# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 03:40:57 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O\N=C\c1cc[n+](C[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
 3VI  3VI  "1,1'-methylenebis{4-[(E)-(hydroxyimino)methyl]pyridin-1-ium}"  ligand  33  19  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3VI
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
 3VI  CAC  C  C1    0  -0.063  94.3967  50.0388  -11.3874
 3VI  CAE  C  CR16  0  -0.373  92.2072  49.8744  -10.1875
 3VI  CAF  C  CR16  0  -0.397  93.3594  51.9722  -10.2727
 3VI  CAG  C  CR16  0  -0.397  90.6029  51.1766   -4.8550
 3VI  CAH  C  CR16  0  -0.374  91.5542  53.3688   -5.0109
 3VI  CAI  C  CR16  0   0.106  91.2223  50.4795   -9.4604
 3VI  CAJ  C  CR16  0   0.118  92.3455  52.5321   -9.5425
 3VI  CAK  C  CR16  0   0.117  90.2732  51.2505   -6.1816
 3VI  CAL  C  CR16  0   0.107  91.2020  53.3947   -6.3302
 3VI  CAM  C  CH2   0  -0.278  90.2461  52.3929   -8.3267
 3VI  CAP  C  CR6   0   0.207  93.3146  50.6180  -10.6103
 3VI  CAQ  C  CR6   0   0.208  91.2613  52.2411   -4.2360
 3VI  NAN  N  N     0  -0.059  94.3250  48.8052  -11.6929
 3VI  NAO  N  N     0  -0.059  92.2055  53.1277   -2.2862
 3VI  NAR  N  NR6   1  -0.433  91.3012  51.7872   -9.1373
 3VI  NAS  N  NR6   1  -0.434  90.5792  52.3441   -6.9037
 3VI  OAA  O  OH1   0  -0.497  95.3625  48.3704  -12.4071
 3VI  OAB  O  OH1   0  -0.497  92.4753  52.9429   -0.9945
 3VI  H1   H  H     0   0.279  95.2266  50.6784  -11.6813
 3VI  H2   H  H     0   0.279  91.3353  51.2399   -2.2880
 3VI  H3   H  HCR6  0   0.319  92.1042  48.8267  -10.4279
 3VI  H4   H  HCR6  0   0.323  94.1818  52.6008  -10.5840
 3VI  H5   H  HCR6  0   0.324  90.3376  50.2849   -4.3045
 3VI  H6   H  HCR6  0   0.320  92.0487  54.2314   -4.5895
 3VI  H7   H  HCR6  0   0.370  90.3452  49.9432   -9.1280
 3VI  H8   H  HCR6  0   0.370  92.3424  53.5807   -9.2807
 3VI  H9   H  HCR6  0   0.371  89.7536  50.4477   -6.6852
 3VI  H10  H  HCR6  0   0.370  91.3959  54.2539   -6.9566
 3VI  H11  H  HCH2  0   0.374  90.1122  53.4288   -8.6252
 3VI  H12  H  HCH2  0   0.374  89.3146  51.8598   -8.4971
 3VI  H13  H  HOH1  0   0.493  95.1850  47.4347  -12.5700
 3VI  H14  H  HOH1  0   0.493  92.9288  53.7480   -0.7121
 3VI  CAD  C  C1    0  -0.063  91.6043  52.1453   -2.8280

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
 3VI  OAA  NAN  single    1.332  0.020  1.332
 3VI  NAN  CAC  double    1.273  0.020  1.273
