# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:50:28 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: ~{N}-[2-(1~{H}-indol-3-yl)ethyl]-2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=CC=CN(CC(=O)NCCc2c[nH]c3ccccc23)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
 K0Q  K0Q  ~{N}-[2-(1~{H}-indol-3-yl)ethyl]-2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)ethanamide  ligand  40  23  .  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_K0Q
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
 K0Q  N    N  NR6   0  -0.494  -3.7803  -0.8062   0.2380
 K0Q  CA   C  CH2   0  -0.453  -2.6468  -1.5345   0.7618
 K0Q  C    C  C     0   0.557  -1.3767  -1.1775   0.0008
 K0Q  O    O  O     0  -0.489  -1.4117  -0.8409  -1.1717
 K0Q  OAY  O  O     0  -0.508  -2.8862   1.0873   1.1090
 K0Q  CAT  C  CR6   0   0.527  -3.7881   0.5505   0.4725
 K0Q  CAU  C  CR6   0   0.169  -4.9248   1.2632  -0.0810
 K0Q  OAZ  O  OH1   0  -0.615  -4.9118   2.5793   0.1904
 K0Q  CAO  C  CR16  0  -0.274  -5.8730   0.6165  -0.8080
 K0Q  CAR  C  CR16  0  -0.386  -5.7714  -0.7795  -1.0309
 K0Q  CAS  C  CR16  0   0.021  -4.7246  -1.4524  -0.5061
 K0Q  NAV  N  NH1   0  -0.646  -0.2481  -1.3198   0.7010
 K0Q  CAN  C  CH2   0  -0.232   1.0653  -1.1391   0.1158
 K0Q  CAM  C  CH2   0  -0.586   2.1414  -1.1874   1.1959
 K0Q  C1   C  CR5   0   0.008   3.5025  -0.9647   0.6265
 K0Q  C2   C  CR56  0   0.029   4.0587   0.2867   0.2027
 K0Q  C9   C  CR16  0  -0.375   3.5909   1.6060   0.2078
 K0Q  C10  C  CR16  0  -0.269   4.4077   2.6074  -0.2797
 K0Q  C11  C  CR16  0  -0.284   5.6898   2.3185  -0.7775
 K0Q  C12  C  CR16  0  -0.305   6.1786   1.0262  -0.7953
 K0Q  C3   C  CR56  0   0.355   5.3512   0.0186  -0.3006
 K0Q  N6   N  NR15  0  -0.686   5.5600  -1.3242  -0.1871
 K0Q  C5   C  CR15  0  -0.083   4.4554  -1.9087   0.3666
 K0Q  H1   H  HCH2  0   0.294  -2.5408  -1.3525   1.8312
 K0Q  H2   H  HCH2  0   0.309  -2.8332  -2.6014   0.6329
 K0Q  H3   H  HOH1  0   0.476  -5.6790   3.0062  -0.2076
 K0Q  H4   H  HCR6  0   0.287  -6.7095   1.1655  -1.2249
 K0Q  H5   H  HCR6  0   0.277  -6.5163  -1.3036  -1.6095
 K0Q  H6   H  HCR6  0   0.301  -4.5823  -2.5145  -0.6369
 K0Q  H7   H  HNH1  0   0.406  -0.3051  -1.6008   1.6672
 K0Q  H8   H  HCH2  0   0.239   1.2589  -1.9158  -0.6292
 K0Q  H9   H  HCH2  0   0.241   1.1012  -0.1798  -0.4049
 K0Q  H10  H  HCH2  0   0.248   1.9229  -0.4285   1.9537
 K0Q  H11  H  HCH2  0   0.257   2.1059  -2.1559   1.7022
 K0Q  H12  H  HCR6  0   0.241   2.6047   1.8420   0.5898
 K0Q  H13  H  HCR6  0   0.245   4.0593   3.6323  -0.2795
