.96  3.000
 6XV  C27  C26  C19  121.12  3.000
 6XV  H5   C27  C16  119.25  3.000
 6XV  H5   C27  C26  119.38  3.000
 6XV  C16  C27  C26  121.36  3.000
 6XV  C16  C02  N03  115.49  3.000
 6XV  N03  C02  O01  123.23  3.000
 6XV  C16  C02  O01  121.28  3.000
 6XV  C15  C04  C05  118.20  3.000
 6XV  C15  C04  N03  124.87  3.000
 6XV  C05  C04  N03  116.93  3.000
 6XV  H7   C05  C06  119.07  3.000
 6XV  H7   C05  C04  119.66  3.000
 6XV  C06  C05  C04  121.27  3.000
 6XV  H8   C06  C07  119.27  3.000
 6XV  H8   C06  C05  119.44  3.000
 6XV  C07  C06  C05  121.29  3.000
 6XV  N08  C07  C06  119.88  3.000
 6XV  N08  C07  C14  123.10  3.000
 6XV  C06  C07  C14  116.92  3.000
 6XV  C09  N08  C07  119.74  3.000
 6XV  N13  C09  N08  122.82  3.000
 6XV  N13  C09  N10  107.63  3.000
 6XV  N08  C09  N10  129.52  3.000
 6XV  H10  C11  H9   108.47  3.000
 6XV  H10  C11  C12  111.16  3.000
 6XV  H9   C11  C12  112.55  3.000
 6XV  H10  C11  N10  111.81  3.000
 6XV  H9   C11  N10  111.82  3.000
 6XV  C12  C11  N10  100.95  3.000
 6XV  H12  C12  H11  108.38  3.000
 6XV  H12  C12  N13  111.89  3.000
 6XV  H11  C12  N13  112.01  3.000
 6XV  H12  C12  C11  112.48  3.000
 6XV  H11  C12  C11  111.09  3.000
 6XV  N13  C12  C11  100.92  3.000
 6XV  H13  N13  C12  119.82  3.000
 6XV  H13  N13  C09  117.77  3.000
 6XV  C12  N13  C09  110.18  3.000
 6XV  H14  C15  C04  120.88  3.000
 6XV  H14  C15  C14  119.10  3.000
 6XV  C04  C15  C14  120.02  3.000
 6XV  C17  C16  C02  124.37  3.000
 6XV  C02  C16  C27  117.77  3.000
 6XV  C17  C16  C27  117.81  3.000
 6XV  H15  C17  C16  121.40  3.000
 6XV  H15  C17  C18  117.51  3.000
 6XV  C16  C17  C18  121.07  3.000
 6XV  N25  C21  N22  107.67  3.000
 6XV  N25  C21  N20  130.07  3.000
 6XV  N22  C21  N20  122.20  3.000
 6XV  H16  N22  C23  120.28  3.000
 6XV  H16  N22  C21  117.87  3.000
 6XV  C23  N22  C21  110.42  3.000
 6XV  H18  C23  H17  108.47  3.000
 6XV  H18  C23  C24  111.05  3.000
 6XV  H17  C23  C24  112.51  3.000
 6XV  H18  C23  N22  111.92  3.000
 6XV  H17  C23  N22  111.83  3.000
 6XV  C24  C23  N22  100.99  3.000
 6XV  H20  C24  H19  108.48  3.000
 6XV  H20  C24  N25  111.79  3.000
 6XV  H19  C24  N25  111.68  3.000
 6XV  H20  C24  C23  112.51  3.000
 6XV  H19  C24  C23  111.35  3.000
 6XV  N25  C24  C23  100.95  3.000
 6XV  H21  N25  C24  120.53  3.000
 6XV  H21  N25  C21  120.93  3.000
 6XV  C24  N25  C21  110.59  3.000
 6XV  H6   N03  C04  114.11  3.000
 6XV  H6   N03  C02  116.91  3.000
 6XV  C04  N03  C02  128.72  3.000
 6XV  C21  N20  C19  122.26  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
 6XV  CONST_01  C05  C06  C07  C14    0.00   0.0  0
 6XV  CONST_02  C05  C04  C15  C14    0.00   0.0  0
 6XV  CONST_03  C27  C26  C19  C18    0.00   0.0  0
 6XV  CONST_04  C27  C16  C17  C18    0.00   0.0  0
 6XV  CONST_05  C16  C17  C18  C19    0.00   0.0  0
 6XV  CONST_06  C16  C27  C26  C19    0.00   0.0  0
 6XV  CONST_07  C17  C18  C19  C26    0.00   0.0  0
 6XV  CONST_08  C17  C16  C27  C26    0.00   0.0  0
 6XV  CONST_09  C07  C06  C05  C04    0.00   0.0  0
 6XV  CONST_10  C07  C14  C15  C04    0.00   0.0  0
 6XV  CONST_11  C15  C04  C05  C06    0.00   0.0  0
 6XV  CONST_12  C15  C14  C07  C06    0.00   0.0  0
 6XV  CONST_13  C12  N13  C09  N10    0.00   0.0  0