 3VI  CAC  CAP  single    1.453  0.020  1.453
 3VI  CAP  CAE  aromatic  1.399  0.020  1.399
 3VI  CAP  CAF  aromatic  1.396  0.020  1.396
 3VI  CAE  CAI  aromatic  1.366  0.020  1.366
 3VI  CAF  CAJ  aromatic  1.369  0.020  1.369
 3VI  CAI  NAR  aromatic  1.349  0.020  1.349
 3VI  CAJ  NAR  aromatic  1.345  0.020  1.345
 3VI  NAR  CAM  single    1.462  0.020  1.462
 3VI  CAM  NAS  single    1.462  0.020  1.462
 3VI  NAS  CAK  aromatic  1.346  0.020  1.346
 3VI  NAS  CAL  aromatic  1.349  0.020  1.349
 3VI  CAK  CAG  aromatic  1.369  0.020  1.369
 3VI  CAL  CAH  aromatic  1.366  0.020  1.366
 3VI  CAG  CAQ  aromatic  1.396  0.020  1.396
 3VI  CAH  CAQ  aromatic  1.399  0.020  1.399
 3VI  CAQ  CAD  single    1.452  0.020  1.452
 3VI  CAD  NAO  double    1.273  0.020  1.273
 3VI  NAO  OAB  single    1.332  0.020  1.332
 3VI  CAC  H1   single    0.930  0.020  1.080
 3VI  CAD  H2   single    0.930  0.020  1.080
 3VI  CAE  H3   single    0.930  0.020  1.080
 3VI  CAF  H4   single    0.930  0.020  1.080
 3VI  CAG  H5   single    0.930  0.020  1.080
 3VI  CAH  H6   single    0.930  0.020  1.080
 3VI  CAI  H7   single    0.930  0.020  1.080
 3VI  CAJ  H8   single    0.930  0.020  1.080
 3VI  CAK  H9   single    0.930  0.020  1.080
 3VI  CAL  H10  single    0.930  0.020  1.080
 3VI  CAM  H11  single    0.970  0.020  1.090
 3VI  CAM  H12  single    0.970  0.020  1.090
 3VI  OAA  H13  single    0.850  0.020  0.980
 3VI  OAB  H14  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
 3VI  H1   CAC  NAN  123.21  3.000
 3VI  H1   CAC  CAP  118.57  3.000
 3VI  NAN  CAC  CAP  118.22  3.000
 3VI  H3   CAE  CAP  121.59  3.000
 3VI  H3   CAE  CAI  118.66  3.000
 3VI  CAP  CAE  CAI  119.75  3.000
 3VI  H4   CAF  CAP  121.25  3.000
 3VI  H4   CAF  CAJ  118.64  3.000
 3VI  CAP  CAF  CAJ  120.11  3.000
 3VI  H5   CAG  CAQ  121.26  3.000
 3VI  H5   CAG  CAK  118.62  3.000
 3VI  CAQ  CAG  CAK  120.13  3.000
 3VI  H6   CAH  CAQ  121.57  3.000
 3VI  H6   CAH  CAL  118.68  3.000
 3VI  CAQ  CAH  CAL  119.75  3.000
 3VI  H7   CAI  NAR  117.06  3.000
 3VI  H7   CAI  CAE  121.96  3.000
 3VI  NAR  CAI  CAE  120.98  3.000
 3VI  H8   CAJ  NAR  117.53  3.000
 3VI  H8   CAJ  CAF  121.87  3.000
 3VI  NAR  CAJ  CAF  120.60  3.000
 3VI  H9   CAK  NAS  117.58  3.000
 3VI  H9   CAK  CAG  121.82  3.000
 3VI  NAS  CAK  CAG  120.60  3.000
 3VI  H10  CAL  NAS  117.10  3.000
 3VI  H10  CAL  CAH  121.91  3.000
 3VI  NAS  CAL  CAH  120.99  3.000
 3VI  H12  CAM  H11  108.60  3.000
 3VI  H12  CAM  NAS  109.36  3.000