 K0Q  H14  H  HCR6  0   0.248   6.3067   3.1249  -1.1532
 K0Q  H15  H  HCR6  0   0.258   7.1669   0.8047  -1.1781
 K0Q  H16  H  HNR5  0   0.408   6.3952  -1.8138  -0.4599
 K0Q  H17  H  HCR5  0   0.281   4.4277  -2.9735   0.5394

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
 K0Q  OAZ  CAU  single    1.344  0.020  1.344
 K0Q  C10  C11  aromatic  1.405  0.020  1.405
 K0Q  C10  C9   aromatic  1.381  0.020  1.381
 K0Q  CAU  CAO  double    1.359  0.020  1.359
 K0Q  CAU  CAT  single    1.451  0.020  1.451
 K0Q  C11  C12  aromatic  1.382  0.020  1.382
 K0Q  CAO  CAR  single    1.417  0.020  1.417
 K0Q  C9   C2   aromatic  1.400  0.020  1.400
 K0Q  OAY  CAT  double    1.227  0.020  1.227
 K0Q  CAT  N    single    1.377  0.020  1.377
 K0Q  C12  C3   aromatic  1.394  0.020  1.394
 K0Q  CAR  CAS  double    1.351  0.020  1.351
 K0Q  C2   C3   aromatic  1.413  0.020  1.413
 K0Q  C2   C1   aromatic  1.433  0.020  1.433
 K0Q  C3   N6   aromatic  1.364  0.020  1.364
 K0Q  N    CAS  single    1.365  0.020  1.365
 K0Q  N    CA   single    1.446  0.020  1.446
 K0Q  C1   CAM  single    1.492  0.020  1.492
 K0Q  C1   C5   aromatic  1.366  0.020  1.366
 K0Q  CAM  CAN  single    1.525  0.020  1.525
 K0Q  O    C    double    1.220  0.020  1.220
 K0Q  N6   C5   aromatic  1.367  0.020  1.367
 K0Q  C    CA   single    1.523  0.020  1.523
 K0Q  C    NAV  single    1.336  0.020  1.336
 K0Q  NAV  CAN  single    1.449  0.020  1.449
 K0Q  CA   H1   single    0.970  0.020  1.090
 K0Q  CA   H2   single    0.970  0.020  1.090
 K0Q  OAZ  H3   single    0.850  0.020  0.980
 K0Q  CAO  H4   single    0.930  0.020  1.080
 K0Q  CAR  H5   single    0.930  0.020  1.080
 K0Q  CAS  H6   single    0.930  0.020  1.080
 K0Q  NAV  H7   single    0.860  0.020  1.020
 K0Q  CAN  H8   single    0.970  0.020  1.090
 K0Q  CAN  H9   single    0.970  0.020  1.090
 K0Q  CAM  H10  single    0.970  0.020  1.090
 K0Q  CAM  H11  single    0.970  0.020  1.090
 K0Q  C9   H12  single    0.930  0.020  1.080
 K0Q  C10  H13  single    0.930  0.020  1.080
 K0Q  C11  H14  single    0.930  0.020  1.080
 K0Q  C12  H15  single    0.930  0.020  1.080
 K0Q  N6   H16  single    0.860  0.020  1.020
 K0Q  C5   H17  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
 K0Q  CAS  N    CAT  123.74  3.000
 K0Q  CAS  N    CA   120.10  3.000
 K0Q  CAT  N    CA   116.05  3.000
 K0Q  H2   CA   H1   107.21  3.000
 K0Q  H2   CA   C    108.22  3.000
 K0Q  H1   CA   C    111.72  3.000
 K0Q  H2   CA   N    108.42  3.000
 K0Q  H1   CA   N    110.35  3.000
