# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:32:08 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-[(2-carbamoylphenyl)amino]-6-[(5-fluoropyridin-2-yl)amino]-N-methylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cnc(Nc2ccc(F)cn2)cc1Nc3ccccc3C(N)=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
 L8Y  L8Y  4-[(2-carbamoylphenyl)amino]-6-[(5-fluoropyridin-2-yl)amino]-N-methylpyridine-3-carboxamide  ligand  45  28  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L8Y
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
 L8Y  C13  C  CR16  0  -0.350  -4.4918  -0.3962   0.2996
 L8Y  C18  C  CR6   0  -0.111   3.8496   1.6176   0.2170
 L8Y  C17  C  CR16  0  -0.269   4.3842   2.8715  -0.0741
 L8Y  C16  C  CR16  0  -0.258   3.8254   3.6809  -1.0490
 L8Y  C15  C  CR16  0  -0.250   2.7324   3.2188  -1.7688
 L8Y  C19  C  C     0   0.453   4.4186   0.8262   1.3565
 L8Y  C11  C  CR6   0   0.412  -6.4680   0.9049   0.5230
 L8Y  C12  C  CR16  0  -0.297  -5.8637  -0.3346   0.4575
 L8Y  C1   C  CR6   0  -0.254   0.5943  -1.8765  -0.1446
 L8Y  C2   C  CR16  0  -0.068  -0.7467  -2.1870   0.0047
 L8Y  N1   N  N     0  -0.495  -1.7410  -1.3155   0.0701
 L8Y  C3   C  CR6   0   0.581  -1.4192  -0.0267  -0.0014
 L8Y  C4   C  CR16  0  -0.513  -0.1036   0.4251  -0.1196
 L8Y  C5   C  CR6   0   0.487   0.9378  -0.4936  -0.1902
 L8Y  N2   N  NH1   0  -0.798   2.2420  -0.1266  -0.2919
 L8Y  N4   N  NH1   0  -0.634   1.2456  -4.1373  -0.6576
 L8Y  O1   O  O     0  -0.516   2.7909  -2.7315   0.1563
 L8Y  C7   C  CH3   0  -0.513   2.1560  -5.2573  -0.7196
 L8Y  C8   C  CR6   0   0.328   2.7409   1.1576  -0.5069
 L8Y  C9   C  CR6   0   0.461  -3.7789   0.8064   0.2171
 L8Y  N5   N  N     0  -0.446  -4.3849   1.9890   0.2807
 L8Y  C10  C  CR16  0  -0.200  -5.6990   2.0454   0.4295
 L8Y  F1   F  F     0  -0.308  -7.7972   1.0080   0.6751
 L8Y  C14  C  CR16  0  -0.304   2.2078   1.9634  -1.5138
 L8Y  N6   N  NH2   0  -0.791   5.7581   0.7731   1.3945
 L8Y  O2   O  O     0  -0.469   3.7025   0.3025   2.1967
 L8Y  H11  H  HCR6  0   0.303  -3.9843  -1.3442   0.2408
 L8Y  H15  H  HCR6  0   0.269   5.2325   3.2334   0.4932
 L8Y  H14  H  HCR6  0   0.263   4.2402   4.6600  -1.2459
 L8Y  H13  H  HCR6  0   0.266   2.2945   3.8283  -2.5483
 L8Y  H10  H  HCR6  0   0.296  -6.4488  -1.2425   0.5274
 L8Y  H1   H  HCR6  0   0.264  -1.0496  -3.2247   0.1000
 L8Y  H2   H  HCR6  0   0.294   0.0904   1.4887  -0.1291
 L8Y  H3   H  HNH1  0   0.421   2.8911  -0.8594  -0.0263
 L8Y  H4   H  HNH1  0   0.409  -2.1043   1.8764  -0.0026
 L8Y  H5   H  HNH1  0   0.411   0.3425  -4.2457  -1.0860
 L8Y  H6   H  HCH3  0   0.252   1.6093  -6.1189  -1.0912
 L8Y  H7   H  HCH3  0   0.239   2.9940  -5.0644  -1.3904
 L8Y  H8   H  HCH3  0   0.242   2.5531  -5.5023   0.2650
 L8Y  H9   H  HCR6  0   0.283  -6.1532   3.0293   0.4768
 L8Y  H12  H  HCR6  0   0.285   1.3861   1.5946  -2.1134
 L8Y  H16  H  HNH2  0   0.413   6.3279   1.1045   0.6352
 L8Y  H17  H  HNH2  0   0.406   6.2219   0.2774   2.1389
