# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:42:23 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 4,4'-[heptane-1,7-diylbis(oxy)]dibenzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(OCCCCCCCOc2ccc(cc2)C(N)=N)cc1
#
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
 AZ3  AZ3  4,4'-[heptane-1,7-diylbis(oxy)]dibenzenecarboximidamide  ligand  55  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AZ3
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
 AZ3  N2   N  NH2   0  -0.824   11.1479  -0.0020   0.3808
 AZ3  C7   C  C     0   0.329   10.2153   0.8319  -0.1715
 AZ3  N1   N  N     0  -0.656   10.4586   1.9427  -0.7562
 AZ3  C3   C  CR6   0   0.021    8.8141   0.3425  -0.1151
 AZ3  C2   C  CR16  0  -0.274    8.5043  -1.0127   0.0207
 AZ3  C1   C  CR16  0  -0.337    7.1930  -1.4455   0.0577
 AZ3  C4   C  CR16  0  -0.261    7.7610   1.2447  -0.2176
 AZ3  C5   C  CR16  0  -0.371    6.4392   0.8284  -0.1728
 AZ3  C6   C  CR6   0   0.387    6.1441  -0.5279  -0.0346
 AZ3  O1   O  O2    0  -0.473    4.9029  -1.0359   0.0175
 AZ3  C8   C  CH2   0  -0.172    3.7852  -0.1609  -0.0503
 AZ3  C9   C  CH2   0  -0.456    2.5283  -1.0018   0.0180
 AZ3  C10  C  CH2   0  -0.427    1.2697  -0.1426  -0.0145
 AZ3  C11  C  CH2   0  -0.414   -0.0022  -0.9803   0.0218
 AZ3  C12  C  CH2   0  -0.427   -1.2736  -0.1410   0.0208
 AZ3  C13  C  CH2   0  -0.456   -2.5325  -1.0003   0.0279
 AZ3  C14  C  CH2   0  -0.172   -3.7892  -0.1564   0.0544
 AZ3  O2   O  O2    0  -0.473   -4.9066  -1.0341   0.0375
 AZ3  C15  C  CR6   0   0.387   -6.1482  -0.5252   0.0646
 AZ3  C16  C  CR16  0  -0.371   -6.4448   0.8365   0.1249
 AZ3  C17  C  CR16  0  -0.261   -7.7669   1.2531   0.1507
 AZ3  C20  C  CR16  0  -0.336   -7.1960  -1.4476   0.0305
 AZ3  C19  C  CR16  0  -0.275   -8.5077  -1.0150   0.0484
 AZ3  C18  C  CR6   0   0.022   -8.8194   0.3452   0.1054
 AZ3  C21  C  C     0   0.331  -10.2213   0.8357   0.1388
 AZ3  N3   N  N     0  -0.656  -10.4613   1.9859   0.6428
 AZ3  N4   N  NH2   0  -0.825  -11.1578  -0.0381  -0.3410
 AZ3  H1   H  HNH2  0   0.393   10.8634  -0.5932   1.1446
 AZ3  H2   H  HNH2  0   0.389   12.0819   0.3615   0.4856
 AZ3  H3   H  H     0   0.321   11.4447   2.1808  -0.6928
 AZ3  H4   H  HCR6  0   0.258    9.2905  -1.7544   0.0784
 AZ3  H5   H  HCR6  0   0.264    6.9717  -2.5011   0.1540
 AZ3  H6   H  HCR6  0   0.257    7.9761   2.2993  -0.3267
 AZ3  H7   H  HCR6  0   0.281    5.6578   1.5720  -0.2438
 AZ3  H8   H  HCH2  0   0.222    3.8122   0.5540   0.7805
 AZ3  H9   H  HCH2  0   0.222    3.8062   0.4142  -0.9831
