# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 04:30:00 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2,2'-[benzene-1,4-diylbis(oxy)]bis(3,5-dichloropyridine)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(Oc2ccc(Oc3ncc(Cl)cc3Cl)cc2)c(Cl)c1
#
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
 TCD  TCD  2,2'-[benzene-1,4-diylbis(oxy)]bis(3,5-dichloropyridine)  ligand  32  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TCD
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
 TCD  C1    C   CR6   0   0.358   1.6879  -0.0226   1.3605
 TCD  O21   O   O2    0  -0.505   1.7525  -0.0115   2.7387
 TCD  C2    C   CR16  0  -0.305   1.7041  -1.2338   0.6910
 TCD  C3    C   CR16  0  -0.305   1.7009  -1.2441  -0.6959
 TCD  C4    C   CR6   0   0.357   1.6821  -0.0429  -1.3831
 TCD  O31   O   O2    0  -0.504   1.7416  -0.0552  -2.7618
 TCD  C5    C   CR16  0  -0.305   1.6689   1.1688  -0.7132
 TCD  C6    C   CR16  0  -0.308   1.6714   1.1792   0.6731
 TCD  C22   C   CR6   0   0.587   0.6057  -0.0042   3.4332
 TCD  N23   N   N     0  -0.437  -0.5441  -0.0302   2.8096
 TCD  C24   C   CR16  0  -0.023  -1.6735  -0.0234   3.5088
 TCD  C25   C   CR6   0  -0.142  -1.6730   0.0105   4.8891
 TCD  CL25  CL  CL    0  -0.105  -3.1596   0.0201   5.7614
 TCD  C26   C   CR16  0  -0.041  -0.4608   0.0376   5.5689
 TCD  C27   C   CR6   0  -0.198   0.7001   0.0301   4.8291
 TCD  CL27  CL  CL    0  -0.081   2.2371   0.0635   5.5944
 TCD  C32   C   CR6   0   0.589   0.5942  -0.0289  -3.4526
 TCD  N33   N   N     0  -0.434  -0.5545  -0.0114  -2.8266
 TCD  C34   C   CR16  0  -0.006  -1.6839   0.0124  -3.5233
 TCD  C35   C   CR6   0  -0.137  -1.6901   0.0185  -4.9038
 TCD  CL35  CL  CL    0  -0.101  -3.1767   0.0486  -5.7723
 TCD  C36   C   CR16  0  -0.019  -0.4784  -0.0001  -5.5842
 TCD  C37   C   CR6   0  -0.195   0.6855  -0.0240  -4.8497
 TCD  CL37  CL  CL    0  -0.078   2.2199  -0.0478  -5.6185
 TCD  H2    H   HCR6  0   0.282   1.7243  -2.1647   1.2427
 TCD  H3    H   HCR6  0   0.282   1.7179  -2.1828  -1.2342
 TCD  H5    H   HCR6  0   0.283   1.6613   2.0999  -1.2649
 TCD  H6    H   HCR6  0   0.290   1.6665   2.1184   1.2108
 TCD  H24   H   HCR6  0   0.307  -2.6001  -0.0464   2.9490
 TCD  H26   H   HCR6  0   0.325  -0.4245   0.0663   6.6494
 TCD  H34   H   HCR6  0   0.280  -2.6090   0.0268  -2.9610
 TCD  H36   H   HCR6  0   0.289  -0.4450   0.0042  -6.6644

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
 TCD  C1   O21   single    1.380  0.020  1.380
 TCD  C1   C2    aromatic  1.384  0.020  1.384
 TCD  C1   C6    aromatic  1.385  0.020  1.385
 TCD  O21  C22   single    1.341  0.020  1.341
 TCD  C2   C3    aromatic  1.387  0.020  1.387
 TCD  C2   H2    single    0.930  0.020  1.080
 TCD  C3   C4    aromatic  1.384  0.020  1.384
 TCD  C3   H3    single    0.930  0.020  1.080
 TCD  C4   O31   single    1.380  0.020  1.380
 TCD  C4   C5    aromatic  1.385  0.020  1.385
 TCD  O31  C32   single    1.340  0.020  1.340
 TCD  C5   C6    aromatic  1.386  0.020  1.386
 TCD  C5   H5    single    0.930  0.020  1.080
 TCD  C6   H6    single    0.930  0.020  1.080
 TCD  C22  N23   aromatic  1.308  0.020  1.308
