# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:35:25 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4,4'-[oxybis(ethane-2,1-diyloxy)]dibenzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(OCCOCCOc2ccc(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
 PET  PET  4,4'-[oxybis(ethane-2,1-diyloxy)]dibenzenecarboximidamide  ligand  47  25  .  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_PET
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
 PET  C1    C  CR6   0   0.393  -0.6793   0.2025   3.6871
 PET  C2    C  CR16  0  -0.338   0.0521   1.3294   4.0739
 PET  C3    C  CR16  0  -0.273   0.9236   1.2594   5.1406
 PET  C4    C  CR6   0  -0.017   1.1048   0.0696   5.8494
 PET  C5    C  CR16  0  -0.266   0.3828  -1.0486   5.4467
 PET  C6    C  CR16  0  -0.371  -0.5067  -0.9925   4.3822
 PET  C7    C  C     0   0.327   2.0245   0.0267   7.0166
 PET  CA    C  CH2   0  -0.224  -2.3098  -0.7323   2.2315
 PET  CB    C  CH2   0  -0.160  -3.1957  -0.2783   1.1026
 PET  C1'   C  CR6   0   0.390  -0.6637  -0.1566  -3.6821
 PET  C2'   C  CR16  0  -0.336   0.0239  -1.3154  -4.0562
 PET  C3'   C  CR16  0  -0.257   0.9261  -1.2831  -5.0981
 PET  C4'   C  CR6   0   0.023   1.1697  -0.1053  -5.8089
 PET  C5'   C  CR16  0  -0.277   0.4858   1.0421  -5.4232
 PET  C6'   C  CR16  0  -0.373  -0.4229   1.0285  -4.3721
 PET  C7'   C  C     0   0.334   2.1508  -0.1123  -6.9249
 PET  CA'   C  CH2   0  -0.223  -2.2646   0.8548  -2.2452
 PET  CB'   C  CH2   0  -0.161  -3.1758   0.4474  -1.1187
 PET  N1    N  N     0  -0.645   2.2376   1.0051   7.8126
 PET  N2    N  NH2   0  -0.805   2.6222  -1.1805   7.2376
 PET  N1'   N  N     0  -0.657   3.0458  -1.0252  -6.9510
 PET  N2'   N  NH2   0  -0.825   2.0316   0.9145  -7.8197
 PET  O1    O  O2    0  -0.466  -1.5137   0.3640   2.6481
 PET  O1'   O  O2    0  -0.467  -1.5255  -0.2808  -2.6597
 PET  O2    O  O2    0  -0.484  -2.4079   0.0615  -0.0085
 PET  H2    H  HCR6  0   0.267  -0.0706   2.2569   3.5289
 PET  H3    H  HCR6  0   0.262   1.4863   2.1442   5.4124
 PET  H5    H  HCR6  0   0.265   0.4889  -1.9858   5.9778
 PET  H6    H  HCR6  0   0.285  -1.0561  -1.8854   4.1170
 PET  HA1   H  HCH2  0   0.236  -1.6811  -1.5694   1.9079
 PET  HA2   H  HCH2  0   0.239  -2.9449  -1.0862   3.0505
 PET  HB1   H  HCH2  0   0.218  -3.8831  -1.1027   0.8690
 PET  HB2   H  HCH2  0   0.215  -3.8133   0.5711   1.4261
 PET  H2'   H  HCR6  0   0.264  -0.1606  -2.2392  -3.5221
 PET  H3'   H  HCR6  0   0.256   1.4505  -2.1873  -5.3763
 PET  H5'   H  HCR6  0   0.259   0.6623   1.9852  -5.9247
 PET  H6'   H  HCR6  0   0.283  -0.9240   1.9500  -4.1086
 PET  HA'1  H  HCH2  0   0.238  -2.8771   1.2434  -3.0659
 PET  HA'2  H  HCH2  0   0.235  -1.5938   1.6571  -1.9182
 PET  HB'1  H  HCH2  0   0.215  -3.8405  -0.3651  -1.4436
 PET  HB'2  H  HCH2  0   0.218  -3.8157   1.3084  -0.8820
 PET  HN1   H  H     0   0.330   1.6401   1.7910   7.5837
