# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:15:07 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1,1'-propane-1,3-diylbis{4-[(E)-(hydroxyimino)methyl]pyridinium}
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O\N=C\c1cc[n+](CCC[n+]2ccc(cc2)\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
 PSP  PSP  1,1'-propane-1,3-diylbis{4-[(E)-(hydroxyimino)methyl]pyridinium}  ligand  39  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PSP
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
 PSP  C1    C  CH2   0  -0.356   1.2407   2.0901  -0.1034
 PSP  C5A   C  CR6   0   0.200   4.6757  -0.3573  -0.2983
 PSP  O10   O  OH1   0  -0.509   7.5716  -2.2663   0.4123
 PSP  N9    N  N     0  -0.069   6.5128  -1.4805   0.6379
 PSP  C8    C  C1    0  -0.066   5.8507  -1.2084  -0.4128
 PSP  C4    C  CR16  0  -0.376   4.2315   0.1616   0.9208
 PSP  C3    C  CR16  0   0.099   3.1215   0.9624   0.9516
 PSP  N2    N  NR6   1  -0.422   2.4524   1.2626  -0.1736
 PSP  C7    C  CR16  0   0.105   2.8496   0.7750  -1.3563
 PSP  C6    C  CR16  0  -0.399   3.9549  -0.0327  -1.4471
 PSP  C2    C  CH2   0  -0.453   0.0010   1.2144  -0.0043
 PSP  C5    C  CH2   0  -0.356  -1.2347   2.0956   0.0963
 PSP  N8    N  NR6   1  -0.422  -2.4493   1.2736   0.1771
 PSP  C9    C  CR16  0   0.099  -3.1356   0.9830  -0.9401
 PSP  C10   C  CR16  0  -0.376  -4.2478   0.1858  -0.8979
 PSP  C11   C  CR6   0   0.200  -4.6755  -0.3401   0.3242
 PSP  C12   C  CR16  0  -0.399  -3.9366  -0.0255   1.4645
 PSP  C13   C  CR16  0   0.105  -2.8310   0.7795   1.3621
 PSP  C14   C  C1    0  -0.066  -5.8508  -1.1894   0.4498
 PSP  N15   N  N     0  -0.069  -6.5294  -1.4513  -0.5929
 PSP  O16   O  OH1   0  -0.509  -7.5862  -2.2372  -0.3580
 PSP  H1A   H  HCH2  0   0.314   1.3369   2.7437   0.7618
 PSP  H2A   H  HCH2  0   0.316   1.2170   2.7181  -0.9925
 PSP  H10A  H  HOH1  0   0.492   7.9827  -2.3894   1.2765
 PSP  H8    H  H     0   0.273   6.1237  -1.5803  -1.3983
 PSP  H4A   H  HCR6  0   0.312   4.7440  -0.0509   1.8470
 PSP  H3A   H  HCR6  0   0.354   2.7446   1.3875   1.8697
 PSP  H7A   H  HCR6  0   0.355   2.2663   1.0537  -2.2213
 PSP  H6A   H  HCR6  0   0.316   4.2500  -0.4014  -2.4189
 PSP  H3    H  HCH2  0   0.286  -0.0734   0.5702  -0.8838
 PSP  H4    H  HCH2  0   0.286   0.0721   0.5689   0.8744
 PSP  H6    H  HCH2  0   0.316  -1.2037   2.7278   0.9824
 PSP  H7    H  HCH2  0   0.314  -1.3322   2.7453  -0.7715
 PSP  H9    H  HCR6  0   0.354  -2.7694   1.4111  -1.8612
 PSP  H10   H  HCR6  0   0.312  -4.7746  -0.0194  -1.8177
 PSP  H12   H  HCR6  0   0.316  -4.2181  -0.4001   2.4381
 PSP  H13   H  HCR6  0   0.355  -2.2336   1.0499   2.2204
 PSP  H14   H  H     0   0.273  -6.1095  -1.5690   1.4362
 PSP  H16   H  HOH1  0   0.492  -8.0109  -2.3517  -1.2168

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
 PSP  C1   N2    single    1.469  0.020  1.469
 PSP  C1   C2    single    1.521  0.020  1.521
 PSP  C1   H1A   single    0.970  0.020  1.090
 PSP  C1   H2A   single    0.970  0.020  1.090
 PSP  C5A  C8    single    1.455  0.020  1.455
 PSP  C5A  C4    aromatic  1.398  0.020  1.398
 PSP  C5A  C6    aromatic  1.394  0.020  1.394
 PSP  O10  N9    single    1.338  0.020  1.338
 PSP  O10  H10A  single    0.850  0.020  0.980
