# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:18:23 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=CC=CN(CC(=O)NCCc2ccc(cc2)c3ccccc3)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
 K8T  K8T  2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide  ligand  46  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K8T
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
 K8T  N    N  NR6   0  -0.492   5.1640   0.6103  -0.3801
 K8T  CA   C  CH2   0  -0.460   4.0158   1.4535  -0.1424
 K8T  C    C  C     0   0.558   2.7181   0.6778  -0.3257
 K8T  O    O  O     0  -0.485   2.6619  -0.3227  -1.0209
 K8T  OAY  O  O     0  -0.508   4.7597  -0.4108   1.6055
 K8T  CAT  C  CR6   0   0.526   5.4484  -0.3206   0.5937
 K8T  CAU  C  CR6   0   0.169   6.6097  -1.1502   0.3279
 K8T  OAZ  O  OH1   0  -0.616   6.8899  -2.0086   1.3232
 K8T  CAO  C  CR16  0  -0.274   7.3030  -1.0367  -0.8349
 K8T  CAR  C  CR16  0  -0.386   6.9098  -0.0854  -1.8095
 K8T  CAS  C  CR16  0   0.020   5.8492   0.7113  -1.5565
 K8T  NAV  N  NH1   0  -0.646   1.6598   1.2211   0.2838
 K8T  CAN  C  CH2   0  -0.230   0.3106   0.7282   0.0959
 K8T  CAM  C  CH2   0  -0.565  -0.6718   1.5405   0.9336
 K8T  CAJ  C  CR6   0   0.112  -2.0817   1.0801   0.6959
 K8T  CAK  C  CR16  0  -0.288  -2.8465   1.6280  -0.3308
 K8T  CAL  C  CR16  0  -0.296  -4.1334   1.1787  -0.5807
 K8T  CAI  C  CR16  0  -0.289  -2.6452   0.0652   1.4639
 K8T  CAH  C  CR16  0  -0.295  -3.9324  -0.3864   1.2174
 K8T  CAG  C  CR6   0   0.074  -4.7006   0.1623   0.1895
 K8T  CAF  C  CR6   0   0.090  -6.0727  -0.3168  -0.0725
 K8T  CAA  C  CR16  0  -0.312  -6.3945  -1.6691   0.0613
 K8T  CAB  C  CR16  0  -0.240  -7.6830  -2.1216  -0.1824
 K8T  CAC  C  CR16  0  -0.267  -8.6764  -1.2303  -0.5664
 K8T  CAD  C  CR16  0  -0.240  -8.3691   0.1171  -0.7040
 K8T  CAE  C  CR16  0  -0.312  -7.0806   0.5690  -0.4591
 K8T  H1   H  HCH2  0   0.298   4.0762   1.9039   0.8482
 K8T  H2   H  HCH2  0   0.312   4.0296   2.2687  -0.8674
 K8T  H3   H  HOH1  0   0.476   7.6826  -2.5137   1.1096
 K8T  H4   H  HCR6  0   0.287   8.1610  -1.6725  -1.0230
 K8T  H5   H  HCR6  0   0.277   7.4464   0.0060  -2.7413
 K8T  H6   H  HCR6  0   0.302   5.4988   1.4616  -2.2489
 K8T  H7   H  HNH1  0   0.408   1.7893   2.0537   0.8367
 K8T  H8   H  HCH2  0   0.242   0.0319   0.7902  -0.9600
 K8T  H9   H  HCH2  0   0.245   0.2545  -0.3249   0.3807
 K8T  H10  H  HCH2  0   0.262  -0.4168   1.4429   1.9919
 K8T  H11  H  HCH2  0   0.260  -0.5784   2.5989   0.6760
 K8T  H12  H  HCR6  0   0.251  -2.4297   2.4162  -0.9475
 K8T  H13  H  HCR6  0   0.253  -4.6956   1.6138  -1.3975
 K8T  H14  H  HCR6  0   0.251  -2.0742  -0.3721   2.2746
 K8T  H15  H  HCR6  0   0.253  -4.3506  -1.1605   1.8495
 K8T  H16  H  HCR6  0   0.253  -5.6259  -2.3798   0.3395
