# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:44:26 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1NC2=C(C(=O)NC=C2)C(=O)Nc3ccc(cc3)N4CCN(C)CC4
#
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
 5Q4  5Q4  4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide  ligand  59  32  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5Q4
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
 5Q4  C4   C  CH2   0  -0.307   -6.0213  -1.1520   0.6877
 5Q4  C6   C  CH2   0  -0.314   -6.5214   1.0929  -0.0017
 5Q4  C11  C  CR6   0   0.349   -1.4281   0.9380   0.0367
 5Q4  C7   C  CH2   0  -0.276   -7.8766   0.6167  -0.4912
 5Q4  C8   C  CR6   0   0.351   -4.2042   0.3308   0.0158
 5Q4  C9   C  CR16  0  -0.318   -3.2294  -0.6527  -0.1946
 5Q4  C10  C  CR16  0  -0.301   -1.8751  -0.3675  -0.1830
 5Q4  C12  C  CR16  0  -0.348   -2.3905   1.9224   0.2502
 5Q4  C13  C  CR16  0  -0.346   -3.7447   1.6308   0.2485
 5Q4  N2   N  NT    0  -0.412   -8.3393  -0.5206   0.2748
 5Q4  C3   C  CH2   0  -0.282   -7.3794  -1.6003   0.1866
 5Q4  C1   C  CH3   0  -0.519   -9.6594  -0.9409  -0.1336
 5Q4  N5   N  NT    0  -0.516   -5.5609   0.0109  -0.0567
 5Q4  C15  C  C     0   0.609    1.0270   0.6130   0.1255
 5Q4  O16  O  O     0  -0.532    0.9837  -0.6180   0.2531
 5Q4  C17  C  CR6   0  -0.464    2.3106   1.3470   0.0785
 5Q4  C18  C  CR6   0   0.512    3.5343   0.6433   0.2170
 5Q4  C19  C  CR16  0  -0.453    4.7640   1.3593   0.1087
 5Q4  C20  C  CR16  0   0.062    4.7363   2.6933  -0.0884
 5Q4  N21  N  NR16  0  -0.669    3.5736   3.3640  -0.1770
 5Q4  C23  C  CR6   0   0.577    2.3325   2.7735  -0.1081
 5Q4  O24  O  O     0  -0.533    1.3428   3.5149  -0.2094
 5Q4  N25  N  NH1   0  -0.764    3.5548  -0.6795   0.4288
 5Q4  C26  C  CR6   0   0.201    4.6903  -1.4700   0.6761
 5Q4  C27  C  CR16  0  -0.273    5.5354  -1.2150   1.7460
 5Q4  C28  C  CR16  0  -0.281    6.6409  -2.0202   1.9855
 5Q4  C29  C  CR16  0  -0.246    6.8821  -3.1056   1.1593
 5Q4  C30  C  CR16  0  -0.388    6.0324  -3.3912   0.0973
 5Q4  C31  C  CR6   0   0.347    4.9333  -2.5756  -0.1554
 5Q4  O32  O  O2    0  -0.459    4.0557  -2.7645  -1.1538
 5Q4  C33  C  CH3   0  -0.438    4.2127  -3.8975  -1.9867
 5Q4  H1   H  HCH2  0   0.214   -6.0869  -0.9242   1.7621
 5Q4  H2   H  HCH2  0   0.254   -5.3201  -1.9761   0.5747
 5Q4  H3   H  HCH2  0   0.250   -6.1958   1.9061  -0.6518
 5Q4  H4   H  HCH2  0   0.210   -6.6209   1.5026   1.0155
 5Q4  H5   H  HCH2  0   0.240   -8.5940   1.4345  -0.3897
 5Q4  H6   H  HCH2  0   0.192   -7.8032   0.3811  -1.5675
 5Q4  H7   H  HCR6  0   0.259   -3.5271  -1.6719  -0.4045
 5Q4  H8   H  HCR6  0   0.270   -1.1786  -1.1686  -0.3687
 5Q4  H9   H  HCR6  0   0.260   -2.0803   2.9444   0.4354
 5Q4  H10  H  HCR6  0   0.268   -4.4353   2.4402   0.4396
 5Q4  H12  H  HCH2  0   0.192   -7.2786  -1.9747  -0.8475
 5Q4  H13  H  HCH2  0   0.239   -7.7229  -2.4377   0.7989
 5Q4  H14  H  HCH3  0   0.192   -9.7054  -1.2695  -1.1838
 5Q4  H15  H  HCH3  0   0.234   -9.9963  -1.7712   0.4888
 5Q4  H16  H  HCH3  0   0.234  -10.3682  -0.1207  -0.0105
 5Q4  H17  H  HNH1  0   0.433    0.0792   2.3600  -0.0533
 5Q4  H18  H  HCR6  0   0.297    5.7142   0.8529   0.1624
 5Q4  H19  H  HCR6  0   0.322    5.6350   3.2838  -0.1875
 5Q4  H22  H  HNR6  0   0.425    3.5907   4.3657  -0.3058
