# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 04:35:23 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: ~{N}-[6-azanyl-4-(1-benzofuran-5-yl)pyridin-2-yl]-2-(methylamino)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC(=O)Nc1cc(cc(N)n1)c2ccc3occc3c2
#
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
 RKW  RKW  ~{N}-[6-azanyl-4-(1-benzofuran-5-yl)pyridin-2-yl]-2-(methylamino)ethanamide  ligand  38  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RKW
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
 RKW  C1   C  CH3   0  -0.521  -15.0288  25.2171  -23.8322
 RKW  N1   N  NH1   0  -0.571  -14.5371  25.0285  -25.1832
 RKW  O1   O  O     0  -0.454  -17.1475  24.8622  -26.2620
 RKW  C2   C  CH2   0  -0.427  -15.0277  25.9905  -26.1273
 RKW  N2   N  NH1   0  -0.712  -17.0340  27.0073  -27.0218
 RKW  O2   O  O     0  -0.430  -24.8496  23.1517  -27.8804
 RKW  C3   C  C     0   0.510  -16.5168  25.8828  -26.4575
 RKW  N3   N  N     0  -0.505  -18.4381  28.4814  -28.0070
 RKW  C4   C  CR6   0   0.497  -18.3154  27.2538  -27.5116
 RKW  C5   C  CR6   0   0.471  -19.6098  28.8568  -28.5090
 RKW  C6   C  CR16  0  -0.469  -20.7207  27.9997  -28.5343
 RKW  C7   C  CR6   0   0.209  -20.5816  26.7226  -28.0211
 RKW  C8   C  CR16  0  -0.478  -19.3481  26.3268  -27.4930
 RKW  C9   C  CR6   0   0.066  -21.7214  25.7812  -28.0185
 RKW  C10  C  CR16  0  -0.312  -22.6186  25.7576  -29.1034
 RKW  C11  C  CR16  0  -0.323  -23.7025  24.8991  -29.1435
 RKW  C12  C  CR56  0   0.357  -23.8679  24.0607  -28.0554
 RKW  C13  C  CR15  0   0.023  -24.6194  22.5575  -26.6798
 RKW  C14  C  CR15  0  -0.385  -23.5244  23.0519  -26.0704
 RKW  C15  C  CR56  0   0.078  -23.0012  24.0516  -26.9610
 RKW  C16  C  CR16  0  -0.394  -21.9136  24.9211  -26.9435
 RKW  H1   H  HCH3  0   0.233  -14.6103  24.4469  -23.1846
 RKW  H2   H  HCH3  0   0.223  -14.6890  26.1821  -23.4512
 RKW  H3   H  HCH3  0   0.201  -16.1196  25.1844  -23.7251
 RKW  H4   H  HNH1  0   0.349  -14.7461  24.0923  -25.5032
 RKW  H6   H  HCH2  0   0.283  -14.4876  25.8799  -27.0745
 RKW  H7   H  HCH2  0   0.255  -14.7983  26.9984  -25.7680
 RKW  H8   H  HNH1  0   0.406  -16.4144  27.7992  -27.1261
 RKW  H9   H  HNH2  0   0.383  -18.8401  30.6173  -29.1469
 RKW  H10  H  HNH2  0   0.391  -20.4549  30.3623  -29.5901
 RKW  H11  H  HCR6  0   0.261  -21.6657  28.3523  -28.9268
 RKW  H12  H  HCR6  0   0.276  -19.2017  25.3318  -27.1099
 RKW  H13  H  HCR6  0   0.259  -22.4466  26.4154  -29.9452
 RKW  H14  H  HCR6  0   0.272  -24.3772  24.8853  -29.9892
 RKW  H15  H  HCR5  0   0.288  -25.3238  21.7944  -26.3887