 K8T  H17  H  HCR6  0   0.257  -7.9084  -3.1751  -0.0784
 K8T  H18  H  HCR6  0   0.257  -9.6818  -1.5823  -0.7577
 K8T  H19  H  HCR6  0   0.257  -9.1376   0.8222  -0.9948
 K8T  H20  H  HCR6  0   0.253  -6.8643   1.6262  -0.5515

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
 K8T  CAN  NAV  single    1.449  0.020  1.449
 K8T  CAN  CAM  single    1.525  0.020  1.525
 K8T  OAY  CAT  double    1.227  0.020  1.227
 K8T  NAV  C    single    1.337  0.020  1.337
 K8T  OAZ  CAU  single    1.344  0.020  1.344
 K8T  CAK  CAJ  aromatic  1.393  0.020  1.393
 K8T  CAK  CAL  aromatic  1.386  0.020  1.386
 K8T  O    C    double    1.220  0.020  1.220
 K8T  C    CA   single    1.523  0.020  1.523
 K8T  CAM  CAJ  single    1.502  0.020  1.502
 K8T  CAT  CAU  single    1.452  0.020  1.452
 K8T  CAT  N    single    1.377  0.020  1.377
 K8T  CAJ  CAI  aromatic  1.392  0.020  1.392
 K8T  CAL  CAG  aromatic  1.396  0.020  1.396
 K8T  CA   N    single    1.444  0.020  1.444
 K8T  CAU  CAO  double    1.359  0.020  1.359
 K8T  N    CAS  single    1.365  0.020  1.365
 K8T  CAE  CAD  aromatic  1.387  0.020  1.387
 K8T  CAE  CAF  aromatic  1.396  0.020  1.396
 K8T  CAI  CAH  aromatic  1.386  0.020  1.386
 K8T  CAG  CAH  aromatic  1.396  0.020  1.396
 K8T  CAG  CAF  single    1.477  0.020  1.477
 K8T  CAO  CAR  single    1.418  0.020  1.418
 K8T  CAD  CAC  aromatic  1.389  0.020  1.389
 K8T  CAF  CAA  aromatic  1.397  0.020  1.397
 K8T  CAS  CAR  double    1.350  0.020  1.350
 K8T  CAC  CAB  aromatic  1.389  0.020  1.389
 K8T  CAA  CAB  aromatic  1.387  0.020  1.387
 K8T  CA   H1   single    0.970  0.020  1.090
 K8T  CA   H2   single    0.970  0.020  1.090
 K8T  OAZ  H3   single    0.850  0.020  0.980
 K8T  CAO  H4   single    0.930  0.020  1.080
 K8T  CAR  H5   single    0.930  0.020  1.080
 K8T  CAS  H6   single    0.930  0.020  1.080
 K8T  NAV  H7   single    0.860  0.020  1.020
 K8T  CAN  H8   single    0.970  0.020  1.090
 K8T  CAN  H9   single    0.970  0.020  1.090
 K8T  CAM  H10  single    0.970  0.020  1.090
 K8T  CAM  H11  single    0.970  0.020  1.090
 K8T  CAK  H12  single    0.930  0.020  1.080
 K8T  CAL  H13  single    0.930  0.020  1.080
 K8T  CAI  H14  single    0.930  0.020  1.080
 K8T  CAH  H15  single    0.930  0.020  1.080
 K8T  CAA  H16  single    0.930  0.020  1.080
 K8T  CAB  H17  single    0.930  0.020  1.080
 K8T  CAC  H18  single    0.930  0.020  1.080
 K8T  CAD  H19  single    0.930  0.020  1.080
 K8T  CAE  H20  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
 K8T  CAS  N    CAT  123.77  3.000
 K8T  CAS  N    CA   119.85  3.000
 K8T  CAT  N    CA   116.27  3.000
 K8T  H2   CA   H1   107.13  3.000
 K8T  H2   CA   C    108.14  3.000
 K8T  H1   CA   C    111.54  3.000
 K8T  H2   CA   N    108.47  3.000
 K8T  H1   CA   N    110.29  3.000
 K8T  C    CA   N    111.12  3.000