 AZ3  H10  H  HCH2  0   0.230    2.5151  -1.7041  -0.8207
 AZ3  H11  H  HCH2  0   0.230    2.5386  -1.5988   0.9349
 AZ3  H12  H  HCH2  0   0.219    1.2754   0.5489   0.8347
 AZ3  H13  H  HCH2  0   0.218    1.2693   0.4792  -0.9162
 AZ3  H14  H  HCH2  0   0.215   -0.0136  -1.6578  -0.8388
 AZ3  H15  H  HCH2  0   0.215    0.0087  -1.6186   0.9119
 AZ3  H16  H  HCH2  0   0.218   -1.2726   0.5200   0.8940
 AZ3  H17  H  HCH2  0   0.218   -1.2792   0.5122  -0.8583
 AZ3  H18  H  HCH2  0   0.230   -2.5425  -1.6413  -0.8587
 AZ3  H19  H  HCH2  0   0.230   -2.5205  -1.6610   0.9000
 AZ3  H20  H  HCH2  0   0.222   -3.8069   0.4676   0.9553
 AZ3  H21  H  HCH2  0   0.222   -3.8179   0.5127  -0.8135
 AZ3  H22  H  HCR6  0   0.281   -5.6642   1.5841   0.1505
 AZ3  H23  H  HCR6  0   0.257   -7.9829   2.3120   0.1993
 AZ3  H24  H  HCR6  0   0.264   -6.9738  -2.5069  -0.0050
 AZ3  H25  H  HCR6  0   0.258   -9.2925  -1.7602   0.0388
 AZ3  H26  H  H     0   0.321  -11.4489   2.2169   0.5751
 AZ3  H27  H  HNH2  0   0.393  -10.8794  -0.6870  -1.0587
 AZ3  H28  H  HNH2  0   0.389  -12.0928   0.3164  -0.4661

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
 AZ3  C13  C14  single    1.514  0.020  1.514
 AZ3  C13  C12  single    1.524  0.020  1.524
 AZ3  C14  O2   single    1.421  0.020  1.421
 AZ3  N1   C7   double    1.279  0.020  1.279
 AZ3  C11  C12  single    1.523  0.020  1.523
 AZ3  C11  C10  single    1.523  0.020  1.523
 AZ3  C9   C10  single    1.524  0.020  1.524
 AZ3  C9   C8   single    1.514  0.020  1.514
 AZ3  C2   C1   aromatic  1.381  0.020  1.381
 AZ3  C2   C3   aromatic  1.397  0.020  1.397
 AZ3  C1   C6   aromatic  1.397  0.020  1.397
 AZ3  O2   C15  single    1.342  0.020  1.342
 AZ3  C7   C3   single    1.485  0.020  1.485
 AZ3  C7   N2   single    1.368  0.020  1.368
 AZ3  C16  C15  aromatic  1.395  0.020  1.395
 AZ3  C16  C17  aromatic  1.386  0.020  1.386
 AZ3  C3   C4   aromatic  1.390  0.020  1.390
 AZ3  C15  C20  aromatic  1.396  0.020  1.396
 AZ3  C8   O1   single    1.421  0.020  1.421
 AZ3  C17  C18  aromatic  1.391  0.020  1.391
 AZ3  C6   O1   single    1.342  0.020  1.342
 AZ3  C6   C5   aromatic  1.395  0.020  1.395
 AZ3  C20  C19  aromatic  1.381  0.020  1.381
 AZ3  C4   C5   aromatic  1.387  0.020  1.387
 AZ3  C18  C19  aromatic  1.397  0.020  1.397
 AZ3  C18  C21  single    1.486  0.020  1.486
 AZ3  C21  N3   double    1.279  0.020  1.279
 AZ3  C21  N4   single    1.368  0.020  1.368
 AZ3  N2   H1   single    0.890  0.020  1.040
 AZ3  N2   H2   single    0.890  0.020  1.040
 AZ3  N1   H3   single    0.890  0.020  1.040
