# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:00:19 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: ~{N}-[8-oxidanyl-4-(pyridin-2-ylamino)quinolin-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(Nc2ccccn2)c3cccc(O)c3n1
#
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
 EC9  EC9  ~{N}-[8-oxidanyl-4-(pyridin-2-ylamino)quinolin-2-yl]ethanamide  ligand  36  22  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EC9
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
 EC9  C1   C  CR16  0  -0.366  10.5241   -5.1679   1.2726
 EC9  C14  C  CR6   0   0.560   8.3825   -7.8792  -1.1488
 EC9  C15  C  CR16  0  -0.427   7.0557   -7.9374  -0.6921
 EC9  C16  C  CR16  0  -0.136   6.1551   -8.7031  -1.3975
 EC9  C17  C  CR16  0  -0.363   6.5819   -9.3937  -2.5305
 EC9  C18  C  CR16  0  -0.039   7.9079   -9.2697  -2.8913
 EC9  C19  C  C     0   0.511  13.4148   -8.7664  -3.4243
 EC9  C2   C  CR16  0  -0.243  11.1868   -4.2596   2.0534
 EC9  C21  C  CH3   0  -0.782  14.6422   -9.1027  -4.2319
 EC9  C3   C  CR16  0  -0.402  12.5599   -4.0271   1.8838
 EC9  C4   C  CR6   0   0.313  13.2627   -4.7135   0.9246
 EC9  C5   C  CR66  0   0.108  12.6034   -5.6683   0.0965
 EC9  C6   C  CR66  0   0.017  11.2198   -5.8921   0.2790
 EC9  C7   C  CR6   0   0.469  10.6076   -6.8608  -0.5920
 EC9  C8   C  CR16  0  -0.489  11.3904   -7.5027  -1.5290
 EC9  C9   C  CR6   0   0.475  12.7599   -7.1846  -1.5932
 EC9  N10  N  N     0  -0.491  13.3506   -6.3074  -0.8242
 EC9  N12  N  NH1   0  -0.709  13.6287   -7.7847  -2.5017
 EC9  N13  N  NH1   0  -0.798   9.2668   -7.0945  -0.4331
 EC9  N22  N  N     0  -0.466   8.7914   -8.5317  -2.2225
 EC9  O11  O  OH1   0  -0.611  14.5757   -4.5409   0.7043
 EC9  O20  O  O     0  -0.458  12.3414   -9.3084  -3.6055
 EC9  H1   H  HCR6  0   0.247   9.4649   -5.3032   1.4457
 EC9  H2   H  HCR6  0   0.281   6.7507   -7.3941   0.1936
 EC9  H3   H  HCR6  0   0.276   5.1261   -8.7646  -1.0690
 EC9  H4   H  HCR6  0   0.269   5.9067  -10.0083  -3.1082
 EC9  H5   H  HCR6  0   0.263   8.2909   -9.7871  -3.7635
 EC9  H6   H  HCR6  0   0.265  10.6477   -3.7093   2.8127
 EC9  H7   H  HCH3  0   0.268  14.5203  -10.0715  -4.7090
 EC9  H8   H  HCH3  0   0.278  14.7804   -8.3527  -5.0132
 EC9  H9   H  HCH3  0   0.263  15.5471   -9.1158  -3.6255
 EC9  H10  H  HCR6  0   0.274  13.0635   -3.3018   2.5126
 EC9  H11  H  HCR6  0   0.334  10.9584   -8.2258  -2.1945
 EC9  H12  H  HNH1  0   0.407  14.5679   -7.4190  -2.4353
 EC9  H13  H  HNH1  0   0.427   8.8313   -6.6225   0.3404
 EC9  H14  H  HOH1  0   0.476  14.9221   -3.8707   1.3046

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
 EC9  C21  C19  single    1.507  0.020  1.507
 EC9  C19  O20  double    1.216  0.020  1.216
 EC9  C19  N12  single    1.364  0.020  1.364
 EC9  C18  C17  aromatic  1.380  0.020  1.380
 EC9  C18  N22  aromatic  1.331  0.020  1.331
 EC9  C17  C16  aromatic  1.394  0.020  1.394
 EC9  N12  C9   single    1.393  0.020  1.393
 EC9  N22  C14  aromatic  1.321  0.020  1.321
 EC9  C9   C8   aromatic  1.407  0.020  1.407
 EC9  C9   N10  aromatic  1.308  0.020  1.308
 EC9  C16  C15  aromatic  1.377  0.020  1.377
 EC9  C8   C7   aromatic  1.379  0.020  1.379
 EC9  C14  C15  aromatic  1.404  0.020  1.404
 EC9  C14  N13  single    1.382  0.020  1.382
 EC9  N10  C5   aromatic  1.347  0.020  1.347
 EC9  C7   N13  single    1.370  0.020  1.370