 PET  HN21  H  HNH2  0   0.382   3.3310  -1.1955   7.9539
 PET  HN22  H  HNH2  0   0.390   2.8349  -1.7563   6.4399
 PET  HN1'  H  H     0   0.321   3.6294  -0.9440  -7.7793
 PET  HN'1  H  HNH2  0   0.390   2.5764   0.8524  -8.6651
 PET  HN'2  H  HNH2  0   0.393   1.1220   1.3217  -7.9619

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
 PET  C1   C2    aromatic  1.398  0.020  1.398
 PET  C1   C6    aromatic  1.393  0.020  1.393
 PET  C1   O1    single    1.342  0.020  1.342
 PET  C2   C3    aromatic  1.379  0.020  1.379
 PET  C2   H2    single    0.930  0.020  1.080
 PET  C3   C4    aromatic  1.397  0.020  1.397
 PET  C3   H3    single    0.930  0.020  1.080
 PET  C4   C5    aromatic  1.391  0.020  1.391
 PET  C4   C7    single    1.487  0.020  1.487
 PET  C5   C6    aromatic  1.388  0.020  1.388
 PET  C5   H5    single    0.930  0.020  1.080
 PET  C6   H6    single    0.930  0.020  1.080
 PET  C7   N1    double    1.279  0.020  1.279
 PET  C7   N2    single    1.365  0.020  1.365
 PET  CA   CB    single    1.505  0.020  1.505
 PET  CA   O1    single    1.417  0.020  1.417
 PET  CA   HA1   single    0.970  0.020  1.090
 PET  CA   HA2   single    0.970  0.020  1.090
 PET  CB   O2    single    1.404  0.020  1.404
 PET  CB   HB1   single    0.970  0.020  1.090
 PET  CB   HB2   single    0.970  0.020  1.090
 PET  C1'  C2'   aromatic  1.398  0.020  1.398
 PET  C1'  C6'   aromatic  1.392  0.020  1.392
 PET  C1'  O1'   single    1.343  0.020  1.343
 PET  C2'  C3'   aromatic  1.379  0.020  1.379
 PET  C2'  H2'   single    0.930  0.020  1.080
 PET  C3'  C4'   aromatic  1.397  0.020  1.397
 PET  C3'  H3'   single    0.930  0.020  1.080
 PET  C4'  C5'   aromatic  1.390  0.020  1.390
 PET  C4'  C7'   single    1.486  0.020  1.486
 PET  C5'  C6'   aromatic  1.389  0.020  1.389
 PET  C5'  H5'   single    0.930  0.020  1.080
 PET  C6'  H6'   single    0.930  0.020  1.080
 PET  C7'  N1'   double    1.279  0.020  1.279
 PET  C7'  N2'   single    1.367  0.020  1.367
 PET  CA'  CB'   single    1.505  0.020  1.505
 PET  CA'  O1'   single    1.417  0.020  1.417
 PET  CA'  HA'1  single    0.970  0.020  1.090
 PET  CA'  HA'2  single    0.970  0.020  1.090
 PET  CB'  O2    single    1.404  0.020  1.404
 PET  CB'  HB'1  single    0.970  0.020  1.090
 PET  CB'  HB'2  single    0.970  0.020  1.090
 PET  N1   HN1   single    0.890  0.020  1.040
 PET  N2   HN21  single    0.890  0.020  1.040
 PET  N2   HN22  single    0.890  0.020  1.040
 PET  N1'  HN1'  single    0.890  0.020  1.040
 PET  N2'  HN'1  single    0.890  0.020  1.040
 PET  N2'  HN'2  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
 PET  O1    C1   C6    124.49  3.000
 PET  O1    C1   C2    116.26  3.000
 PET  C6    C1   C2    119.25  3.000
 PET  H2    C2   C3    120.29  3.000
 PET  H2    C2   C1    119.46  3.000
 PET  C3    C2   C1    120.25  3.000
 PET  H3    C3   C4    120.07  3.000
 PET  H3    C3   C2    118.74  3.000