 AZ3  C2   H4   single    0.930  0.020  1.080
 AZ3  C1   H5   single    0.930  0.020  1.080
 AZ3  C4   H6   single    0.930  0.020  1.080
 AZ3  C5   H7   single    0.930  0.020  1.080
 AZ3  C8   H8   single    0.970  0.020  1.090
 AZ3  C8   H9   single    0.970  0.020  1.090
 AZ3  C9   H10  single    0.970  0.020  1.090
 AZ3  C9   H11  single    0.970  0.020  1.090
 AZ3  C10  H12  single    0.970  0.020  1.090
 AZ3  C10  H13  single    0.970  0.020  1.090
 AZ3  C11  H14  single    0.970  0.020  1.090
 AZ3  C11  H15  single    0.970  0.020  1.090
 AZ3  C12  H16  single    0.970  0.020  1.090
 AZ3  C12  H17  single    0.970  0.020  1.090
 AZ3  C13  H18  single    0.970  0.020  1.090
 AZ3  C13  H19  single    0.970  0.020  1.090
 AZ3  C14  H20  single    0.970  0.020  1.090
 AZ3  C14  H21  single    0.970  0.020  1.090
 AZ3  C16  H22  single    0.930  0.020  1.080
 AZ3  C17  H23  single    0.930  0.020  1.080
 AZ3  C20  H24  single    0.930  0.020  1.080
 AZ3  C19  H25  single    0.930  0.020  1.080
 AZ3  N3   H26  single    0.890  0.020  1.040
 AZ3  N4   H27  single    0.890  0.020  1.040
 AZ3  N4   H28  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
 AZ3  H2   N2   H1   113.26  3.000
 AZ3  H2   N2   C7   117.00  3.000
 AZ3  H1   N2   C7   118.15  3.000
 AZ3  C3   C7   N1   118.89  3.000
 AZ3  C3   C7   N2   115.28  3.000
 AZ3  N1   C7   N2   125.78  3.000
 AZ3  H3   N1   C7   111.07  3.000
 AZ3  C4   C3   C2   117.95  3.000
 AZ3  C4   C3   C7   119.86  3.000
 AZ3  C2   C3   C7   122.19  3.000
 AZ3  H4   C2   C1   118.25  3.000
 AZ3  H4   C2   C3   120.59  3.000
 AZ3  C1   C2   C3   121.14  3.000
 AZ3  H5   C1   C6   119.53  3.000
 AZ3  H5   C1   C2   120.12  3.000
 AZ3  C6   C1   C2   120.35  3.000
 AZ3  H6   C4   C5   119.04  3.000
 AZ3  H6   C4   C3   119.30  3.000
 AZ3  C5   C4   C3   121.66  3.000
 AZ3  H7   C5   C6   121.50  3.000
 AZ3  H7   C5   C4   118.71  3.000
 AZ3  C6   C5   C4   119.79  3.000
 AZ3  O1   C6   C5   124.57  3.000
 AZ3  C5   C6   C1   119.11  3.000
 AZ3  O1   C6   C1   116.32  3.000
 AZ3  C8   O1   C6   119.50  3.000
 AZ3  H9   C8   H8   107.60  3.000
 AZ3  H9   C8   C9   110.23  3.000
 AZ3  H8   C8   C9   110.39  3.000
 AZ3  H9   C8   O1   110.40  3.000
 AZ3  H8   C8   O1   110.24  3.000
 AZ3  C9   C8   O1   107.99  3.000
 AZ3  H11  C9   H10  107.00  3.000
 AZ3  H11  C9   C10  109.46  3.000
 AZ3  H10  C9   C10  109.61  3.000
 AZ3  H11  C9   C8   109.46  3.000
 AZ3  H10  C9   C8   109.39  3.000
 AZ3  C10  C9   C8   111.80  3.000
 AZ3  H13  C10  H12  106.26  3.000
 AZ3  H13  C10  C11  109.36  3.000
 AZ3  H12  C10  C11  109.46  3.000