 PSP  N9   C8    double    1.271  0.020  1.271
 PSP  C8   H8    single    0.930  0.020  1.080
 PSP  C4   C3    aromatic  1.369  0.020  1.369
 PSP  C4   H4A   single    0.930  0.020  1.080
 PSP  C3   N2    aromatic  1.343  0.020  1.343
 PSP  C3   H3A   single    0.930  0.020  1.080
 PSP  N2   C7    aromatic  1.339  0.020  1.339
 PSP  C7   C6    aromatic  1.372  0.020  1.372
 PSP  C7   H7A   single    0.930  0.020  1.080
 PSP  C6   H6A   single    0.930  0.020  1.080
 PSP  C2   C5    single    1.521  0.020  1.521
 PSP  C2   H3    single    0.970  0.020  1.090
 PSP  C2   H4    single    0.970  0.020  1.090
 PSP  C5   N8    single    1.469  0.020  1.469
 PSP  C5   H6    single    0.970  0.020  1.090
 PSP  C5   H7    single    0.970  0.020  1.090
 PSP  N8   C9    aromatic  1.343  0.020  1.343
 PSP  N8   C13   aromatic  1.339  0.020  1.339
 PSP  C9   C10   aromatic  1.369  0.020  1.369
 PSP  C9   H9    single    0.930  0.020  1.080
 PSP  C10  C11   aromatic  1.397  0.020  1.397
 PSP  C10  H10   single    0.930  0.020  1.080
 PSP  C11  C12   aromatic  1.395  0.020  1.395
 PSP  C11  C14   single    1.455  0.020  1.455
 PSP  C12  C13   aromatic  1.371  0.020  1.371
 PSP  C12  H12   single    0.930  0.020  1.080
 PSP  C13  H13   single    0.930  0.020  1.080
 PSP  C14  N15   double    1.271  0.020  1.271
 PSP  C14  H14   single    0.930  0.020  1.080
 PSP  N15  O16   single    1.338  0.020  1.338
 PSP  O16  H16   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
 PSP  H2A   C1   H1A  107.74  3.000
 PSP  H2A   C1   C2   111.56  3.000
 PSP  H1A   C1   C2   111.46  3.000
 PSP  H2A   C1   N2   107.69  3.000
 PSP  H1A   C1   N2   107.66  3.000
 PSP  C2    C1   N2   110.55  3.000
 PSP  C6    C5A  C4   117.90  3.000
 PSP  C6    C5A  C8   119.25  3.000
 PSP  C4    C5A  C8   122.84  3.000
 PSP  H10A  O10  N9   105.14  3.000
 PSP  C8    N9   O10  113.49  3.000
 PSP  H8    C8   N9   123.00  3.000
 PSP  H8    C8   C5A  118.27  3.000
 PSP  N9    C8   C5A  118.73  3.000
 PSP  H4A   C4   C3   118.73  3.000
 PSP  H4A   C4   C5A  121.63  3.000
 PSP  C3    C4   C5A  119.64  3.000
 PSP  H3A   C3   N2   116.77  3.000
 PSP  H3A   C3   C4   122.17  3.000
 PSP  N2    C3   C4   121.05  3.000
 PSP  C7    N2   C3   120.70  3.000
 PSP  C7    N2   C1   119.47  3.000
 PSP  C3    N2   C1   119.79  3.000
 PSP  H7A   C7   C6   122.28  3.000
 PSP  H7A   C7   N2   116.94  3.000
 PSP  C6    C7   N2   120.78  3.000
 PSP  H6A   C6   C7   118.72  3.000
 PSP  H6A   C6   C5A  121.35  3.000
 PSP  C7    C6   C5A  119.93  3.000
 PSP  H4    C2   H3   107.66  3.000
 PSP  H4    C2   C5   110.00  3.000
 PSP  H3    C2   C5   109.85  3.000
 PSP  H4    C2   C1   109.84  3.000
 PSP  H3    C2   C1   110.03  3.000
 PSP  C5    C2   C1   109.44  3.000
 PSP  H7    C5   H6   107.75  3.000
 PSP  H7    C5   N8   107.69  3.000
 PSP  H6    C5   N8   107.68  3.000
 PSP  H7    C5   C2   111.46  3.000
 PSP  H6    C5   C2   111.53  3.000
 PSP  N8    C5   C2   110.56  3.000
 PSP  C13   N8   C9   120.70  3.000
 PSP  C13   N8   C5   119.39  3.000
 PSP  C9    N8   C5   119.86  3.000
 PSP  H9    C9   C10  122.19  3.000
 PSP  H9    C9   N8   116.78  3.000
 PSP  C10   C9   N8   121.03  3.000
 PSP  H10   C10  C11  121.62  3.000
 PSP  H10   C10  C9   118.73  3.000