 3VI  H11  CAM  NAS  109.10  3.000
 3VI  H12  CAM  NAR  109.17  3.000
 3VI  H11  CAM  NAR  109.38  3.000
 3VI  NAS  CAM  NAR  111.18  3.000
 3VI  CAF  CAP  CAE  117.89  3.000
 3VI  CAF  CAP  CAC  119.47  3.000
 3VI  CAE  CAP  CAC  122.64  3.000
 3VI  CAH  CAQ  CAG  117.89  3.000
 3VI  CAH  CAQ  CAD  122.72  3.000
 3VI  CAG  CAQ  CAD  119.39  3.000
 3VI  OAA  NAN  CAC  113.64  3.000
 3VI  OAB  NAO  CAD  113.66  3.000
 3VI  CAM  NAR  CAJ  119.86  3.000
 3VI  CAM  NAR  CAI  119.48  3.000
 3VI  CAJ  NAR  CAI  120.66  3.000
 3VI  CAM  NAS  CAL  119.52  3.000
 3VI  CAL  NAS  CAK  120.64  3.000
 3VI  CAM  NAS  CAK  119.83  3.000
 3VI  H13  OAA  NAN  105.27  3.000
 3VI  H14  OAB  NAO  105.24  3.000
 3VI  H2   CAD  NAO  123.22  3.000
 3VI  H2   CAD  CAQ  118.53  3.000
 3VI  NAO  CAD  CAQ  118.25  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
 3VI  CONST_01  CAJ  CAF  CAP  CAE     0.00   0.0  0
 3VI  CONST_02  CAJ  NAR  CAI  CAE     0.00   0.0  0
 3VI  CONST_03  CAI  CAE  CAP  CAF     0.00   0.0  0
 3VI  CONST_04  CAI  NAR  CAJ  CAF     0.00   0.0  0
 3VI  CONST_05  CAL  NAS  CAK  CAG     0.00   0.0  0
 3VI  CONST_06  CAL  CAH  CAQ  CAG     0.00   0.0  0
 3VI  CONST_07  CAK  NAS  CAL  CAH     0.00   0.0  0
 3VI  CONST_08  CAK  CAG  CAQ  CAH     0.00   0.0  0
 3VI  CONST_09  NAR  CAI  CAE  CAP     0.00   0.0  0
 3VI  CONST_10  NAR  CAJ  CAF  CAP     0.00   0.0  0
 3VI  CONST_11  NAS  CAK  CAG  CAQ     0.00   0.0  0
 3VI  CONST_12  NAS  CAL  CAH  CAQ     0.00   0.0  0
 3VI  CONST_13  CAI  CAE  CAP  CAC   180.00   0.0  0
 3VI  CONST_14  CAJ  CAF  CAP  CAC   180.00   0.0  0
 3VI  CONST_15  CAK  CAG  CAQ  CAD   180.00   0.0  0
 3VI  CONST_16  CAL  CAH  CAQ  CAD   180.00   0.0  0
 3VI  CONST_17  CAM  NAR  CAI  CAE   180.00   0.0  0
 3VI  CONST_18  CAM  NAR  CAJ  CAF   180.00   0.0  0
 3VI  CONST_19  CAM  NAS  CAK  CAG   180.00   0.0  0
 3VI  CONST_20  CAM  NAS  CAL  CAH   180.00   0.0  0
 3VI  CONST_21  H4   CAF  CAP  CAE   180.00   0.0  0
 3VI  CONST_22  H3   CAE  CAP  CAF   180.00   0.0  0
 3VI  CONST_23  H6   CAH  CAQ  CAG   180.00   0.0  0
 3VI  CONST_24  H5   CAG  CAQ  CAH   180.00   0.0  0
 3VI  CONST_25  H8   CAJ  NAR  CAI   180.00   0.0  0
 3VI  CONST_26  H7   CAI  NAR  CAJ   180.00   0.0  0
 3VI  CONST_27  H10  CAL  NAS  CAK   180.00   0.0  0
 3VI  CONST_28  H9   CAK  NAS  CAL   180.00   0.0  0
 3VI  CONST_29  H7   CAI  CAE  CAP   180.00   0.0  0
 3VI  CONST_30  H8   CAJ  CAF  CAP   180.00   0.0  0