 AZ3  H13  C10  C9   109.75  3.000
 AZ3  H12  C10  C9   109.58  3.000
 AZ3  C11  C10  C9   112.26  3.000
 AZ3  H15  C11  H14  106.14  3.000
 AZ3  H15  C11  C12  109.26  3.000
 AZ3  H14  C11  C12  109.36  3.000
 AZ3  H15  C11  C10  109.36  3.000
 AZ3  H14  C11  C10  109.28  3.000
 AZ3  C12  C11  C10  113.19  3.000
 AZ3  H17  C12  H16  106.26  3.000
 AZ3  H17  C12  C13  109.62  3.000
 AZ3  H16  C12  C13  109.71  3.000
 AZ3  H17  C12  C11  109.47  3.000
 AZ3  H16  C12  C11  109.35  3.000
 AZ3  C13  C12  C11  112.26  3.000
 AZ3  H19  C13  H18  106.99  3.000
 AZ3  H19  C13  C14  109.38  3.000
 AZ3  H18  C13  C14  109.46  3.000
 AZ3  H19  C13  C12  109.58  3.000
 AZ3  H18  C13  C12  109.51  3.000
 AZ3  C14  C13  C12  111.80  3.000
 AZ3  H21  C14  H20  107.63  3.000
 AZ3  H21  C14  O2   110.30  3.000
 AZ3  H20  C14  O2   110.41  3.000
 AZ3  H21  C14  C13  110.37  3.000
 AZ3  H20  C14  C13  110.19  3.000
 AZ3  O2   C14  C13  107.95  3.000
 AZ3  C15  O2   C14  119.53  3.000
 AZ3  C20  C15  C16  119.10  3.000
 AZ3  C20  C15  O2   116.30  3.000
 AZ3  C16  C15  O2   124.59  3.000
 AZ3  H22  C16  C17  118.71  3.000
 AZ3  H22  C16  C15  121.50  3.000
 AZ3  C17  C16  C15  119.79  3.000
 AZ3  H23  C17  C18  119.30  3.000
 AZ3  H23  C17  C16  119.03  3.000
 AZ3  C18  C17  C16  121.67  3.000
 AZ3  H24  C20  C19  120.11  3.000
 AZ3  H24  C20  C15  119.54  3.000
 AZ3  C19  C20  C15  120.35  3.000
 AZ3  H25  C19  C18  120.60  3.000
 AZ3  H25  C19  C20  118.22  3.000
 AZ3  C18  C19  C20  121.17  3.000
 AZ3  C21  C18  C19  122.21  3.000
 AZ3  C21  C18  C17  119.86  3.000
 AZ3  C19  C18  C17  117.92  3.000
 AZ3  N4   C21  N3   125.76  3.000
 AZ3  N4   C21  C18  115.30  3.000
 AZ3  N3   C21  C18  118.88  3.000
 AZ3  H26  N3   C21  111.13  3.000
 AZ3  H28  N4   H27  113.25  3.000
 AZ3  H28  N4   C21  117.01  3.000
 AZ3  H27  N4   C21  118.20  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
 AZ3  CONST_01  C6   C1   C2   C3     0.00   0.0  0
 AZ3  CONST_02  C6   C5   C4   C3     0.00   0.0  0
 AZ3  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 AZ3  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 AZ3  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 AZ3  CONST_06  C4   C5   C6   C1     0.00   0.0  0
 AZ3  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 AZ3  CONST_08  C18  C19  C20  C15    0.00   0.0  0
 AZ3  CONST_09  C19  C20  C15  C16    0.00   0.0  0
 AZ3  CONST_10  C19  C18  C17  C16    0.00   0.0  0
 AZ3  CONST_11  C20  C15  C16  C17    0.00   0.0  0
 AZ3  CONST_12  C20  C19  C18  C17    0.00   0.0  0