 K8T  NAV  C    O    123.85  3.000
 K8T  O    C    CA   121.71  3.000
 K8T  NAV  C    CA   114.38  3.000
 K8T  CAU  CAT  OAY  123.90  3.000
 K8T  CAU  CAT  N    114.97  3.000
 K8T  OAY  CAT  N    121.13  3.000
 K8T  CAO  CAU  OAZ  125.51  3.000
 K8T  CAO  CAU  CAT  121.14  3.000
 K8T  OAZ  CAU  CAT  113.34  3.000
 K8T  H3   OAZ  CAU  110.01  3.000
 K8T  H4   CAO  CAR  119.59  3.000
 K8T  H4   CAO  CAU  120.22  3.000
 K8T  CAR  CAO  CAU  120.19  3.000
 K8T  H5   CAR  CAS  120.15  3.000
 K8T  H5   CAR  CAO  120.83  3.000
 K8T  CAS  CAR  CAO  119.02  3.000
 K8T  H6   CAS  CAR  123.02  3.000
 K8T  H6   CAS  N    116.19  3.000
 K8T  CAR  CAS  N    120.79  3.000
 K8T  H7   NAV  CAN  118.16  3.000
 K8T  H7   NAV  C    118.96  3.000
 K8T  CAN  NAV  C    122.68  3.000
 K8T  H9   CAN  H8   107.05  3.000
 K8T  H9   CAN  CAM  109.70  3.000
 K8T  H8   CAN  CAM  109.62  3.000
 K8T  H9   CAN  NAV  110.00  3.000
 K8T  H8   CAN  NAV  110.07  3.000
 K8T  CAM  CAN  NAV  110.33  3.000
 K8T  H11  CAM  H10  107.14  3.000
 K8T  H11  CAM  CAJ  109.86  3.000
 K8T  H10  CAM  CAJ  110.18  3.000
 K8T  H11  CAM  CAN  109.33  3.000
 K8T  H10  CAM  CAN  109.51  3.000
 K8T  CAJ  CAM  CAN  110.76  3.000
 K8T  CAI  CAJ  CAK  118.12  3.000
 K8T  CAI  CAJ  CAM  121.07  3.000
 K8T  CAK  CAJ  CAM  120.77  3.000
 K8T  H12  CAK  CAL  119.36  3.000
 K8T  H12  CAK  CAJ  119.62  3.000
 K8T  CAL  CAK  CAJ  121.02  3.000
 K8T  H13  CAL  CAG  119.86  3.000
 K8T  H13  CAL  CAK  119.20  3.000
 K8T  CAG  CAL  CAK  120.93  3.000
 K8T  H14  CAI  CAH  119.40  3.000
 K8T  H14  CAI  CAJ  119.58  3.000
 K8T  CAH  CAI  CAJ  121.02  3.000
 K8T  H15  CAH  CAG  119.88  3.000
 K8T  H15  CAH  CAI  119.17  3.000
 K8T  CAG  CAH  CAI  120.93  3.000
 K8T  CAF  CAG  CAH  120.97  3.000
 K8T  CAF  CAG  CAL  121.06  3.000
 K8T  CAH  CAG  CAL  117.98  3.000
 K8T  CAE  CAF  CAA  118.32  3.000
 K8T  CAA  CAF  CAG  120.75  3.000
 K8T  CAE  CAF  CAG  120.93  3.000
 K8T  H16  CAA  CAB  119.35  3.000
 K8T  H16  CAA  CAF  119.77  3.000
 K8T  CAB  CAA  CAF  120.87  3.000
 K8T  H17  CAB  CAC  120.15  3.000
 K8T  H17  CAB  CAA  119.61  3.000
 K8T  CAC  CAB  CAA  120.24  3.000
 K8T  H18  CAC  CAD  120.23  3.000
 K8T  H18  CAC  CAB  120.31  3.000
 K8T  CAD  CAC  CAB  119.46  3.000
 K8T  H19  CAD  CAE  119.64  3.000
 K8T  H19  CAD  CAC  120.09  3.000
 K8T  CAE  CAD  CAC  120.27  3.000
 K8T  H20  CAE  CAD  119.24  3.000
 K8T  H20  CAE  CAF  119.91  3.000
 K8T  CAD  CAE  CAF  120.84  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
 K8T  CONST_01  CAG  CAL  CAK  CAJ    0.00   0.0  0
 K8T  CONST_02  CAG  CAH  CAI  CAJ    0.00   0.0  0
 K8T  CONST_03  CAH  CAI  CAJ  CAK    0.00   0.0  0
 K8T  CONST_04  CAH  CAG  CAL  CAK    0.00   0.0  0
 K8T  CONST_05  CAF  CAG  CAL  CAK  180.00   0.0  0
 K8T  CONST_06  CAI  CAJ  CAK  CAL    0.00   0.0  0