 TCD  C22  C27   aromatic  1.400  0.020  1.400
 TCD  N23  C24   aromatic  1.328  0.020  1.328
 TCD  C24  C25   aromatic  1.381  0.020  1.381
 TCD  C24  H24   single    0.930  0.020  1.080
 TCD  C25  CL25  single    1.724  0.020  1.724
 TCD  C25  C26   aromatic  1.390  0.020  1.390
 TCD  C26  C27   aromatic  1.377  0.020  1.377
 TCD  C26  H26   single    0.930  0.020  1.080
 TCD  C27  CL27  single    1.717  0.020  1.717
 TCD  C32  N33   aromatic  1.308  0.020  1.308
 TCD  C32  C37   aromatic  1.400  0.020  1.400
 TCD  N33  C34   aromatic  1.327  0.020  1.327
 TCD  C34  C35   aromatic  1.380  0.020  1.380
 TCD  C34  H34   single    0.930  0.020  1.080
 TCD  C35  CL35  single    1.722  0.020  1.722
 TCD  C35  C36   aromatic  1.390  0.020  1.390
 TCD  C36  C37   aromatic  1.377  0.020  1.377
 TCD  C36  H36   single    0.930  0.020  1.080
 TCD  C37  CL37  single    1.716  0.020  1.716

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
 TCD  C6    C1   C2    121.31  3.000
 TCD  C6    C1   O21   119.30  3.000
 TCD  C2    C1   O21   119.32  3.000
 TCD  C22   O21  C1    118.52  3.000
 TCD  H2    C2   C3    120.23  3.000
 TCD  H2    C2   C1    120.42  3.000
 TCD  C3    C2   C1    119.35  3.000
 TCD  H3    C3   C4    120.41  3.000
 TCD  H3    C3   C2    120.24  3.000
 TCD  C4    C3   C2    119.35  3.000
 TCD  C5    C4   O31   119.44  3.000
 TCD  C5    C4   C3    121.30  3.000
 TCD  O31   C4   C3    119.19  3.000
 TCD  C32   O31  C4    118.56  3.000
 TCD  H5    C5   C6    120.21  3.000
 TCD  H5    C5   C4    120.42  3.000
 TCD  C6    C5   C4    119.36  3.000
 TCD  H6    C6   C5    120.22  3.000
 TCD  H6    C6   C1    120.44  3.000
 TCD  C5    C6   C1    119.34  3.000
 TCD  C27   C22  N23   122.35  3.000
 TCD  C27   C22  O21   117.33  3.000
 TCD  N23   C22  O21   120.32  3.000
 TCD  C24   N23  C22   119.76  3.000
 TCD  H24   C24  C25   121.17  3.000
 TCD  H24   C24  N23   117.09  3.000
 TCD  C25   C24  N23   121.74  3.000
 TCD  C26   C25  CL25  120.30  3.000
 TCD  C26   C25  C24   119.32  3.000
 TCD  CL25  C25  C24   120.38  3.000
 TCD  H26   C26  C27   120.58  3.000
 TCD  H26   C26  C25   121.23  3.000
 TCD  C27   C26  C25   118.20  3.000
 TCD  CL27  C27  C26   121.01  3.000
 TCD  CL27  C27  C22   120.35  3.000
 TCD  C26   C27  C22   118.64  3.000
 TCD  C37   C32  N33   122.32  3.000
 TCD  C37   C32  O31   117.31  3.000
 TCD  N33   C32  O31   120.37  3.000
 TCD  C34   N33  C32   119.75  3.000
 TCD  H34   C34  C35   121.03  3.000
 TCD  H34   C34  N33   117.05  3.000
 TCD  C35   C34  N33   121.93  3.000
 TCD  C36   C35  CL35  120.39  3.000
 TCD  C36   C35  C34   119.05  3.000
 TCD  CL35  C35  C34   120.55  3.000
 TCD  H36   C36  C37   120.49  3.000
 TCD  H36   C36  C35   121.08  3.000
 TCD  C37   C36  C35   118.43  3.000
 TCD  CL37  C37  C36   121.14  3.000
 TCD  CL37  C37  C32   120.35  3.000
 TCD  C36   C37  C32   118.52  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