 L8Y  N3   N  NH1   0  -0.754  -2.4097   0.9163   0.0580
 L8Y  C6   C  C     0   0.560   1.6283  -2.9374  -0.2020

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
 L8Y  N6   C19  single    1.341  0.020  1.341
 L8Y  C17  C16  aromatic  1.385  0.020  1.385
 L8Y  C17  C18  aromatic  1.394  0.020  1.394
 L8Y  C16  C15  aromatic  1.388  0.020  1.388
 L8Y  C19  C18  single    1.500  0.020  1.500
 L8Y  C19  O2   double    1.222  0.020  1.222
 L8Y  C18  C8   aromatic  1.402  0.020  1.402
 L8Y  C15  C14  aromatic  1.384  0.020  1.384
 L8Y  C8   C14  aromatic  1.395  0.020  1.395
 L8Y  C8   N2   single    1.394  0.020  1.394
 L8Y  N2   C5   single    1.359  0.020  1.359
 L8Y  O1   C6   double    1.234  0.020  1.234
 L8Y  C5   C4   aromatic  1.390  0.020  1.390
 L8Y  C5   C1   aromatic  1.426  0.020  1.426
 L8Y  C10  N5   aromatic  1.324  0.020  1.324
 L8Y  C10  C11  aromatic  1.379  0.020  1.379
 L8Y  F1   C11  single    1.342  0.020  1.342
 L8Y  C4   C3   aromatic  1.396  0.020  1.396
 L8Y  C6   C1   single    1.483  0.020  1.483
 L8Y  C6   N4   single    1.339  0.020  1.339
 L8Y  N5   C9   aromatic  1.330  0.020  1.330
 L8Y  C11  C12  aromatic  1.381  0.020  1.381
 L8Y  C1   C2   aromatic  1.384  0.020  1.384
 L8Y  C7   N4   single    1.445  0.020  1.445
 L8Y  C3   N3   single    1.369  0.020  1.369
 L8Y  C3   N1   aromatic  1.330  0.020  1.330
 L8Y  C9   N3   single    1.383  0.020  1.383
 L8Y  C9   C13  aromatic  1.400  0.020  1.400
 L8Y  C12  C13  aromatic  1.382  0.020  1.382
 L8Y  C2   N1   aromatic  1.324  0.020  1.324
 L8Y  C13  H11  single    0.930  0.020  1.080
 L8Y  C17  H15  single    0.930  0.020  1.080
 L8Y  C16  H14  single    0.930  0.020  1.080
 L8Y  C15  H13  single    0.930  0.020  1.080
 L8Y  C12  H10  single    0.930  0.020  1.080
 L8Y  C2   H1   single    0.930  0.020  1.080
 L8Y  C4   H2   single    0.930  0.020  1.080
 L8Y  N2   H3   single    0.860  0.020  1.020
 L8Y  N3   H4   single    0.860  0.020  1.020
 L8Y  N4   H5   single    0.860  0.020  1.020
 L8Y  C7   H6   single    0.970  0.020  1.090
 L8Y  C7   H7   single    0.970  0.020  1.090
 L8Y  C7   H8   single    0.970  0.020  1.090
 L8Y  C10  H9   single    0.930  0.020  1.080
 L8Y  C14  H12  single    0.930  0.020  1.080
 L8Y  N6   H16  single    0.860  0.020  1.020
 L8Y  N6   H17  single    0.860  0.020  1.020

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
 L8Y  H11  C13  C9   120.86  3.000
 L8Y  H11  C13  C12  120.87  3.000
 L8Y  C9   C13  C12  118.28  3.000
 L8Y  C8   C18  C19  121.29  3.000
 L8Y  C8   C18  C17  119.39  3.000
 L8Y  C19  C18  C17  119.20  3.000
 L8Y  H15  C17  C16  119.32  3.000
 L8Y  H15  C17  C18  119.45  3.000
 L8Y  C16  C17  C18  121.20  3.000
 L8Y  H14  C16  C15  120.61  3.000
 L8Y  H14  C16  C17  120.17  3.000
 L8Y  C15  C16  C17  119.22  3.000
 L8Y  H13  C15  C14  119.36  3.000
 L8Y  H13  C15  C16  120.31  3.000
 L8Y  C14  C15  C16  120.32  3.000
 L8Y  O2   C19  N6   123.29  3.000
 L8Y  O2   C19  C18  121.76  3.000
 L8Y  N6   C19  C18  114.93  3.000