 EC9  C7   C6   aromatic  1.439  0.020  1.439
 EC9  C5   C6   aromatic  1.413  0.020  1.413
 EC9  C5   C4   aromatic  1.425  0.020  1.425
 EC9  C6   C1   aromatic  1.413  0.020  1.413
 EC9  O11  C4   single    1.342  0.020  1.342
 EC9  C4   C3   aromatic  1.373  0.020  1.373
 EC9  C1   C2   aromatic  1.369  0.020  1.369
 EC9  C3   C2   aromatic  1.403  0.020  1.403
 EC9  C1   H1   single    0.930  0.020  1.080
 EC9  C15  H2   single    0.930  0.020  1.080
 EC9  C16  H3   single    0.930  0.020  1.080
 EC9  C17  H4   single    0.930  0.020  1.080
 EC9  C18  H5   single    0.930  0.020  1.080
 EC9  C2   H6   single    0.930  0.020  1.080
 EC9  C21  H7   single    0.970  0.020  1.090
 EC9  C21  H8   single    0.970  0.020  1.090
 EC9  C21  H9   single    0.970  0.020  1.090
 EC9  C3   H10  single    0.930  0.020  1.080
 EC9  C8   H11  single    0.930  0.020  1.080
 EC9  N12  H12  single    0.860  0.020  1.020
 EC9  N13  H13  single    0.860  0.020  1.020
 EC9  O11  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
 EC9  H1   C1   C6   122.05  3.000
 EC9  H1   C1   C2   117.75  3.000
 EC9  C6   C1   C2   120.20  3.000
 EC9  N22  C14  N13  120.21  3.000
 EC9  N13  C14  C15  117.36  3.000
 EC9  N22  C14  C15  122.43  3.000
 EC9  H2   C15  C16  120.93  3.000
 EC9  H2   C15  C14  120.74  3.000
 EC9  C16  C15  C14  118.32  3.000
 EC9  H3   C16  C17  120.66  3.000
 EC9  H3   C16  C15  119.88  3.000
 EC9  C17  C16  C15  119.46  3.000
 EC9  H4   C17  C18  120.78  3.000
 EC9  H4   C17  C16  121.68  3.000
 EC9  C18  C17  C16  117.53  3.000
 EC9  H5   C18  N22  115.73  3.000
 EC9  H5   C18  C17  120.47  3.000
 EC9  N22  C18  C17  123.80  3.000
 EC9  O20  C19  N12  124.05  3.000
 EC9  N12  C19  C21  113.29  3.000
 EC9  O20  C19  C21  122.65  3.000
 EC9  H6   C2   C3   119.23  3.000
 EC9  H6   C2   C1   119.78  3.000
 EC9  C3   C2   C1   120.98  3.000
 EC9  H9   C21  H8   107.55  3.000
 EC9  H9   C21  H7   109.08  3.000
 EC9  H8   C21  H7   108.21  3.000
 EC9  H9   C21  C19  112.38  3.000
 EC9  H8   C21  C19  109.47  3.000
 EC9  H7   C21  C19  110.04  3.000
 EC9  H10  C3   C4   120.13  3.000
 EC9  H10  C3   C2   119.70  3.000
 EC9  C4   C3   C2   120.17  3.000
 EC9  O11  C4   C5   116.30  3.000
 EC9  O11  C4   C3   123.43  3.000
 EC9  C5   C4   C3   120.26  3.000
 EC9  N10  C5   C6   123.79  3.000
 EC9  C6   C5   C4   118.93  3.000
 EC9  N10  C5   C4   117.28  3.000
 EC9  C7   C6   C5   116.41  3.000
 EC9  C5   C6   C1   119.45  3.000
 EC9  C7   C6   C1   124.14  3.000
 EC9  N13  C7   C8   123.69  3.000
 EC9  N13  C7   C6   117.44  3.000
 EC9  C8   C7   C6   118.88  3.000
 EC9  H11  C8   C9   121.03  3.000
 EC9  H11  C8   C7   120.41  3.000
 EC9  C9   C8   C7   118.56  3.000
 EC9  N12  C9   N10  113.01  3.000
 EC9  N10  C9   C8   124.36  3.000
 EC9  N12  C9   C8   122.63  3.000
 EC9  C9   N10  C5   118.01  3.000
 EC9  H12  N12  C9   112.40  3.000
 EC9  H12  N12  C19  116.79  3.000
 EC9  C9   N12  C19  130.80  3.000
 EC9  H13  N13  C7   115.65  3.000
 EC9  H13  N13  C14  112.82  3.000
 EC9  C7   N13  C14  131.52  3.000
 EC9  C18  N22  C14  118.46  3.000
 EC9  H14  O11  C4   109.80  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
 EC9  CONST_01  C8   C7   C6   C1   180.00   0.0  0
 EC9  CONST_02  N10  C5   C6   C1   180.00   0.0  0