 6XV  CONST_17  N13  C09  N10  C11    0.00   0.0  0
 6XV  CONST_21  C24  N25  C21  N22    0.00   0.0  0
 6XV  CONST_22  N25  C21  N22  C23    0.00   0.0  0
 6XV  CONST_23  N03  C04  C15  C14  180.00   0.0  0
 6XV  CONST_24  C02  C16  C17  C18  180.00   0.0  0
 6XV  CONST_25  C02  C16  C27  C26  180.00   0.0  0
 6XV  CONST_26  N20  C19  C26  C27  180.00   0.0  0
 6XV  CONST_27  C06  C05  C04  N03  180.00   0.0  0
 6XV  CONST_28  N08  C07  C06  C05  180.00   0.0  0
 6XV  CONST_29  C15  C14  C07  N08  180.00   0.0  0
 6XV  CONST_30  N20  C19  C18  C17  180.00   0.0  0
 6XV  CONST_31  C07  N08  C09  N10    0.00   0.0  0
 6XV  CONST_32  N22  C21  N20  C19  180.00   0.0  0
 6XV  CONST_33  N25  C21  N20  C19    0.00   0.0  0
 6XV  CONST_34  N13  C09  N08  C07  180.00   0.0  0
 6XV  CONST_35  C12  N13  C09  N08  180.00   0.0  0
 6XV  CONST_36  C11  N10  C09  N08  180.00   0.0  0
 6XV  CONST_37  C23  N22  C21  N20  180.00   0.0  0
 6XV  CONST_38  C24  N25  C21  N20  180.00   0.0  0
 6XV  CONST_39  H8   C06  C07  C14  180.00   0.0  0
 6XV  CONST_40  H4   C26  C19  C18  180.00   0.0  0
 6XV  CONST_41  H15  C17  C18  C19  180.00   0.0  0
 6XV  CONST_42  H5   C27  C26  C19  180.00   0.0  0
 6XV  CONST_43  H3   C18  C19  C26  180.00   0.0  0
 6XV  CONST_44  H2   C14  C15  C04  180.00   0.0  0
 6XV  CONST_45  H14  C15  C04  C05  180.00   0.0  0
 6XV  CONST_46  H7   C05  C06  C07  180.00   0.0  0
 6XV  CONST_48  H1   N10  C11  C12  180.00   0.0  0
 6XV  CONST_50  H16  N22  C23  C24  180.00   0.0  0
 6XV  CONST_51  C16  C02  N03  C04  180.00   0.0  0
 6XV  CONST_52  C05  C04  N03  C02  180.00   0.0  0
 6XV  CONST_53  C15  C04  N03  C02    0.00   0.0  0
 6XV  CONST_54  H6   N03  C04  C05    0.00   0.0  0
 6XV  CONST_55  C04  N03  C02  O01    0.00   0.0  0
 6XV  Var_01    H11  C12  C11  N10   88.74  30.0  1
 6XV  Var_02    H9   C11  N10  C09  145.79  30.0  1
 6XV  Var_03    H17  C23  N22  C21  145.76  30.0  1
 6XV  Var_04    H19  C24  N25  C21  -93.27  30.0  1
 6XV  Var_05    O01  C02  C16  C27  -16.69  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
 6XV  plan-1  C18  0.020
 6XV  plan-1  C19  0.020
 6XV  plan-1  C26  0.020
 6XV  plan-1  C27  0.020
 6XV  plan-1  C02  0.020
 6XV  plan-1  C16  0.020
 6XV  plan-1  C17  0.020
 6XV  plan-1  H3   0.020
 6XV  plan-1  H4   0.020
 6XV  plan-1  H5   0.020
 6XV  plan-1  H15  0.020
 6XV  plan-1  N20  0.020
 6XV  plan-2  C14  0.020
 6XV  plan-2  C04  0.020
 6XV  plan-2  C05  0.020
 6XV  plan-2  C06  0.020
 6XV  plan-2  C07  0.020
 6XV  plan-2  N08  0.020
 6XV  plan-2  C15  0.020
 6XV  plan-2  H2   0.020
 6XV  plan-2  H7   0.020
 6XV  plan-2  H8   0.020
 6XV  plan-2  H14  0.020
 6XV  plan-2  N03  0.020
 6XV  plan-3  C02  0.020
 6XV  plan-3  C04  0.020
 6XV  plan-3  C16  0.020
 6XV  plan-3  H6   0.020
 6XV  plan-3  N03  0.020
 6XV  plan-3  O01  0.020
 6XV  plan-4  N10  0.020
 6XV  plan-4  C07  0.020
 6XV  plan-4  N08  0.020
 6XV  plan-4  C09  0.020
 6XV  plan-4  C11  0.020
 6XV  plan-4  C12  0.020
 6XV  plan-4  N13  0.020
 6XV  plan-4  H1   0.020
 6XV  plan-4  H13  0.020
 6XV  plan-5  C19  0.020
 6XV  plan-5  C21  0.020
 6XV  plan-5  N22  0.020
 6XV  plan-5  C23  0.020
 6XV  plan-5  C24  0.020
 6XV  plan-5  N25  0.020
 6XV  plan-5  H16  0.020
 6XV  plan-5  H21  0.020
 6XV  plan-5  N20  0.020