 RKW  H16  H  HCR5  0   0.267  -23.1320  22.7474  -25.1138
 RKW  H17  H  HCR6  0   0.260  -21.2442  24.9372  -26.0927
 RKW  N4   N  NH2   0  -0.837  -19.7051  30.1385  -28.9575

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
 RKW  N4   C5   single    1.361  0.020  1.361
 RKW  C5   C6   aromatic  1.403  0.020  1.403
 RKW  C5   N3   aromatic  1.329  0.020  1.329
 RKW  C6   C7   aromatic  1.383  0.020  1.383
 RKW  C10  C11  aromatic  1.383  0.020  1.383
 RKW  C10  C9   aromatic  1.408  0.020  1.408
 RKW  C11  C12  aromatic  1.384  0.020  1.384
 RKW  N3   C4   aromatic  1.329  0.020  1.329
 RKW  C7   C9   single    1.478  0.020  1.478
 RKW  C7   C8   aromatic  1.399  0.020  1.399
 RKW  C9   C16  aromatic  1.390  0.020  1.390
 RKW  C12  O2   aromatic  1.349  0.020  1.349
 RKW  C12  C15  aromatic  1.396  0.020  1.396
 RKW  O2   C13  aromatic  1.359  0.020  1.359
 RKW  C4   C8   aromatic  1.388  0.020  1.388
 RKW  C4   N2   single    1.394  0.020  1.394
 RKW  C16  C15  aromatic  1.393  0.020  1.393
 RKW  C15  C14  aromatic  1.438  0.020  1.438
 RKW  N2   C3   single    1.360  0.020  1.360
 RKW  C13  C14  aromatic  1.347  0.020  1.347
 RKW  C3   C2   single    1.529  0.020  1.529
 RKW  C3   O1   double    1.216  0.020  1.216
 RKW  C2   N1   single    1.434  0.020  1.434
 RKW  N1   C1   single    1.450  0.020  1.450
 RKW  C1   H1   single    0.970  0.020  1.090
 RKW  C1   H2   single    0.970  0.020  1.090
 RKW  C1   H3   single    0.970  0.020  1.090
 RKW  N1   H4   single    0.890  0.020  1.040
 RKW  C2   H6   single    0.970  0.020  1.090
 RKW  C2   H7   single    0.970  0.020  1.090
 RKW  N2   H8   single    0.860  0.020  1.020
 RKW  N4   H9   single    0.890  0.020  1.040
 RKW  N4   H10  single    0.890  0.020  1.040
 RKW  C6   H11  single    0.930  0.020  1.080
 RKW  C8   H12  single    0.930  0.020  1.080
 RKW  C10  H13  single    0.930  0.020  1.080
 RKW  C11  H14  single    0.930  0.020  1.080
 RKW  C13  H15  single    0.930  0.020  1.080
 RKW  C14  H16  single    0.930  0.020  1.080
 RKW  C16  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
 RKW  H3   C1   H2   107.57  3.000
 RKW  H3   C1   H1   107.63  3.000
 RKW  H2   C1   H1   107.33  3.000
 RKW  H3   C1   N1   115.11  3.000
 RKW  H2   C1   N1   109.55  3.000
 RKW  H1   C1   N1   109.36  3.000
 RKW  H4   N1   C2   110.00  3.000
 RKW  H4   N1   C1   110.19  3.000
 RKW  C2   N1   C1   114.21  3.000
 RKW  H7   C2   H6   105.87  3.000
 RKW  H7   C2   C3   109.87  3.000
 RKW  H6   C2   C3   106.63  3.000
 RKW  H7   C2   N1   109.26  3.000
 RKW  H6   C2   N1   109.43  3.000