 EC9  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 EC9  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 EC9  CONST_05  C17  C18  N22  C14    0.00   0.0  0
 EC9  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 EC9  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 EC9  CONST_08  C18  N22  C14  C15    0.00   0.0  0
 EC9  CONST_09  N22  C18  C17  C16    0.00   0.0  0
 EC9  CONST_10  N22  C14  C15  C16    0.00   0.0  0
 EC9  CONST_11  C7   C6   C1   C2   180.00   0.0  0
 EC9  CONST_12  C5   C6   C1   C2     0.00   0.0  0
 EC9  CONST_13  C5   C4   C3   C2     0.00   0.0  0
 EC9  CONST_14  N10  C5   C4   C3   180.00   0.0  0
 EC9  CONST_15  C6   C5   C4   C3     0.00   0.0  0
 EC9  CONST_16  C6   C1   C2   C3     0.00   0.0  0
 EC9  CONST_17  C9   N10  C5   C4   180.00   0.0  0
 EC9  CONST_18  C7   C6   C5   C4   180.00   0.0  0
 EC9  CONST_19  C8   C9   N10  C5     0.00   0.0  0
 EC9  CONST_20  C8   C7   C6   C5     0.00   0.0  0
 EC9  CONST_21  C9   C8   C7   C6     0.00   0.0  0
 EC9  CONST_22  C9   N10  C5   C6     0.00   0.0  0
 EC9  CONST_23  N10  C9   C8   C7     0.00   0.0  0
 EC9  CONST_24  N10  C5   C6   C7     0.00   0.0  0
 EC9  CONST_25  N13  C7   C6   C1     0.00   0.0  0
 EC9  CONST_26  N13  C14  C15  C16  180.00   0.0  0
 EC9  CONST_27  N13  C14  N22  C18  180.00   0.0  0
 EC9  CONST_28  O11  C4   C3   C2   180.00   0.0  0
 EC9  CONST_29  N12  C9   N10  C5   180.00   0.0  0
 EC9  CONST_30  N13  C7   C6   C5   180.00   0.0  0
 EC9  CONST_31  O11  C4   C5   C6   180.00   0.0  0
 EC9  CONST_32  N12  C9   C8   C7   180.00   0.0  0
 EC9  CONST_33  N13  C7   C8   C9   180.00   0.0  0
 EC9  CONST_34  O11  C4   C5   N10    0.00   0.0  0
 EC9  CONST_35  H10  C3   C2   C1   180.00   0.0  0
 EC9  CONST_36  H5   C18  N22  C14  180.00   0.0  0
 EC9  CONST_37  H3   C16  C15  C14  180.00   0.0  0
 EC9  CONST_38  H4   C17  C16  C15  180.00   0.0  0
 EC9  CONST_39  H2   C15  C16  C17  180.00   0.0  0
 EC9  CONST_40  H1   C1   C2   C3   180.00   0.0  0
 EC9  CONST_41  H6   C2   C3   C4   180.00   0.0  0
 EC9  CONST_42  H11  C8   C7   C6   180.00   0.0  0
 EC9  CONST_43  C8   C9   N12  C19    0.00   0.0  0
 EC9  CONST_44  N10  C9   N12  C19  180.00   0.0  0
 EC9  CONST_45  H12  N12  C9   C8   180.00   0.0  0
 EC9  CONST_46  C9   N12  C19  C21  180.00   0.0  0
 EC9  CONST_47  O20  C19  N12  C9     0.00   0.0  0
 EC9  Var_01    C8   C7   N13  C14   -5.02  30.0  3
 EC9  Var_02    C7   N13  C14  C15  177.96  30.0  2
 EC9  Var_03    H7   C21  C19  N12  161.98  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
 EC9  plan-1  C14  0.020
 EC9  plan-1  C15  0.020
 EC9  plan-1  C16  0.020
 EC9  plan-1  C17  0.020
 EC9  plan-1  C18  0.020
 EC9  plan-1  N13  0.020
 EC9  plan-1  N22  0.020
 EC9  plan-1  H2   0.020
 EC9  plan-1  H3   0.020
 EC9  plan-1  H4   0.020
 EC9  plan-1  H5   0.020
 EC9  plan-2  C1   0.020
 EC9  plan-2  C2   0.020
 EC9  plan-2  C3   0.020
 EC9  plan-2  C4   0.020
 EC9  plan-2  C5   0.020
 EC9  plan-2  C6   0.020
 EC9  plan-2  C7   0.020
 EC9  plan-2  C8   0.020
 EC9  plan-2  C9   0.020
 EC9  plan-2  N10  0.020
 EC9  plan-2  N12  0.020
 EC9  plan-2  N13  0.020
 EC9  plan-2  O11  0.020
 EC9  plan-2  H1   0.020
 EC9  plan-2  H6   0.020
 EC9  plan-2  H10  0.020
 EC9  plan-2  H11  0.020
 EC9  plan-3  C19  0.020
 EC9  plan-3  C21  0.020
 EC9  plan-3  C9   0.020
 EC9  plan-3  N12  0.020
 EC9  plan-3  O20  0.020
 EC9  plan-3  H12  0.020