 L8Y  F1   C11  C10  119.78  3.000
 L8Y  F1   C11  C12  120.53  3.000
 L8Y  C10  C11  C12  119.69  3.000
 L8Y  H10  C12  C11  120.89  3.000
 L8Y  H10  C12  C13  120.43  3.000
 L8Y  C11  C12  C13  118.67  3.000
 L8Y  C6   C1   C5   121.66  3.000
 L8Y  C6   C1   C2   121.28  3.000
 L8Y  C5   C1   C2   117.02  3.000
 L8Y  H1   C2   N1   114.55  3.000
 L8Y  H1   C2   C1   119.62  3.000
 L8Y  N1   C2   C1   125.82  3.000
 L8Y  C3   N1   C2   116.96  3.000
 L8Y  N3   C3   C4   117.56  3.000
 L8Y  N3   C3   N1   119.34  3.000
 L8Y  C4   C3   N1   123.10  3.000
 L8Y  H2   C4   C5   121.01  3.000
 L8Y  H2   C4   C3   119.22  3.000
 L8Y  C5   C4   C3   119.75  3.000
 L8Y  N2   C5   C4   122.97  3.000
 L8Y  C4   C5   C1   117.31  3.000
 L8Y  N2   C5   C1   119.72  3.000
 L8Y  H3   N2   C8   118.48  3.000
 L8Y  H3   N2   C5   113.55  3.000
 L8Y  C8   N2   C5   127.14  3.000
 L8Y  H5   N4   C7   117.66  3.000
 L8Y  H5   N4   C6   119.88  3.000
 L8Y  C7   N4   C6   121.94  3.000
 L8Y  H8   C7   H7   108.39  3.000
 L8Y  H8   C7   H6   108.32  3.000
 L8Y  H7   C7   H6   108.46  3.000
 L8Y  H8   C7   N4   111.43  3.000
 L8Y  H7   C7   N4   111.93  3.000
 L8Y  H6   C7   N4   108.21  3.000
 L8Y  C14  C8   N2   120.42  3.000
 L8Y  N2   C8   C18  120.37  3.000
 L8Y  C14  C8   C18  119.04  3.000
 L8Y  N5   C9   N3   112.70  3.000
 L8Y  N3   C9   C13  125.39  3.000
 L8Y  N5   C9   C13  121.91  3.000
 L8Y  C10  N5   C9   119.70  3.000
 L8Y  H9   C10  N5   117.33  3.000
 L8Y  H9   C10  C11  120.92  3.000
 L8Y  N5   C10  C11  121.75  3.000
 L8Y  H12  C14  C8   119.55  3.000
 L8Y  H12  C14  C15  119.66  3.000
 L8Y  C8   C14  C15  120.78  3.000
 L8Y  H17  N6   H16  117.34  3.000
 L8Y  H17  N6   C19  120.01  3.000
 L8Y  H16  N6   C19  122.11  3.000
 L8Y  H4   N3   C9   112.47  3.000
 L8Y  H4   N3   C3   115.70  3.000
 L8Y  C9   N3   C3   131.81  3.000
 L8Y  O1   C6   N4   121.17  3.000
 L8Y  N4   C6   C1   117.06  3.000
 L8Y  O1   C6   C1   121.77  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
 L8Y  CONST_01  C10  N5   C9   C13     0.00   0.0  0
 L8Y  CONST_02  C10  C11  C12  C13     0.00   0.0  0
 L8Y  CONST_03  C15  C16  C17  C18     0.00   0.0  0
 L8Y  CONST_04  C15  C14  C8   C18     0.00   0.0  0
 L8Y  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 L8Y  CONST_06  C14  C8   C18  C17     0.00   0.0  0
 L8Y  CONST_07  C8   C18  C17  C16     0.00   0.0  0
 L8Y  CONST_08  C8   C14  C15  C16     0.00   0.0  0
 L8Y  CONST_09  C9   N5   C10  C11     0.00   0.0  0
 L8Y  CONST_10  C9   C13  C12  C11     0.00   0.0  0
 L8Y  CONST_11  N5   C10  C11  C12     0.00   0.0  0
 L8Y  CONST_12  N5   C9   C13  C12     0.00   0.0  0
 L8Y  CONST_13  C3   C4   C5   C1      0.00   0.0  0
 L8Y  CONST_14  C3   N1   C2   C1      0.00   0.0  0
 L8Y  CONST_15  C4   C5   C1   C2      0.00   0.0  0
 L8Y  CONST_16  C4   C3   N1   C2      0.00   0.0  0
 L8Y  CONST_17  C5   C4   C3   N1      0.00   0.0  0
 L8Y  CONST_18  C5   C1   C2   N1      0.00   0.0  0
 L8Y  CONST_19  F1   C11  C12  C13   180.00   0.0  0