 AZ3  CONST_13  C1   C2   C3   C7   180.00   0.0  0
 AZ3  CONST_14  C5   C4   C3   C7   180.00   0.0  0
 AZ3  CONST_15  O1   C6   C1   C2   180.00   0.0  0
 AZ3  CONST_16  O1   C6   C5   C4   180.00   0.0  0
 AZ3  CONST_17  C17  C16  C15  O2   180.00   0.0  0
 AZ3  CONST_18  C19  C20  C15  O2   180.00   0.0  0
 AZ3  CONST_19  C21  C18  C17  C16  180.00   0.0  0
 AZ3  CONST_20  C21  C18  C19  C20  180.00   0.0  0
 AZ3  CONST_21  H5   C1   C2   C3   180.00   0.0  0
 AZ3  CONST_22  H7   C5   C4   C3   180.00   0.0  0
 AZ3  CONST_23  H6   C4   C3   C2   180.00   0.0  0
 AZ3  CONST_24  H4   C2   C3   C4   180.00   0.0  0
 AZ3  CONST_25  H23  C17  C16  C15  180.00   0.0  0
 AZ3  CONST_26  H25  C19  C20  C15  180.00   0.0  0
 AZ3  CONST_27  H24  C20  C15  C16  180.00   0.0  0
 AZ3  CONST_28  H22  C16  C15  C20  180.00   0.0  0
 AZ3  CONST_29  H3   N1   C7   C3   180.00   0.0  0
 AZ3  CONST_31  H2   N2   C7   C3   180.00   0.0  0
 AZ3  CONST_32  H26  N3   C21  C18  180.00   0.0  0
 AZ3  CONST_34  H28  N4   C21  C18  180.00   0.0  0
 AZ3  Var_01    C2   C3   C7   N2   -22.48  30.0  2
 AZ3  Var_02    C16  C15  O2   C14   -0.77  30.0  2
 AZ3  Var_03    N3   C21  C18  C17  -23.08  30.0  2
 AZ3  Var_04    C9   C8   O1   C6   179.50  30.0  1
 AZ3  Var_05    H20  C14  O2   C15   59.06  30.0  2
 AZ3  Var_06    C10  C9   C8   O1   178.63  30.0  1
 AZ3  Var_07    C11  C10  C9   C8   178.70  30.0  3
 AZ3  Var_08    C12  C11  C10  C9   178.74  30.0  1
 AZ3  Var_09    C13  C12  C11  C10  178.81  30.0  3
 AZ3  Var_10    C14  C13  C12  C11  178.88  30.0  1
 AZ3  Var_11    O2   C14  C13  C12  179.07  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
 AZ3  plan-1  C7   0.020
 AZ3  plan-1  C3   0.020
 AZ3  plan-1  C2   0.020
 AZ3  plan-1  C1   0.020
 AZ3  plan-1  C4   0.020
 AZ3  plan-1  C5   0.020
 AZ3  plan-1  C6   0.020
 AZ3  plan-1  O1   0.020
 AZ3  plan-1  H4   0.020
 AZ3  plan-1  H5   0.020
 AZ3  plan-1  H6   0.020
 AZ3  plan-1  H7   0.020
 AZ3  plan-2  O2   0.020
 AZ3  plan-2  C15  0.020
 AZ3  plan-2  C16  0.020
 AZ3  plan-2  C17  0.020
 AZ3  plan-2  C20  0.020
 AZ3  plan-2  C19  0.020
 AZ3  plan-2  C18  0.020
 AZ3  plan-2  C21  0.020
 AZ3  plan-2  H22  0.020
 AZ3  plan-2  H23  0.020
 AZ3  plan-2  H24  0.020
 AZ3  plan-2  H25  0.020
 AZ3  plan-3  N2   0.020
 AZ3  plan-3  C7   0.020
 AZ3  plan-3  N1   0.020
 AZ3  plan-3  C3   0.020
 AZ3  plan-3  H1   0.020
 AZ3  plan-3  H2   0.020
 AZ3  plan-3  H3   0.020
 AZ3  plan-4  C18  0.020
 AZ3  plan-4  C21  0.020
 AZ3  plan-4  N3   0.020
 AZ3  plan-4  N4   0.020
 AZ3  plan-4  H26  0.020
 AZ3  plan-4  H27  0.020
 AZ3  plan-4  H28  0.020