 PET  C4    C3   C2    121.17  3.000
 PET  C7    C4   C5    121.69  3.000
 PET  C7    C4   C3    120.21  3.000
 PET  C5    C4   C3    118.08  3.000
 PET  H5    C5   C6    118.29  3.000
 PET  H5    C5   C4    120.21  3.000
 PET  C6    C5   C4    121.48  3.000
 PET  H6    C6   C5    118.70  3.000
 PET  H6    C6   C1    121.53  3.000
 PET  C5    C6   C1    119.77  3.000
 PET  N2    C7   N1    120.19  3.000
 PET  N2    C7   C4    115.05  3.000
 PET  N1    C7   C4    124.72  3.000
 PET  HA2   CA   HA1   107.86  3.000
 PET  HA2   CA   O1    110.85  3.000
 PET  HA1   CA   O1    110.81  3.000
 PET  HA2   CA   CB    108.49  3.000
 PET  HA1   CA   CB    110.28  3.000
 PET  O1    CA   CB    108.53  3.000
 PET  HB2   CB   HB1   106.91  3.000
 PET  HB2   CB   O2    111.18  3.000
 PET  HB1   CB   O2    111.38  3.000
 PET  HB2   CB   CA    110.07  3.000
 PET  HB1   CB   CA    107.54  3.000
 PET  O2    CB   CA    109.66  3.000
 PET  O1'   C1'  C6'   124.54  3.000
 PET  O1'   C1'  C2'   116.27  3.000
 PET  C6'   C1'  C2'   119.19  3.000
 PET  H2'   C2'  C3'   120.28  3.000
 PET  H2'   C2'  C1'   119.42  3.000
 PET  C3'   C2'  C1'   120.30  3.000
 PET  H3'   C3'  C4'   119.29  3.000
 PET  H3'   C3'  C2'   119.48  3.000
 PET  C4'   C3'  C2'   121.22  3.000
 PET  C7'   C4'  C5'   122.48  3.000
 PET  C7'   C4'  C3'   119.56  3.000
 PET  C5'   C4'  C3'   117.96  3.000
 PET  H5'   C5'  C6'   117.74  3.000
 PET  H5'   C5'  C4'   120.68  3.000
 PET  C6'   C5'  C4'   121.57  3.000
 PET  H6'   C6'  C5'   118.62  3.000
 PET  H6'   C6'  C1'   121.63  3.000
 PET  C5'   C6'  C1'   119.75  3.000
 PET  N2'   C7'  N1'   125.72  3.000
 PET  N2'   C7'  C4'   115.50  3.000
 PET  N1'   C7'  C4'   118.74  3.000
 PET  HA'2  CA'  HA'1  107.83  3.000
 PET  HA'2  CA'  O1'   110.78  3.000
 PET  HA'1  CA'  O1'   110.91  3.000
 PET  HA'2  CA'  CB'   110.20  3.000
 PET  HA'1  CA'  CB'   108.56  3.000
 PET  O1'   CA'  CB'   108.53  3.000
 PET  HB'2  CB'  HB'1  106.91  3.000
 PET  HB'2  CB'  O2    111.33  3.000
 PET  HB'1  CB'  O2    111.19  3.000
 PET  HB'2  CB'  CA'   107.57  3.000
 PET  HB'1  CB'  CA'   110.18  3.000
 PET  O2    CB'  CA'   109.58  3.000
 PET  HN1   N1   C7    110.76  3.000
 PET  HN22  N2   HN21  113.96  3.000
 PET  HN22  N2   C7    118.04  3.000
 PET  HN21  N2   C7    115.86  3.000
 PET  HN1'  N1'  C7'   111.19  3.000
 PET  HN'2  N2'  HN'1  113.26  3.000
 PET  HN'2  N2'  C7'   118.36  3.000
 PET  HN'1  N2'  C7'   117.11  3.000
 PET  CA    O1   C1    118.92  3.000
 PET  CA'   O1'  C1'   118.90  3.000
 PET  CB'   O2   CB    112.67  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
 PET  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 PET  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 PET  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 PET  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PET  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 PET  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PET  CONST_07  C4'   C3'  C2'  C1'    0.00   0.0  0