 K0Q  C    CA   N    110.78  3.000
 K0Q  NAV  C    O    123.87  3.000
 K0Q  NAV  C    CA   114.69  3.000
 K0Q  O    C    CA   121.38  3.000
 K0Q  CAU  CAT  OAY  123.95  3.000
 K0Q  OAY  CAT  N    121.00  3.000
 K0Q  CAU  CAT  N    115.04  3.000
 K0Q  CAO  CAU  OAZ  125.52  3.000
 K0Q  CAO  CAU  CAT  121.13  3.000
 K0Q  OAZ  CAU  CAT  113.35  3.000
 K0Q  H3   OAZ  CAU  110.04  3.000
 K0Q  H4   CAO  CAR  119.59  3.000
 K0Q  H4   CAO  CAU  120.22  3.000
 K0Q  CAR  CAO  CAU  120.20  3.000
 K0Q  H5   CAR  CAS  120.09  3.000
 K0Q  H5   CAR  CAO  120.88  3.000
 K0Q  CAS  CAR  CAO  119.03  3.000
 K0Q  H6   CAS  CAR  123.05  3.000
 K0Q  H6   CAS  N    116.15  3.000
 K0Q  CAR  CAS  N    120.80  3.000
 K0Q  H7   NAV  CAN  118.24  3.000
 K0Q  H7   NAV  C    118.98  3.000
 K0Q  CAN  NAV  C    122.73  3.000
 K0Q  H9   CAN  H8   107.05  3.000
 K0Q  H9   CAN  CAM  110.01  3.000
 K0Q  H8   CAN  CAM  109.57  3.000
 K0Q  H9   CAN  NAV  109.38  3.000
 K0Q  H8   CAN  NAV  110.31  3.000
 K0Q  CAM  CAN  NAV  110.46  3.000
 K0Q  H11  CAM  H10  106.68  3.000
 K0Q  H11  CAM  C1   109.78  3.000
 K0Q  H10  CAM  C1   110.05  3.000
 K0Q  H11  CAM  CAN  109.45  3.000
 K0Q  H10  CAM  CAN  109.11  3.000
 K0Q  C1   CAM  CAN  111.63  3.000
 K0Q  C5   C1   C2   106.04  3.000
 K0Q  C5   C1   CAM  127.28  3.000
 K0Q  C2   C1   CAM  126.66  3.000
 K0Q  C3   C2   C9   119.07  3.000
 K0Q  C3   C2   C1   107.14  3.000
 K0Q  C9   C2   C1   133.79  3.000
 K0Q  H12  C9   C10  120.32  3.000
 K0Q  H12  C9   C2   120.71  3.000
 K0Q  C10  C9   C2   118.97  3.000
 K0Q  H13  C10  C11  119.23  3.000
 K0Q  H13  C10  C9   119.74  3.000
 K0Q  C11  C10  C9   121.03  3.000
 K0Q  H14  C11  C12  119.38  3.000
 K0Q  H14  C11  C10  119.32  3.000
 K0Q  C12  C11  C10  121.30  3.000
 K0Q  H15  C12  C3   121.27  3.000
 K0Q  H15  C12  C11  121.25  3.000
 K0Q  C3   C12  C11  117.47  3.000
 K0Q  N6   C3   C12  130.56  3.000
 K0Q  N6   C3   C2   107.29  3.000
 K0Q  C12  C3   C2   122.15  3.000
 K0Q  H16  N6   C5   124.94  3.000
 K0Q  H16  N6   C3   125.73  3.000
 K0Q  C5   N6   C3   109.33  3.000
 K0Q  H17  C5   N6   120.50  3.000
 K0Q  H17  C5   C1   129.30  3.000
 K0Q  N6   C5   C1   110.20  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
 K0Q  CONST_01  C10  C9   C2   C1    180.00   0.0  0
 K0Q  CONST_02  C12  C3   C2   C1    180.00   0.0  0
 K0Q  CONST_03  N6   C3   C2   C1      0.00   0.0  0
 K0Q  CONST_04  C3   N6   C5   C1      0.00   0.0  0
 K0Q  CONST_05  C11  C10  C9   C2      0.00   0.0  0
 K0Q  CONST_06  C11  C12  C3   C2      0.00   0.0  0
 K0Q  CONST_07  C5   N6   C3   C2      0.00   0.0  0
