# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:36:14 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-[[2,2-bis(fluoranyl)-1,3-benzodioxol-5-yl]methyl]-~{N}-methyl-2-oxidanylidene-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C1=CC=CN(Cc2ccc3OC(F)(F)Oc3c2)C1=O
#
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
 GZT  GZT  1-[[2,2-bis(fluoranyl)-1,3-benzodioxol-5-yl]methyl]-~{N}-methyl-2-oxidanylidene-pyridine-3-carboxamide  ligand  35  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GZT
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
 GZT  CAA  C  CH3   0  -0.515   5.1223   2.5379  -0.9976
 GZT  NAB  N  NH1   0  -0.659   4.2277   1.5257  -0.4943
 GZT  CAC  C  C     0   0.557   4.2878   0.2575  -0.9081
 GZT  OAK  O  O     0  -0.507   5.1041  -0.1248  -1.7429
 GZT  CAD  C  CR6   0  -0.308   3.3082  -0.7047  -0.3112
 GZT  CAE  C  CR6   0   0.618   2.3380  -0.3128   0.6846
 GZT  OAF  O  O     0  -0.503   2.1967   0.8189   1.1499
 GZT  CAG  C  CR16  0  -0.122   3.3567  -2.0039  -0.7419
 GZT  CAH  C  CR16  0  -0.392   2.4864  -2.9813  -0.2383
 GZT  CAI  C  CR16  0   0.065   1.5806  -2.6041   0.7015
 GZT  NAJ  N  NR6   0  -0.497   1.5063  -1.3298   1.1430
 GZT  CAW  C  CH2   0  -0.424   0.4890  -0.9675   2.1315
 GZT  CAR  C  CR6   0   0.126  -0.6583  -0.2089   1.5174
 GZT  CAQ  C  CR16  0  -0.365  -1.4461  -0.8348   0.5412
 GZT  CAP  C  CR56  0   0.320  -2.4828  -0.1000   0.0336
 GZT  OAU  O  O     0  -0.495  -3.4041  -0.4496  -0.9164
 GZT  CAM  C  CR5   0   1.035  -4.2399   0.6231  -1.0764
 GZT  FAL  F  F     0  -0.290  -4.2245   1.0382  -2.3449
 GZT  FAV  F  F     0  -0.290  -5.5009   0.2695  -0.8156
 GZT  OAN  O  O     0  -0.494  -3.8493   1.6354  -0.2413
 GZT  CAO  C  CR56  0   0.297  -2.7586   1.1839   0.4510
 GZT  CAT  C  CR16  0  -0.320  -2.0112   1.8185   1.4066
 GZT  CAS  C  CR16  0  -0.302  -0.9412   1.0872   1.9298
 GZT  H1   H  HCH3  0   0.247   4.8502   3.4882  -0.5470
 GZT  H2   H  HCH3  0   0.236   6.1624   2.3249  -0.7461
 GZT  H3   H  HCH3  0   0.236   5.0501   2.6395  -2.0812
 GZT  H4   H  HNH1  0   0.416   3.5309   1.7639   0.1987
 GZT  H5   H  HCR6  0   0.282   4.0898  -2.2785  -1.4891
 GZT  H6   H  HCR6  0   0.284   2.5253  -4.0056  -0.5744
 GZT  H7   H  HCR6  0   0.323   0.8798  -3.3004   1.1401
 GZT  H8   H  HCH2  0   0.298   0.1352  -1.8964   2.5778
 GZT  H9   H  HCH2  0   0.299   0.9543  -0.3849   2.9236
 GZT  H10  H  HCR6  0   0.286  -1.2538  -1.8462   0.2069
 GZT  H11  H  HCR6  0   0.290  -2.2250   2.8259   1.7344
 GZT  H12  H  HCR6  0   0.268  -0.3158   1.5504   2.6808

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
 GZT  CAA  NAB  single    1.442  0.020  1.442
 GZT  NAB  CAC  single    1.335  0.020  1.335
 GZT  OAF  CAE  double    1.232  0.020  1.232
 GZT  CAC  OAK  double    1.229  0.020  1.229
 GZT  CAC  CAD  single    1.497  0.020  1.497
 GZT  CAE  CAD  single    1.444  0.020  1.444