 TCD  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 TCD  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 TCD  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 TCD  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 TCD  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 TCD  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 TCD  CONST_07  C25   C24  N23  C22     0.00   0.0  0
 TCD  CONST_08  C25   C26  C27  C22     0.00   0.0  0
 TCD  CONST_09  C26   C27  C22  N23     0.00   0.0  0
 TCD  CONST_10  C26   C25  C24  N23     0.00   0.0  0
 TCD  CONST_11  C27   C22  N23  C24     0.00   0.0  0
 TCD  CONST_12  C27   C26  C25  C24     0.00   0.0  0
 TCD  CONST_13  C35   C34  N33  C32     0.00   0.0  0
 TCD  CONST_14  C35   C36  C37  C32     0.00   0.0  0
 TCD  CONST_15  C36   C37  C32  N33     0.00   0.0  0
 TCD  CONST_16  C36   C35  C34  N33     0.00   0.0  0
 TCD  CONST_17  C37   C32  N33  C34     0.00   0.0  0
 TCD  CONST_18  C37   C36  C35  C34     0.00   0.0  0
 TCD  CONST_19  C3    C2   C1   O21   180.00   0.0  0
 TCD  CONST_20  C5    C6   C1   O21   180.00   0.0  0
 TCD  CONST_21  C24   N23  C22  O21   180.00   0.0  0
 TCD  CONST_22  C26   C27  C22  O21   180.00   0.0  0
 TCD  CONST_23  O31   C4   C3   C2    180.00   0.0  0
 TCD  CONST_24  C6    C5   C4   O31   180.00   0.0  0
 TCD  CONST_25  C34   N33  C32  O31   180.00   0.0  0
 TCD  CONST_26  C36   C37  C32  O31   180.00   0.0  0
 TCD  CONST_27  CL27  C27  C22  N23   180.00   0.0  0
 TCD  CONST_28  CL25  C25  C24  N23   180.00   0.0  0
 TCD  CONST_29  CL27  C27  C26  C25   180.00   0.0  0
 TCD  CONST_30  C27   C26  C25  CL25  180.00   0.0  0
 TCD  CONST_31  CL37  C37  C32  N33   180.00   0.0  0
 TCD  CONST_32  CL35  C35  C34  N33   180.00   0.0  0
 TCD  CONST_33  CL37  C37  C36  C35   180.00   0.0  0
 TCD  CONST_34  C37   C36  C35  CL35  180.00   0.0  0
 TCD  CONST_35  H3    C3   C2   C1    180.00   0.0  0
 TCD  CONST_36  H5    C5   C6   C1    180.00   0.0  0
 TCD  CONST_37  H6    C6   C1   C2    180.00   0.0  0
 TCD  CONST_38  H2    C2   C3   C4    180.00   0.0  0
 TCD  CONST_39  H24   C24  N23  C22   180.00   0.0  0
 TCD  CONST_40  H26   C26  C27  C22   180.00   0.0  0
 TCD  CONST_41  H34   C34  N33  C32   180.00   0.0  0
 TCD  CONST_42  H36   C36  C37  C32   180.00   0.0  0
 TCD  Var_01    N23   C22  O21  C1      1.15  30.0  2
 TCD  Var_02    N33   C32  O31  C4     -0.96  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
 TCD  plan-1  C1    0.020
 TCD  plan-1  O21   0.020
 TCD  plan-1  C2    0.020
 TCD  plan-1  C3    0.020
 TCD  plan-1  C4    0.020
 TCD  plan-1  O31   0.020
 TCD  plan-1  C5    0.020
 TCD  plan-1  C6    0.020
 TCD  plan-1  H2    0.020
 TCD  plan-1  H3    0.020
 TCD  plan-1  H5    0.020
 TCD  plan-1  H6    0.020
 TCD  plan-2  O21   0.020
 TCD  plan-2  C22   0.020
 TCD  plan-2  N23   0.020
 TCD  plan-2  C24   0.020
 TCD  plan-2  C25   0.020
 TCD  plan-2  CL25  0.020
 TCD  plan-2  C26   0.020
 TCD  plan-2  C27   0.020
 TCD  plan-2  CL27  0.020
 TCD  plan-2  H24   0.020
 TCD  plan-2  H26   0.020
 TCD  plan-3  O31   0.020
 TCD  plan-3  C32   0.020
 TCD  plan-3  N33   0.020
 TCD  plan-3  C34   0.020
 TCD  plan-3  C35   0.020
 TCD  plan-3  CL35  0.020
 TCD  plan-3  C36   0.020
 TCD  plan-3  C37   0.020
 TCD  plan-3  CL37  0.020
 TCD  plan-3  H34   0.020
 TCD  plan-3  H36   0.020