 K0Q  CONST_08  N6   C5   C1   C2      0.00   0.0  0
 K0Q  CONST_09  C12  C11  C10  C9      0.00   0.0  0
 K0Q  CONST_10  C12  C3   C2   C9      0.00   0.0  0
 K0Q  CONST_11  N6   C3   C2   C9    180.00   0.0  0
 K0Q  CONST_12  C5   C1   C2   C9    180.00   0.0  0
 K0Q  CONST_13  C3   C12  C11  C10     0.00   0.0  0
 K0Q  CONST_14  C3   C2   C9   C10     0.00   0.0  0
 K0Q  CONST_15  N6   C3   C12  C11   180.00   0.0  0
 K0Q  CONST_16  C5   N6   C3   C12   180.00   0.0  0
 K0Q  CONST_17  C5   C1   C2   C3      0.00   0.0  0
 K0Q  CONST_18  CAS  N    CAT  CAU     0.00   0.0  0
 K0Q  CONST_19  C9   C2   C1   CAM     0.00   0.0  0
 K0Q  CONST_20  C3   C2   C1   CAM   180.00   0.0  0
 K0Q  CONST_21  N6   C5   C1   CAM   180.00   0.0  0
 K0Q  CONST_22  CAU  CAT  N    CA    180.00   0.0  0
 K0Q  CONST_23  CAS  N    CAT  OAY   180.00   0.0  0
 K0Q  CONST_24  H12  C9   C2   C1      0.00   0.0  0
 K0Q  CONST_25  H16  N6   C5   C1    180.00   0.0  0
 K0Q  CONST_26  H13  C10  C9   C2    180.00   0.0  0
 K0Q  CONST_27  H15  C12  C3   C2    180.00   0.0  0
 K0Q  CONST_28  H17  C5   C1   C2    180.00   0.0  0
 K0Q  CONST_29  H14  C11  C10  C9    180.00   0.0  0
 K0Q  CONST_30  OAY  CAT  N    CA      0.00   0.0  0
 K0Q  CONST_31  CAN  NAV  C    CA    180.00   0.0  0
 K0Q  CONST_32  CAN  NAV  C    O       0.00   0.0  0
 K0Q  CONST_33  H7   NAV  C    CA      0.00   0.0  0
 K0Q  Var_01    CAT  N    CA   C     -69.30  30.0  2
 K0Q  Var_02    C2   C1   CAM  CAN    75.77  30.0  2
 K0Q  Var_03    O    C    CA   N     -29.54  30.0  1
 K0Q  Var_04    C1   CAM  CAN  NAV  -178.36  30.0  2
 K0Q  Var_05    CAM  CAN  NAV  C     172.61  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
 K0Q  plan-1  N    0.020
 K0Q  plan-1  CA   0.020
 K0Q  plan-1  OAY  0.020
 K0Q  plan-1  CAT  0.020
 K0Q  plan-1  CAU  0.020
 K0Q  plan-1  OAZ  0.020
 K0Q  plan-1  CAO  0.020
 K0Q  plan-1  CAR  0.020
 K0Q  plan-1  CAS  0.020
 K0Q  plan-1  H4   0.020
 K0Q  plan-1  H5   0.020
 K0Q  plan-1  H6   0.020
 K0Q  plan-2  CAM  0.020
 K0Q  plan-2  C1   0.020
 K0Q  plan-2  C2   0.020
 K0Q  plan-2  C9   0.020
 K0Q  plan-2  C10  0.020
 K0Q  plan-2  C11  0.020
 K0Q  plan-2  C12  0.020
 K0Q  plan-2  C3   0.020
 K0Q  plan-2  N6   0.020
 K0Q  plan-2  C5   0.020
 K0Q  plan-2  H12  0.020
 K0Q  plan-2  H13  0.020
 K0Q  plan-2  H14  0.020
 K0Q  plan-2  H15  0.020
 K0Q  plan-2  H16  0.020
 K0Q  plan-2  H17  0.020
 K0Q  plan-3  CA   0.020
 K0Q  plan-3  C    0.020
 K0Q  plan-3  O    0.020
 K0Q  plan-3  NAV  0.020
 K0Q  plan-3  CAN  0.020
 K0Q  plan-3  H7   0.020