 GZT  CAE  NAJ  single    1.391  0.020  1.391
 GZT  CAD  CAG  double    1.370  0.020  1.370
 GZT  CAW  NAJ  single    1.464  0.020  1.464
 GZT  CAW  CAR  single    1.506  0.020  1.506
 GZT  NAJ  CAI  single    1.351  0.020  1.351
 GZT  CAG  CAH  single    1.402  0.020  1.402
 GZT  CAS  CAR  aromatic  1.389  0.020  1.389
 GZT  CAS  CAT  aromatic  1.398  0.020  1.398
 GZT  CAR  CAQ  aromatic  1.402  0.020  1.402
 GZT  CAI  CAH  double    1.359  0.020  1.359
 GZT  CAT  CAO  aromatic  1.369  0.020  1.369
 GZT  CAQ  CAP  aromatic  1.368  0.020  1.368
 GZT  CAO  CAP  aromatic  1.378  0.020  1.378
 GZT  CAO  OAN  single    1.369  0.020  1.369
 GZT  CAP  OAU  single    1.369  0.020  1.369
 GZT  OAN  CAM  single    1.369  0.020  1.369
 GZT  OAU  CAM  single    1.369  0.020  1.369
 GZT  CAM  FAL  single    1.335  0.020  1.335
 GZT  CAM  FAV  single    1.335  0.020  1.335
 GZT  CAA  H1   single    0.970  0.020  1.090
 GZT  CAA  H2   single    0.970  0.020  1.090
 GZT  CAA  H3   single    0.970  0.020  1.090
 GZT  NAB  H4   single    0.860  0.020  1.020
 GZT  CAG  H5   single    0.930  0.020  1.080
 GZT  CAH  H6   single    0.930  0.020  1.080
 GZT  CAI  H7   single    0.930  0.020  1.080
 GZT  CAW  H8   single    0.970  0.020  1.090
 GZT  CAW  H9   single    0.970  0.020  1.090
 GZT  CAQ  H10  single    0.930  0.020  1.080
 GZT  CAT  H11  single    0.930  0.020  1.080
 GZT  CAS  H12  single    0.930  0.020  1.080

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
 GZT  H3   CAA  H2   108.08  3.000
 GZT  H3   CAA  H1   108.30  3.000
 GZT  H2   CAA  H1   108.30  3.000
 GZT  H3   CAA  NAB  111.79  3.000
 GZT  H2   CAA  NAB  111.96  3.000
 GZT  H1   CAA  NAB  108.30  3.000
 GZT  H4   NAB  CAC  117.84  3.000
 GZT  H4   NAB  CAA  120.10  3.000
 GZT  CAC  NAB  CAA  122.05  3.000
 GZT  CAD  CAC  OAK  120.37  3.000
 GZT  CAD  CAC  NAB  117.21  3.000
 GZT  OAK  CAC  NAB  122.41  3.000
 GZT  CAG  CAD  CAE  119.86  3.000
 GZT  CAG  CAD  CAC  117.46  3.000
 GZT  CAE  CAD  CAC  122.68  3.000
 GZT  NAJ  CAE  OAF  118.59  3.000
 GZT  NAJ  CAE  CAD  115.48  3.000
 GZT  OAF  CAE  CAD  125.92  3.000
 GZT  H5   CAG  CAH  119.44  3.000
 GZT  H5   CAG  CAD  118.80  3.000
 GZT  CAH  CAG  CAD  121.76  3.000
 GZT  H6   CAH  CAI  120.21  3.000
 GZT  H6   CAH  CAG  121.85  3.000
 GZT  CAI  CAH  CAG  117.95  3.000
 GZT  H7   CAI  NAJ  116.07  3.000
 GZT  H7   CAI  CAH  122.28  3.000
 GZT  NAJ  CAI  CAH  121.64  3.000
 GZT  CAW  NAJ  CAI  119.50  3.000
 GZT  CAI  NAJ  CAE  123.30  3.000
 GZT  CAW  NAJ  CAE  117.19  3.000
 GZT  H9   CAW  H8   107.29  3.000
 GZT  H9   CAW  CAR  110.67  3.000
 GZT  H8   CAW  CAR  110.43  3.000
 GZT  H9   CAW  NAJ  109.08  3.000
 GZT  H8   CAW  NAJ  106.93  3.000
 GZT  CAR  CAW  NAJ  112.25  3.000
 GZT  CAS  CAR  CAQ  120.59  3.000
 GZT  CAQ  CAR  CAW  119.15  3.000
 GZT  CAS  CAR  CAW  120.26  3.000
 GZT  H10  CAQ  CAP  121.45  3.000
 GZT  H10  CAQ  CAR  122.17  3.000