 RKW  C3   C2   N1   115.34  3.000
 RKW  H8   N2   C4   112.88  3.000
 RKW  H8   N2   C3   117.21  3.000
 RKW  C4   N2   C3   129.90  3.000
 RKW  C13  O2   C12  106.61  3.000
 RKW  N2   C3   C2   113.68  3.000
 RKW  C2   C3   O1   121.98  3.000
 RKW  N2   C3   O1   124.30  3.000
 RKW  C5   N3   C4   118.88  3.000
 RKW  C8   C4   N3   123.58  3.000
 RKW  C8   C4   N2   124.15  3.000
 RKW  N3   C4   N2   112.28  3.000
 RKW  C6   C5   N4   120.91  3.000
 RKW  C6   C5   N3   122.16  3.000
 RKW  N4   C5   N3   116.88  3.000
 RKW  H11  C6   C7   121.54  3.000
 RKW  H11  C6   C5   119.92  3.000
 RKW  C7   C6   C5   118.53  3.000
 RKW  C9   C7   C8   119.93  3.000
 RKW  C8   C7   C6   119.34  3.000
 RKW  C9   C7   C6   120.73  3.000
 RKW  H12  C8   C7   121.06  3.000
 RKW  H12  C8   C4   121.40  3.000
 RKW  C7   C8   C4   117.52  3.000
 RKW  C16  C9   C10  119.83  3.000
 RKW  C16  C9   C7   120.13  3.000
 RKW  C10  C9   C7   120.04  3.000
 RKW  H13  C10  C11  118.64  3.000
 RKW  H13  C10  C9   119.21  3.000
 RKW  C11  C10  C9   122.14  3.000
 RKW  H14  C11  C12  122.17  3.000
 RKW  H14  C11  C10  121.28  3.000
 RKW  C12  C11  C10  116.55  3.000
 RKW  C15  C12  C11  123.11  3.000
 RKW  C15  C12  O2   110.22  3.000
 RKW  C11  C12  O2   126.67  3.000
 RKW  H15  C13  C14  131.95  3.000
 RKW  H15  C13  O2   115.91  3.000
 RKW  C14  C13  O2   112.13  3.000
 RKW  H16  C14  C15  127.87  3.000
 RKW  H16  C14  C13  126.42  3.000
 RKW  C15  C14  C13  105.71  3.000
 RKW  C16  C15  C14  135.29  3.000
 RKW  C14  C15  C12  105.32  3.000
 RKW  C16  C15  C12  119.39  3.000
 RKW  H17  C16  C15  120.14  3.000
 RKW  H17  C16  C9   120.87  3.000
 RKW  C15  C16  C9   118.98  3.000
 RKW  H10  N4   H9   114.60  3.000
 RKW  H10  N4   C5   117.95  3.000
 RKW  H9   N4   C5   116.72  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
 RKW  CONST_01  C10  C11  C12  O2   180.00   0.0  0
 RKW  CONST_02  C16  C15  C12  O2   180.00   0.0  0
 RKW  CONST_03  C14  C15  C12  O2     0.00   0.0  0
 RKW  CONST_04  C15  C14  C13  O2     0.00   0.0  0
 RKW  CONST_05  C7   C6   C5   N3     0.00   0.0  0
 RKW  CONST_06  C7   C8   C4   N3     0.00   0.0  0
 RKW  CONST_07  C6   C5   N3   C4     0.00   0.0  0
 RKW  CONST_08  C6   C7   C8   C4     0.00   0.0  0
 RKW  CONST_09  C9   C7   C8   C4   180.00   0.0  0
 RKW  CONST_10  C9   C7   C6   C5   180.00   0.0  0
 RKW  CONST_11  C8   C7   C6   C5     0.00   0.0  0
 RKW  CONST_12  C8   C4   N3   C5     0.00   0.0  0
 RKW  CONST_15  C11  C10  C9   C7   180.00   0.0  0
 RKW  CONST_16  C15  C16  C9   C7   180.00   0.0  0
