# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:02:13 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2E,2'E)-N,N'-[1,4-diazepane-1,4-diyldi(ethane-2,1-diyl)]bis[2-(hydroxyimino)acetamide]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O\N=C\C(=O)NCCN1CCCN(CCNC(=O)\C=N\O)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
 PQY  PQY  (2E,2'E)-N,N'-[1,4-diazepane-1,4-diyldi(ethane-2,1-diyl)]bis[2-(hydroxyimino)acetamide]  ligand  47  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PQY
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
 PQY  N1   N  NT    0  -0.417  -1.4487   1.2831   0.0731
 PQY  N3   N  NH1   0  -0.652  -4.8766  -0.0652   0.5875
 PQY  C4   C  CH2   0  -0.325   0.7754   2.4025   0.4107
 PQY  C5   C  CH2   0  -0.255  -0.6286   2.1186   0.9283
 PQY  C7   C  CH2   0  -0.272   3.4817  -0.1626   0.1419
 PQY  C8   C  CH2   0  -0.301  -2.8269   1.2606   0.5138
 PQY  C10  C  C     0   0.512  -5.8518  -0.7158  -0.0648
 PQY  C13  C  C1    0  -0.180   7.1853  -0.5685   0.5678
 PQY  C1   C  CH2   0  -0.313  -1.2941   1.5204  -1.3522
 PQY  C11  C  C1    0  -0.180  -7.1786  -0.5837   0.6008
 PQY  C12  C  C     0   0.511   5.8633  -0.7650  -0.0918
 PQY  C2   C  CH2   0  -0.412  -0.1532   0.6994  -1.9404
 PQY  C3   C  CH2   0  -0.300   1.2538   1.1275  -1.5547
 PQY  C9   C  CH2   0  -0.264  -3.4894  -0.0716   0.1825
 PQY  N2   N  NT    0  -0.418   1.4755   1.2415  -0.1193
 PQY  N4   N  NH1   0  -0.650   4.8644  -0.1493   0.5593
 PQY  N5   N  N     0  -0.063   8.1963  -1.0988   0.0192
 PQY  N6   N  N     0  -0.063  -8.1506  -1.2237   0.1007
 PQY  O1   O  O     0  -0.489  -5.6889  -1.3488  -1.0964
 PQY  O2   O  O     0  -0.488   5.7264  -1.4147  -1.1167
 PQY  O3   O  OH1   0  -0.530   9.3457  -0.8641   0.6831
 PQY  O4   O  OH1   0  -0.530  -9.3056  -1.0426   0.7721
 PQY  H2   H  HNH1  0   0.405  -5.0971   0.3630   1.4735
 PQY  H3   H  HCH2  0   0.207   0.7479   3.2133  -0.3327
 PQY  H4   H  HCH2  0   0.246   1.3297   2.8045   1.2605
 PQY  H5   H  HCH2  0   0.191  -1.0921   3.1022   1.1147
 PQY  H6   H  HCH2  0   0.220  -0.5524   1.6260   1.9028
 PQY  H7   H  HCH2  0   0.237   3.0183   1.6200   1.2179
 PQY  H8   H  HCH2  0   0.205   3.4759   1.9117  -0.4555
 PQY  H9   H  HCH2  0   0.243   2.8957  -0.8236   0.7863
 PQY  H10  H  HCH2  0   0.249   3.4388  -0.5689  -0.8668
 PQY  H11  H  HCH2  0   0.241  -2.8462   1.3969   1.5990
 PQY  H12  H  HCH2  0   0.209  -3.4201   2.0853   0.0881
 PQY  H13  H  H     0   0.269   7.2530   0.0187   1.4828
 PQY  H15  H  HCH2  0   0.242  -2.2131   1.2093  -1.8534
 PQY  H16  H  HCH2  0   0.210  -1.1767   2.5893  -1.5910
 PQY  H17  H  H     0   0.269  -7.2807   0.0425   1.4862
 PQY  H19  H  HCH2  0   0.217  -0.3089  -0.3428  -1.6498
 PQY  H20  H  HCH2  0   0.221  -0.2164   0.7373  -3.0316
 PQY  H21  H  HCH2  0   0.237   1.9445   0.3907  -1.9683
 PQY  H22  H  HCH2  0   0.195   1.4937   2.0847  -2.0499
 PQY  H23  H  HCH2  0   0.240  -2.9433  -0.8788   0.6795
 PQY  H24  H  HCH2  0   0.247  -3.4461  -0.2682  -0.8884
 PQY  H26  H  HNH1  0   0.405   5.0803   0.3374   1.4155
 PQY  H29  H  HOH1  0   0.485  10.0268  -1.2979   0.1562
 PQY  H30  H  HOH1  0   0.485  -9.9482  -1.5927   0.3096
 PQY  C6   C  CH2   0  -0.292   2.8925   1.2442   0.1993