 GZT  CAP  CAQ  CAR  116.38  3.000
 GZT  CAO  CAP  OAU  108.27  3.000
 GZT  OAU  CAP  CAQ  129.07  3.000
 GZT  CAO  CAP  CAQ  122.66  3.000
 GZT  CAM  OAU  CAP  106.97  3.000
 GZT  OAN  CAM  FAV  110.24  3.000
 GZT  FAV  CAM  FAL  106.19  3.000
 GZT  OAN  CAM  FAL  110.27  3.000
 GZT  FAV  CAM  OAU  110.26  3.000
 GZT  FAL  CAM  OAU  110.34  3.000
 GZT  OAN  CAM  OAU  109.50  3.000
 GZT  CAO  OAN  CAM  106.98  3.000
 GZT  CAT  CAO  OAN  129.44  3.000
 GZT  OAN  CAO  CAP  108.28  3.000
 GZT  CAT  CAO  CAP  122.28  3.000
 GZT  H11  CAT  CAS  121.71  3.000
 GZT  H11  CAT  CAO  122.39  3.000
 GZT  CAS  CAT  CAO  115.90  3.000
 GZT  H12  CAS  CAT  118.59  3.000
 GZT  H12  CAS  CAR  119.21  3.000
 GZT  CAT  CAS  CAR  122.20  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
 GZT  CONST_01  CAO  CAT  CAS  CAR     0.00   0.0  0
 GZT  CONST_02  CAO  CAP  CAQ  CAR     0.00   0.0  0
 GZT  CONST_03  CAT  CAS  CAR  CAQ     0.00   0.0  0
 GZT  CONST_04  CAT  CAO  CAP  CAQ     0.00   0.0  0
 GZT  CONST_05  CAS  CAR  CAQ  CAP     0.00   0.0  0
 GZT  CONST_06  CAS  CAT  CAO  CAP     0.00   0.0  0
 GZT  CONST_07  CAI  NAJ  CAE  CAD     0.00   0.0  0
 GZT  CONST_08  CAT  CAS  CAR  CAW   180.00   0.0  0
 GZT  CONST_09  CAP  CAQ  CAR  CAW   180.00   0.0  0
 GZT  CONST_10  CAW  NAJ  CAE  CAD   180.00   0.0  0
 GZT  CONST_11  CAI  NAJ  CAE  OAF   180.00   0.0  0
 GZT  CONST_12  H11  CAT  CAS  CAR   180.00   0.0  0
 GZT  CONST_13  H12  CAS  CAR  CAQ   180.00   0.0  0
 GZT  CONST_14  H10  CAQ  CAP  OAU     0.00   0.0  0
 GZT  CONST_15  CAW  NAJ  CAE  OAF     0.00   0.0  0
 GZT  CONST_16  CAD  CAC  NAB  CAA   180.00   0.0  0
 GZT  CONST_17  H4   NAB  CAC  CAD     0.00   0.0  0
 GZT  CONST_18  OAK  CAC  NAB  CAA     0.00   0.0  0
 GZT  Var_01    OAN  CAM  OAU  CAP     0.13  30.0  1
 GZT  Var_02    CAT  CAO  OAN  CAM  -179.64  30.0  1
 GZT  Var_03    CAO  CAP  OAU  CAM     0.01  30.0  1
 GZT  Var_04    CAR  CAW  NAJ  CAE    74.49  30.0  2
 GZT  Var_05    CAS  CAR  CAW  NAJ  -118.54  30.0  2
 GZT  Var_06    CAE  CAD  CAC  NAB    -0.77  30.0  2
 GZT  Var_07    H1   CAA  NAB  CAC   177.55  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
 GZT  plan-1  CAC  0.020
 GZT  plan-1  CAD  0.020
 GZT  plan-1  CAE  0.020
 GZT  plan-1  OAF  0.020
 GZT  plan-1  CAG  0.020
 GZT  plan-1  CAH  0.020
 GZT  plan-1  CAI  0.020
 GZT  plan-1  NAJ  0.020
 GZT  plan-1  CAW  0.020
 GZT  plan-1  H5   0.020
 GZT  plan-1  H6   0.020
 GZT  plan-1  H7   0.020
 GZT  plan-2  CAW  0.020
 GZT  plan-2  CAR  0.020
 GZT  plan-2  CAQ  0.020
 GZT  plan-2  CAP  0.020
 GZT  plan-2  OAU  0.020
 GZT  plan-2  OAN  0.020
 GZT  plan-2  CAO  0.020
 GZT  plan-2  CAT  0.020
 GZT  plan-2  CAS  0.020
 GZT  plan-2  H10  0.020
 GZT  plan-2  H11  0.020
 GZT  plan-2  H12  0.020
 GZT  plan-3  CAA  0.020
 GZT  plan-3  NAB  0.020
 GZT  plan-3  CAC  0.020
 GZT  plan-3  OAK  0.020
 GZT  plan-3  CAD  0.020
 GZT  plan-3  H4   0.020