 RKW  CONST_19  C12  C11  C10  C9     0.00   0.0  0
 RKW  CONST_20  C12  C15  C16  C9     0.00   0.0  0
 RKW  CONST_21  C14  C15  C16  C9   180.00   0.0  0
 RKW  CONST_22  C15  C12  C11  C10    0.00   0.0  0
 RKW  CONST_23  C15  C16  C9   C10    0.00   0.0  0
 RKW  CONST_24  C16  C9   C10  C11    0.00   0.0  0
 RKW  CONST_25  C13  O2   C12  C11  180.00   0.0  0
 RKW  CONST_26  C16  C15  C12  C11    0.00   0.0  0
 RKW  CONST_27  C14  C15  C12  C11  180.00   0.0  0
 RKW  CONST_28  C14  C13  O2   C12    0.00   0.0  0
 RKW  CONST_29  C13  C14  C15  C12    0.00   0.0  0
 RKW  CONST_30  C15  C12  O2   C13    0.00   0.0  0
 RKW  CONST_31  C16  C15  C14  C13  180.00   0.0  0
 RKW  CONST_32  C5   N3   C4   N2   180.00   0.0  0
 RKW  CONST_33  C7   C8   C4   N2   180.00   0.0  0
 RKW  CONST_34  N4   C5   N3   C4   180.00   0.0  0
 RKW  CONST_35  C7   C6   C5   N4   180.00   0.0  0
 RKW  CONST_36  H14  C11  C12  O2     0.00   0.0  0
 RKW  CONST_37  H16  C14  C13  O2   180.00   0.0  0
 RKW  CONST_38  H11  C6   C5   N3   180.00   0.0  0
 RKW  CONST_39  H12  C8   C4   N3   180.00   0.0  0
 RKW  CONST_40  H13  C10  C9   C7     0.00   0.0  0
 RKW  CONST_41  H17  C16  C9   C7     0.00   0.0  0
 RKW  CONST_42  H15  C13  O2   C12  180.00   0.0  0
 RKW  CONST_43  N3   C4   N2   C3   180.00   0.0  0
 RKW  CONST_44  C8   C4   N2   C3     0.00   0.0  0
 RKW  CONST_47  H8   N2   C4   N3     0.00   0.0  0
 RKW  CONST_48  C4   N2   C3   O1     0.00   0.0  0
 RKW  CONST_49  C4   N2   C3   C2   180.00   0.0  0
 RKW  Var_01    C3   C2   N1   C1   -69.00  30.0  1
 RKW  Var_02    N2   C3   C2   N1   161.65  30.0  2
 RKW  Var_03    H1   C1   N1   C2   179.91  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
 RKW  plan-1  N2   0.020
 RKW  plan-1  N3   0.020
 RKW  plan-1  C4   0.020
 RKW  plan-1  C5   0.020
 RKW  plan-1  C6   0.020
 RKW  plan-1  C7   0.020
 RKW  plan-1  C8   0.020
 RKW  plan-1  C9   0.020
 RKW  plan-1  H11  0.020
 RKW  plan-1  H12  0.020
 RKW  plan-1  N4   0.020
 RKW  plan-2  O2   0.020
 RKW  plan-2  C7   0.020
 RKW  plan-2  C9   0.020
 RKW  plan-2  C10  0.020
 RKW  plan-2  C11  0.020
 RKW  plan-2  C12  0.020
 RKW  plan-2  C13  0.020
 RKW  plan-2  C14  0.020
 RKW  plan-2  C15  0.020
 RKW  plan-2  C16  0.020
 RKW  plan-2  H13  0.020
 RKW  plan-2  H14  0.020
 RKW  plan-2  H15  0.020
 RKW  plan-2  H16  0.020
 RKW  plan-2  H17  0.020
 RKW  plan-3  O1   0.020
 RKW  plan-3  C2   0.020
 RKW  plan-3  N2   0.020
 RKW  plan-3  C3   0.020
 RKW  plan-3  C4   0.020
 RKW  plan-3  H8   0.020
 RKW  plan-4  C5   0.020
 RKW  plan-4  H9   0.020
 RKW  plan-4  H10  0.020
 RKW  plan-4  N4   0.020