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
 PQY  O3   N5   single  1.348  0.020  1.348
 PQY  N5   C13  double  1.267  0.020  1.267
 PQY  C13  C12  single  1.491  0.020  1.491
 PQY  C12  N4   single  1.342  0.020  1.342
 PQY  C12  O2   double  1.221  0.020  1.221
 PQY  N4   C7   single  1.444  0.020  1.444
 PQY  C7   C6   single  1.526  0.020  1.526
 PQY  C6   N2   single  1.452  0.020  1.452
 PQY  N2   C3   single  1.457  0.020  1.457
 PQY  N2   C4   single  1.456  0.020  1.456
 PQY  C3   C2   single  1.520  0.020  1.520
 PQY  C2   C1   single  1.524  0.020  1.524
 PQY  C4   C5   single  1.523  0.020  1.523
 PQY  C5   N1   single  1.450  0.020  1.450
 PQY  C1   N1   single  1.453  0.020  1.453
 PQY  N1   C8   single  1.447  0.020  1.447
 PQY  C8   C9   single  1.524  0.020  1.524
 PQY  C9   N3   single  1.445  0.020  1.445
 PQY  O1   C10  double  1.221  0.020  1.221
 PQY  N3   C10  single  1.342  0.020  1.342
 PQY  C10  C11  single  1.490  0.020  1.490
 PQY  C11  N6   double  1.267  0.020  1.267
 PQY  N6   O4   single  1.348  0.020  1.348
 PQY  N3   H2   single  0.860  0.020  1.020
 PQY  C4   H3   single  0.970  0.020  1.090
 PQY  C4   H4   single  0.970  0.020  1.090
 PQY  C5   H5   single  0.970  0.020  1.090
 PQY  C5   H6   single  0.970  0.020  1.090
 PQY  C6   H7   single  0.970  0.020  1.090
 PQY  C6   H8   single  0.970  0.020  1.090
 PQY  C7   H9   single  0.970  0.020  1.090
 PQY  C7   H10  single  0.970  0.020  1.090
 PQY  C8   H11  single  0.970  0.020  1.090
 PQY  C8   H12  single  0.970  0.020  1.090
 PQY  C13  H13  single  0.930  0.020  1.080
 PQY  C1   H15  single  0.970  0.020  1.090
 PQY  C1   H16  single  0.970  0.020  1.090
 PQY  C11  H17  single  0.930  0.020  1.080
 PQY  C2   H19  single  0.970  0.020  1.090
 PQY  C2   H20  single  0.970  0.020  1.090
 PQY  C3   H21  single  0.970  0.020  1.090
 PQY  C3   H22  single  0.970  0.020  1.090
 PQY  C9   H23  single  0.970  0.020  1.090
 PQY  C9   H24  single  0.970  0.020  1.090
 PQY  N4   H26  single  0.860  0.020  1.020
 PQY  O3   H29  single  0.850  0.020  0.980
 PQY  O4   H30  single  0.850  0.020  0.980

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
 PQY  C1   N1   C8   113.73  3.000
 PQY  C8   N1   C5   111.60  3.000
 PQY  C1   N1   C5   115.10  3.000
 PQY  H2   N3   C9   117.26  3.000
 PQY  H2   N3   C10  118.30  3.000
 PQY  C9   N3   C10  124.01  3.000
 PQY  H4   C4   H3   105.51  3.000
 PQY  H4   C4   N2   109.45  3.000
 PQY  H3   C4   N2   110.72  3.000
 PQY  H4   C4   C5   105.80  3.000
 PQY  H3   C4   C5   110.12  3.000
 PQY  N2   C4   C5   114.73  3.000
 PQY  H6   C5   H5   106.26  3.000
 PQY  H6   C5   C4   108.81  3.000
 PQY  H5   C5   C4   106.17  3.000
 PQY  H6   C5   N1   107.76  3.000
 PQY  H5   C5   N1   112.07  3.000
 PQY  C4   C5   N1   115.37  3.000
 PQY  H10  C7   H9   107.42  3.000
 PQY  H10  C7   N4   108.00  3.000
 PQY  H9   C7   N4   110.38  3.000
 PQY  H10  C7   C6   111.34  3.000
 PQY  H9   C7   C6   109.15  3.000
 PQY  N4   C7   C6   110.50  3.000
 PQY  H12  C8   H11  106.30  3.000
 PQY  H12  C8   C9   109.65  3.000
 PQY  H11  C8   C9   108.47  3.000
 PQY  H12  C8   N1   112.56  3.000
 PQY  H11  C8   N1   108.48  3.000
 PQY  C9   C8   N1   111.18  3.000