 PSP  C11   C10  C9   119.65  3.000
 PSP  C14   C11  C12  119.27  3.000
 PSP  C14   C11  C10  122.83  3.000
 PSP  C12   C11  C10  117.90  3.000
 PSP  H12   C12  C13  118.74  3.000
 PSP  H12   C12  C11  121.37  3.000
 PSP  C13   C12  C11  119.90  3.000
 PSP  H13   C13  C12  122.25  3.000
 PSP  H13   C13  N8   116.93  3.000
 PSP  C12   C13  N8   120.82  3.000
 PSP  H14   C14  N15  123.01  3.000
 PSP  H14   C14  C11  118.28  3.000
 PSP  N15   C14  C11  118.72  3.000
 PSP  O16   N15  C14  113.49  3.000
 PSP  H16   O16  N15  105.13  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
 PSP  CONST_01  N2   C3   C4   C5A    0.00   0.0  0
 PSP  CONST_02  N2   C7   C6   C5A    0.00   0.0  0
 PSP  CONST_03  C7   C6   C5A  C4     0.00   0.0  0
 PSP  CONST_04  C7   N2   C3   C4     0.00   0.0  0
 PSP  CONST_05  C6   C5A  C4   C3     0.00   0.0  0
 PSP  CONST_06  C6   C7   N2   C3     0.00   0.0  0
 PSP  CONST_07  C11  C10  C9   N8     0.00   0.0  0
 PSP  CONST_08  C11  C12  C13  N8     0.00   0.0  0
 PSP  CONST_09  C12  C13  N8   C9     0.00   0.0  0
 PSP  CONST_10  C12  C11  C10  C9     0.00   0.0  0
 PSP  CONST_11  C13  N8   C9   C10    0.00   0.0  0
 PSP  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 PSP  CONST_13  C4   C3   N2   C1   180.00   0.0  0
 PSP  CONST_14  C6   C7   N2   C1   180.00   0.0  0
 PSP  CONST_15  C3   C4   C5A  C8   180.00   0.0  0
 PSP  CONST_16  C7   C6   C5A  C8   180.00   0.0  0
 PSP  CONST_17  C10  C9   N8   C5   180.00   0.0  0
 PSP  CONST_18  C12  C13  N8   C5   180.00   0.0  0
 PSP  CONST_19  C14  C11  C10  C9   180.00   0.0  0
 PSP  CONST_20  C14  C11  C12  C13  180.00   0.0  0
 PSP  CONST_21  H3A  C3   C4   C5A  180.00   0.0  0
 PSP  CONST_22  H7A  C7   C6   C5A  180.00   0.0  0
 PSP  CONST_23  H6A  C6   C5A  C4   180.00   0.0  0
 PSP  CONST_24  H4A  C4   C3   N2   180.00   0.0  0
 PSP  CONST_25  H10  C10  C9   N8   180.00   0.0  0
 PSP  CONST_26  H12  C12  C13  N8   180.00   0.0  0
 PSP  CONST_27  H13  C13  N8   C9   180.00   0.0  0
 PSP  CONST_28  H9   C9   C10  C11  180.00   0.0  0
 PSP  Var_01    C4   C5A  C8   N9    -0.85  30.0  3
 PSP  Var_02    C2   C1   N2   C3   -93.41  30.0  2
 PSP  Var_03    C9   N8   C5   C2   -94.23  30.0  2
 PSP  Var_04    N15  C14  C11  C10   -0.95  30.0  2
 PSP  Var_05    N8   C5   C2   C1   179.32  30.0  3
 PSP  Var_06    C5   C2   C1   N2   178.82  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
 PSP  plan-1  C1   0.020
 PSP  plan-1  C5A  0.020
 PSP  plan-1  C8   0.020
 PSP  plan-1  C4   0.020
 PSP  plan-1  C3   0.020
 PSP  plan-1  N2   0.020
 PSP  plan-1  C7   0.020
 PSP  plan-1  C6   0.020
 PSP  plan-1  H4A  0.020
 PSP  plan-1  H3A  0.020
 PSP  plan-1  H7A  0.020
 PSP  plan-1  H6A  0.020
 PSP  plan-2  C5   0.020
 PSP  plan-2  N8   0.020
 PSP  plan-2  C9   0.020
 PSP  plan-2  C10  0.020
 PSP  plan-2  C11  0.020
 PSP  plan-2  C12  0.020
 PSP  plan-2  C13  0.020
 PSP  plan-2  C14  0.020
 PSP  plan-2  H9   0.020
 PSP  plan-2  H10  0.020
 PSP  plan-2  H12  0.020
 PSP  plan-2  H13  0.020
 PSP  plan-3  C5A  0.020
 PSP  plan-3  O10  0.020
 PSP  plan-3  N9   0.020
 PSP  plan-3  C8   0.020
 PSP  plan-3  H8   0.020
 PSP  plan-4  C11  0.020
 PSP  plan-4  C14  0.020
 PSP  plan-4  N15  0.020
 PSP  plan-4  O16  0.020
 PSP  plan-4  H14  0.020