 PET  CONST_08  C4'   C5'  C6'  C1'    0.00   0.0  0
 PET  CONST_09  C5'   C6'  C1'  C2'    0.00   0.0  0
 PET  CONST_10  C5'   C4'  C3'  C2'    0.00   0.0  0
 PET  CONST_11  C6'   C1'  C2'  C3'    0.00   0.0  0
 PET  CONST_12  C6'   C5'  C4'  C3'    0.00   0.0  0
 PET  CONST_13  C7    C4   C3   C2   180.00   0.0  0
 PET  CONST_14  O1    C1   C2   C3   180.00   0.0  0
 PET  CONST_15  O1    C1   C6   C5   180.00   0.0  0
 PET  CONST_16  C7    C4   C5   C6   180.00   0.0  0
 PET  CONST_17  C7'   C4'  C3'  C2'  180.00   0.0  0
 PET  CONST_18  O1'   C1'  C2'  C3'  180.00   0.0  0
 PET  CONST_19  O1'   C1'  C6'  C5'  180.00   0.0  0
 PET  CONST_20  C7'   C4'  C5'  C6'  180.00   0.0  0
 PET  CONST_21  H3    C3   C2   C1   180.00   0.0  0
 PET  CONST_22  H5    C5   C6   C1   180.00   0.0  0
 PET  CONST_23  H6    C6   C1   C2   180.00   0.0  0
 PET  CONST_24  H2    C2   C3   C4   180.00   0.0  0
 PET  CONST_25  H3'   C3'  C2'  C1'  180.00   0.0  0
 PET  CONST_26  H5'   C5'  C6'  C1'  180.00   0.0  0
 PET  CONST_27  H6'   C6'  C1'  C2'  180.00   0.0  0
 PET  CONST_28  H2'   C2'  C3'  C4'  180.00   0.0  0
 PET  CONST_29  HN1   N1   C7   C4     0.00   0.0  0
 PET  CONST_30  HN21  N2   C7   C4   180.00   0.0  0
 PET  CONST_32  HN1'  N1'  C7'  C4'  180.00   0.0  0
 PET  CONST_33  HN'1  N2'  C7'  C4'  180.00   0.0  0
 PET  Var_01    N1    C7   C4   C3    32.23  30.0  2
 PET  Var_02    N1'   C7'  C4'  C3'  -22.12  30.0  2
 PET  Var_03    CB    CA   O1   C1   177.38  30.0  2
 PET  Var_04    CB'   CA'  O1'  C1'  178.52  30.0  2
 PET  Var_05    CA'   CB'  O2   CB   177.46  30.0  1
 PET  Var_06    O2    CB   CA   O1    65.05  30.0  3
 PET  Var_07    O2    CB'  CA'  O1'   64.76  30.0  3
 PET  Var_08    HB1   CB   O2   CB'   58.83  30.0  1

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
 PET  plan-1  C1    0.020
 PET  plan-1  C2    0.020
 PET  plan-1  C3    0.020
 PET  plan-1  C4    0.020
 PET  plan-1  C5    0.020
 PET  plan-1  C6    0.020
 PET  plan-1  C7    0.020
 PET  plan-1  O1    0.020
 PET  plan-1  H2    0.020
 PET  plan-1  H3    0.020
 PET  plan-1  H5    0.020
 PET  plan-1  H6    0.020
 PET  plan-2  C1'   0.020
 PET  plan-2  C2'   0.020
 PET  plan-2  C3'   0.020
 PET  plan-2  C4'   0.020
 PET  plan-2  C5'   0.020
 PET  plan-2  C6'   0.020
 PET  plan-2  C7'   0.020
 PET  plan-2  O1'   0.020
 PET  plan-2  H2'   0.020
 PET  plan-2  H3'   0.020
 PET  plan-2  H5'   0.020
 PET  plan-2  H6'   0.020
 PET  plan-3  C4    0.020
 PET  plan-3  C7    0.020
 PET  plan-3  N1    0.020
 PET  plan-3  N2    0.020
 PET  plan-3  HN1   0.020
 PET  plan-3  HN21  0.020
 PET  plan-3  HN22  0.020
 PET  plan-4  C4'   0.020
 PET  plan-4  C7'   0.020
 PET  plan-4  N1'   0.020
 PET  plan-4  N2'   0.020
 PET  plan-4  HN1'  0.020
 PET  plan-4  HN'1  0.020
 PET  plan-4  HN'2  0.020