 K8T  CONST_07  CAI  CAH  CAG  CAL    0.00   0.0  0
 K8T  CONST_10  CAF  CAG  CAH  CAI  180.00   0.0  0
 K8T  CONST_13  CAD  CAE  CAF  CAG  180.00   0.0  0
 K8T  CONST_14  CAB  CAA  CAF  CAG  180.00   0.0  0
 K8T  CONST_15  CAC  CAD  CAE  CAF    0.00   0.0  0
 K8T  CONST_16  CAC  CAB  CAA  CAF    0.00   0.0  0
 K8T  CONST_17  CAD  CAE  CAF  CAA    0.00   0.0  0
 K8T  CONST_18  CAD  CAC  CAB  CAA    0.00   0.0  0
 K8T  CONST_19  CAE  CAD  CAC  CAB    0.00   0.0  0
 K8T  CONST_20  CAE  CAF  CAA  CAB    0.00   0.0  0
 K8T  CONST_21  CAS  N    CAT  CAU    0.00   0.0  0
 K8T  CONST_22  CAL  CAK  CAJ  CAM  180.00   0.0  0
 K8T  CONST_23  CAH  CAI  CAJ  CAM  180.00   0.0  0
 K8T  CONST_24  CAU  CAT  N    CA   180.00   0.0  0
 K8T  CONST_25  CAS  N    CAT  OAY  180.00   0.0  0
 K8T  CONST_26  H13  CAL  CAK  CAJ  180.00   0.0  0
 K8T  CONST_27  H15  CAH  CAI  CAJ  180.00   0.0  0
 K8T  CONST_28  H14  CAI  CAJ  CAK  180.00   0.0  0
 K8T  CONST_29  H12  CAK  CAJ  CAI  180.00   0.0  0
 K8T  CONST_30  H20  CAE  CAF  CAG    0.00   0.0  0
 K8T  CONST_31  H16  CAA  CAF  CAG    0.00   0.0  0
 K8T  CONST_32  H19  CAD  CAE  CAF  180.00   0.0  0
 K8T  CONST_33  H17  CAB  CAA  CAF  180.00   0.0  0
 K8T  CONST_34  H18  CAC  CAB  CAA  180.00   0.0  0
 K8T  CONST_35  OAY  CAT  N    CA     0.00   0.0  0
 K8T  CONST_36  CAN  NAV  C    CA   180.00   0.0  0
 K8T  CONST_37  CAN  NAV  C    O      0.00   0.0  0
 K8T  CONST_38  H7   NAV  C    CA     0.00   0.0  0
 K8T  Var_01    CAT  N    CA   C    -73.13  30.0  3
 K8T  Var_02    CAK  CAJ  CAM  CAN  -88.36  30.0  2
 K8T  Var_03    NAV  C    CA   N    158.97  30.0  1
 K8T  Var_04    CAJ  CAM  CAN  NAV  177.29  30.0  3
 K8T  Var_05    CAM  CAN  NAV  C    179.34  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
 K8T  plan-1  N    0.020
 K8T  plan-1  CA   0.020
 K8T  plan-1  OAY  0.020
 K8T  plan-1  CAT  0.020
 K8T  plan-1  CAU  0.020
 K8T  plan-1  OAZ  0.020
 K8T  plan-1  CAO  0.020
 K8T  plan-1  CAR  0.020
 K8T  plan-1  CAS  0.020
 K8T  plan-1  H4   0.020
 K8T  plan-1  H5   0.020
 K8T  plan-1  H6   0.020
 K8T  plan-2  CAM  0.020
 K8T  plan-2  CAJ  0.020
 K8T  plan-2  CAK  0.020
 K8T  plan-2  CAL  0.020
 K8T  plan-2  CAI  0.020
 K8T  plan-2  CAH  0.020
 K8T  plan-2  CAG  0.020
 K8T  plan-2  CAF  0.020
 K8T  plan-2  H12  0.020
 K8T  plan-2  H13  0.020
 K8T  plan-2  H14  0.020
 K8T  plan-2  H15  0.020
 K8T  plan-3  CAG  0.020
 K8T  plan-3  CAF  0.020
 K8T  plan-3  CAA  0.020
 K8T  plan-3  CAB  0.020
 K8T  plan-3  CAC  0.020
 K8T  plan-3  CAD  0.020
 K8T  plan-3  CAE  0.020
 K8T  plan-3  H16  0.020
 K8T  plan-3  H17  0.020
 K8T  plan-3  H18  0.020
 K8T  plan-3  H19  0.020
 K8T  plan-3  H20  0.020
 K8T  plan-4  CA   0.020
 K8T  plan-4  C    0.020
 K8T  plan-4  O    0.020
 K8T  plan-4  NAV  0.020
 K8T  plan-4  CAN  0.020
 K8T  plan-4  H7   0.020