 3VI  CONST_31  H9   CAK  CAG  CAQ   180.00   0.0  0
 3VI  CONST_32  H10  CAL  CAH  CAQ   180.00   0.0  0
 3VI  CONST_33  H3   CAE  CAI  NAR   180.00   0.0  0
 3VI  CONST_34  H4   CAF  CAJ  NAR   180.00   0.0  0
 3VI  CONST_35  H5   CAG  CAK  NAS   180.00   0.0  0
 3VI  CONST_36  H6   CAH  CAL  NAS   180.00   0.0  0
 3VI  Var_01    NAS  CAM  NAR  CAI    92.56  30.0  2
 3VI  Var_02    NAS  CAM  NAR  CAJ   -86.80  30.0  2
 3VI  Var_03    NAR  CAM  NAS  CAK   -86.11  30.0  3
 3VI  Var_04    NAR  CAM  NAS  CAL    93.33  30.0  3
 3VI  Var_05    NAN  CAC  CAP  CAE     0.11  30.0  2
 3VI  Var_06    NAN  CAC  CAP  CAF  -179.32  30.0  2
 3VI  Var_07    NAO  CAD  CAQ  CAG   179.92  30.0  2
 3VI  Var_08    NAO  CAD  CAQ  CAH    -0.57  30.0  2
 3VI  Var_09    H1   CAC  CAP  CAE   180.00  30.0  2
 3VI  Var_10    H1   CAC  CAP  CAF     0.57  30.0  2
 3VI  Var_11    H2   CAD  CAQ  CAG    -0.11  30.0  2
 3VI  Var_12    H2   CAD  CAQ  CAH   179.40  30.0  2
 3VI  Var_13    H11  CAM  NAR  CAI  -146.89  30.0  2
 3VI  Var_14    H12  CAM  NAR  CAI   -28.18  30.0  2
 3VI  Var_15    H11  CAM  NAR  CAJ    33.75  30.0  2
 3VI  Var_16    H12  CAM  NAR  CAJ   152.46  30.0  2
 3VI  Var_17    H11  CAM  NAS  CAK   153.18  30.0  3
 3VI  Var_18    H12  CAM  NAS  CAK    34.52  30.0  3
 3VI  Var_19    H11  CAM  NAS  CAL   -27.39  30.0  3
 3VI  Var_20    H12  CAM  NAS  CAL  -146.04  30.0  3
 3VI  Var_21    OAA  NAN  CAC  CAP   179.88   0.0  2
 3VI  Var_22    OAB  NAO  CAD  CAQ   179.99   0.0  2
 3VI  Var_23    H1   CAC  NAN  OAA     0.00   0.0  2
 3VI  Var_24    H2   CAD  NAO  OAB     0.02   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
 3VI  plan-1  CAC  0.020
 3VI  plan-1  CAE  0.020
 3VI  plan-1  CAF  0.020
 3VI  plan-1  CAI  0.020
 3VI  plan-1  CAJ  0.020
 3VI  plan-1  CAM  0.020
 3VI  plan-1  CAP  0.020
 3VI  plan-1  NAR  0.020
 3VI  plan-1  H3   0.020
 3VI  plan-1  H4   0.020
 3VI  plan-1  H7   0.020
 3VI  plan-1  H8   0.020
 3VI  plan-2  CAG  0.020
 3VI  plan-2  CAH  0.020
 3VI  plan-2  CAK  0.020
 3VI  plan-2  CAL  0.020
 3VI  plan-2  CAM  0.020
 3VI  plan-2  CAQ  0.020
 3VI  plan-2  NAS  0.020
 3VI  plan-2  H5   0.020
 3VI  plan-2  H6   0.020
 3VI  plan-2  H9   0.020
 3VI  plan-2  H10  0.020
 3VI  plan-2  CAD  0.020
 3VI  plan-3  CAC  0.020
 3VI  plan-3  CAP  0.020
 3VI  plan-3  NAN  0.020
 3VI  plan-3  OAA  0.020
 3VI  plan-3  H1   0.020
 3VI  plan-4  CAQ  0.020
 3VI  plan-4  NAO  0.020
 3VI  plan-4  OAB  0.020
 3VI  plan-4  H2   0.020
 3VI  plan-4  CAD  0.020