 L8Y  CONST_20  N2   C8   C18  C17   180.00   0.0  0
 L8Y  CONST_21  C19  C18  C17  C16   180.00   0.0  0
 L8Y  CONST_22  N2   C8   C14  C15   180.00   0.0  0
 L8Y  CONST_23  C14  C8   C18  C19   180.00   0.0  0
 L8Y  CONST_24  N3   C9   C13  C12   180.00   0.0  0
 L8Y  CONST_25  N2   C5   C1   C2    180.00   0.0  0
 L8Y  CONST_26  N3   C3   N1   C2    180.00   0.0  0
 L8Y  CONST_27  C6   C1   C2   N1    180.00   0.0  0
 L8Y  CONST_28  N2   C5   C4   C3    180.00   0.0  0
 L8Y  CONST_29  C6   C1   C5   C4    180.00   0.0  0
 L8Y  CONST_30  N3   C3   C4   C5    180.00   0.0  0
 L8Y  CONST_31  C10  N5   C9   N3    180.00   0.0  0
 L8Y  CONST_32  F1   C11  C10  N5    180.00   0.0  0
 L8Y  CONST_33  H14  C16  C17  C18   180.00   0.0  0
 L8Y  CONST_34  H12  C14  C8   C18   180.00   0.0  0
 L8Y  CONST_35  H13  C15  C16  C17   180.00   0.0  0
 L8Y  CONST_36  H15  C17  C16  C15   180.00   0.0  0
 L8Y  CONST_37  H11  C13  C12  C11   180.00   0.0  0
 L8Y  CONST_38  H9   C10  C11  C12   180.00   0.0  0
 L8Y  CONST_39  H2   C4   C5   C1    180.00   0.0  0
 L8Y  CONST_40  H1   C2   N1   C3    180.00   0.0  0
 L8Y  CONST_41  H10  C12  C13  C9    180.00   0.0  0
 L8Y  CONST_42  C7   N4   C6   C1    180.00   0.0  0
 L8Y  CONST_43  H16  N6   C19  C18     0.00   0.0  0
 L8Y  CONST_44  H17  N6   C19  C18   180.00   0.0  0
 L8Y  CONST_45  H5   N4   C6   C1      0.00   0.0  0
 L8Y  CONST_46  C7   N4   C6   O1      0.00   0.0  0
 L8Y  Var_01    C3   N3   C9   C13    -3.13  30.0  2
 L8Y  Var_02    C5   N2   C8   C18   137.12  30.0  2
 L8Y  Var_03    C8   N2   C5   C1    171.78  30.0  3
 L8Y  Var_04    C9   N3   C3   N1      1.70  30.0  2
 L8Y  Var_05    N6   C19  C18  C17   -46.27  30.0  2
 L8Y  Var_06    O1   C6   C1   C2   -152.65  30.0  2
 L8Y  Var_07    H6   C7   N4   C6    178.27  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
 L8Y  plan-1  C18  0.020
 L8Y  plan-1  C17  0.020
 L8Y  plan-1  C16  0.020
 L8Y  plan-1  C15  0.020
 L8Y  plan-1  C19  0.020
 L8Y  plan-1  N2   0.020
 L8Y  plan-1  C8   0.020
 L8Y  plan-1  C14  0.020
 L8Y  plan-1  H15  0.020
 L8Y  plan-1  H14  0.020
 L8Y  plan-1  H13  0.020
 L8Y  plan-1  H12  0.020
 L8Y  plan-2  C1   0.020
 L8Y  plan-2  C2   0.020
 L8Y  plan-2  N1   0.020
 L8Y  plan-2  C3   0.020
 L8Y  plan-2  C4   0.020
 L8Y  plan-2  C5   0.020
 L8Y  plan-2  N2   0.020
 L8Y  plan-2  H1   0.020
 L8Y  plan-2  H2   0.020
 L8Y  plan-2  N3   0.020
 L8Y  plan-2  C6   0.020
 L8Y  plan-3  C13  0.020
 L8Y  plan-3  C11  0.020
 L8Y  plan-3  C12  0.020
 L8Y  plan-3  C9   0.020
 L8Y  plan-3  N5   0.020
 L8Y  plan-3  C10  0.020
 L8Y  plan-3  F1   0.020
 L8Y  plan-3  H11  0.020
 L8Y  plan-3  H10  0.020
 L8Y  plan-3  H9   0.020
 L8Y  plan-3  N3   0.020
 L8Y  plan-4  C18  0.020
 L8Y  plan-4  C19  0.020
 L8Y  plan-4  N6   0.020
 L8Y  plan-4  O2   0.020
 L8Y  plan-4  H16  0.020
 L8Y  plan-4  H17  0.020
 L8Y  plan-5  C1   0.020
 L8Y  plan-5  N4   0.020
 L8Y  plan-5  O1   0.020
 L8Y  plan-5  C7   0.020
 L8Y  plan-5  H5   0.020
 L8Y  plan-5  C6   0.020