 PQY  O1   C10  C11  122.82  3.000
 PQY  C11  C10  N3   112.77  3.000
 PQY  O1   C10  N3   124.41  3.000
 PQY  H13  C13  N5   122.68  3.000
 PQY  H13  C13  C12  119.86  3.000
 PQY  N5   C13  C12  117.46  3.000
 PQY  H16  C1   H15  105.46  3.000
 PQY  H16  C1   C2   111.06  3.000
 PQY  H15  C1   C2   107.42  3.000
 PQY  H16  C1   N1   112.49  3.000
 PQY  H15  C1   N1   108.31  3.000
 PQY  C2   C1   N1   111.73  3.000
 PQY  H17  C11  N6   122.65  3.000
 PQY  H17  C11  C10  119.83  3.000
 PQY  N6   C11  C10  117.52  3.000
 PQY  O2   C12  N4   124.60  3.000
 PQY  O2   C12  C13  122.75  3.000
 PQY  N4   C12  C13  112.64  3.000
 PQY  H20  C2   H19  106.86  3.000
 PQY  H20  C2   C3   107.26  3.000
 PQY  H19  C2   C3   109.44  3.000
 PQY  H20  C2   C1   108.86  3.000
 PQY  H19  C2   C1   107.73  3.000
 PQY  C3   C2   C1   116.31  3.000
 PQY  H22  C3   H21  106.14  3.000
 PQY  H22  C3   N2   109.94  3.000
 PQY  H21  C3   N2   109.26  3.000
 PQY  H22  C3   C2   109.35  3.000
 PQY  H21  C3   C2   107.42  3.000
 PQY  N2   C3   C2   114.38  3.000
 PQY  H24  C9   H23  107.07  3.000
 PQY  H24  C9   C8   110.73  3.000
 PQY  H23  C9   C8   109.22  3.000
 PQY  H24  C9   N3   108.33  3.000
 PQY  H23  C9   N3   110.80  3.000
 PQY  C8   C9   N3   110.63  3.000
 PQY  C3   N2   C6   111.39  3.000
 PQY  C3   N2   C4   110.36  3.000
 PQY  C6   N2   C4   112.82  3.000
 PQY  H26  N4   C12  118.30  3.000
 PQY  H26  N4   C7   117.05  3.000
 PQY  C12  N4   C7   124.62  3.000
 PQY  O3   N5   C13  113.22  3.000
 PQY  O4   N6   C11  113.13  3.000
 PQY  H29  O3   N5   104.76  3.000
 PQY  H30  O4   N6   104.80  3.000
 PQY  H8   C6   H7   106.54  3.000
 PQY  H8   C6   N2   112.78  3.000
 PQY  H7   C6   N2   108.50  3.000
 PQY  H8   C6   C7   109.36  3.000
 PQY  H7   C6   C7   107.91  3.000
 PQY  N2   C6   C7   111.51  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
 PQY  CONST_01  C13  C12  N4   C7    180.00   0.0  0
 PQY  CONST_02  O2   C12  N4   C7      0.00   0.0  0
 PQY  CONST_03  C9   N3   C10  C11   180.00   0.0  0
 PQY  CONST_04  O1   C10  N3   C9      0.00   0.0  0
 PQY  CONST_05  H26  N4   C12  C13     0.00   0.0  0
 PQY  CONST_06  H2   N3   C10  C11     0.00   0.0  0
 PQY  Var_01    N3   C9   C8   N1   -178.11  30.0  3
 PQY  Var_02    N4   C7   C6   N2   -175.69  30.0  1
 PQY  Var_03    N6   C11  C10  N3   -176.23  30.0  2
 PQY  Var_04    C12  N4   C7   C6   -133.39  30.0  2
 PQY  Var_05    C10  N3   C9   C8    146.70  30.0  3
 PQY  Var_06    N5   C13  C12  N4   -179.19  30.0  1
 PQY  Var_07    H13  C13  N5   O3      0.18   0.0  2
 PQY  Var_08    H17  C11  N6   O4      0.21   0.0  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
 PQY  plan-1  N3   0.020
 PQY  plan-1  C10  0.020
 PQY  plan-1  C11  0.020
 PQY  plan-1  C9   0.020
 PQY  plan-1  O1   0.020
 PQY  plan-1  H2   0.020
 PQY  plan-2  C7   0.020
 PQY  plan-2  C13  0.020
 PQY  plan-2  C12  0.020
 PQY  plan-2  N4   0.020
 PQY  plan-2  O2   0.020
 PQY  plan-2  H26  0.020
 PQY  plan-3  C13  0.020
 PQY  plan-3  C12  0.020
 PQY  plan-3  N5   0.020
 PQY  plan-3  O3   0.020
 PQY  plan-3  H13  0.020
 PQY  plan-4  C10  0.020
 PQY  plan-4  C11  0.020
 PQY  plan-4  N6   0.020
 PQY  plan-4  O4   0.020
 PQY  plan-4  H17  0.020