 5Q4  H20  H  HNH1  0   0.426    2.6346  -1.1204   0.3864
 5Q4  H21  H  HCR6  0   0.275    5.3231  -0.3795   2.4016
 5Q4  H23  H  HCR6  0   0.259    7.2960  -1.8056   2.8187
 5Q4  H24  H  HCR6  0   0.263    7.7350  -3.7473   1.3366
 5Q4  H25  H  HCR6  0   0.286    6.2432  -4.2461  -0.5311
 5Q4  H26  H  HCH3  0   0.232    5.1514  -3.8657  -2.5452
 5Q4  H27  H  HCH3  0   0.232    4.1711  -4.8296  -1.4182
 5Q4  H28  H  HCH3  0   0.262    3.3847  -3.8773  -2.6903
 5Q4  N14  N  NH1   0  -0.786   -0.0929   1.3547   0.0164

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
 5Q4  C33  O32  single    1.415  0.020  1.415
 5Q4  O32  C31  single    1.343  0.020  1.343
 5Q4  C30  C31  aromatic  1.392  0.020  1.392
 5Q4  C30  C29  aromatic  1.390  0.020  1.390
 5Q4  C31  C26  aromatic  1.404  0.020  1.404
 5Q4  C19  C20  double    1.349  0.020  1.349
 5Q4  C19  C18  single    1.427  0.020  1.427
 5Q4  C20  N21  single    1.345  0.020  1.345
 5Q4  C29  C28  aromatic  1.385  0.020  1.385
 5Q4  C26  N25  single    1.405  0.020  1.405
 5Q4  C26  C27  aromatic  1.387  0.020  1.387
 5Q4  N25  C18  single    1.340  0.020  1.340
 5Q4  C18  C17  double    1.418  0.020  1.418
 5Q4  N21  C23  single    1.376  0.020  1.376
 5Q4  C28  C27  aromatic  1.388  0.020  1.388
 5Q4  C23  C17  single    1.439  0.020  1.439
 5Q4  C23  O24  double    1.241  0.020  1.241
 5Q4  C17  C15  single    1.479  0.020  1.479
 5Q4  O16  C15  double    1.238  0.020  1.238
 5Q4  C15  N14  single    1.348  0.020  1.348
 5Q4  N14  C11  single    1.399  0.020  1.399
 5Q4  C11  C12  aromatic  1.393  0.020  1.393
 5Q4  C11  C10  aromatic  1.397  0.020  1.397
 5Q4  C12  C13  aromatic  1.385  0.020  1.385
 5Q4  C10  C9   aromatic  1.384  0.020  1.384
 5Q4  C13  C8   aromatic  1.398  0.020  1.398
 5Q4  C9   C8   aromatic  1.401  0.020  1.401
 5Q4  C8   N5   single    1.396  0.020  1.396
 5Q4  N5   C6   single    1.448  0.020  1.448
 5Q4  N5   C4   single    1.455  0.020  1.455
 5Q4  C6   C7   single    1.517  0.020  1.517
 5Q4  C4   C3   single    1.515  0.020  1.515
 5Q4  C7   N2   single    1.447  0.020  1.447
 5Q4  C3   N2   single    1.447  0.020  1.447
 5Q4  N2   C1   single    1.444  0.020  1.444
 5Q4  C4   H1   single    0.970  0.020  1.090
 5Q4  C4   H2   single    0.970  0.020  1.090
 5Q4  C6   H3   single    0.970  0.020  1.090
 5Q4  C6   H4   single    0.970  0.020  1.090
 5Q4  C7   H5   single    0.970  0.020  1.090
 5Q4  C7   H6   single    0.970  0.020  1.090
 5Q4  C9   H7   single    0.930  0.020  1.080
 5Q4  C10  H8   single    0.930  0.020  1.080
 5Q4  C12  H9   single    0.930  0.020  1.080
 5Q4  C13  H10  single    0.930  0.020  1.080
 5Q4  C3   H12  single    0.970  0.020  1.090
 5Q4  C3   H13  single    0.970  0.020  1.090
 5Q4  C1   H14  single    0.970  0.020  1.090
 5Q4  C1   H15  single    0.970  0.020  1.090
 5Q4  C1   H16  single    0.970  0.020  1.090
 5Q4  N14  H17  single    0.860  0.020  1.020
 5Q4  C19  H18  single    0.930  0.020  1.080
 5Q4  C20  H19  single    0.930  0.020  1.080
 5Q4  N21  H22  single    0.860  0.020  1.020
 5Q4  N25  H20  single    0.860  0.020  1.020
 5Q4  C27  H21  single    0.930  0.020  1.080
 5Q4  C28  H23  single    0.930  0.020  1.080
 5Q4  C29  H24  single    0.930  0.020  1.080
 5Q4  C30  H25  single    0.930  0.020  1.080
 5Q4  C33  H26  single    0.970  0.020  1.090
 5Q4  C33  H27  single    0.970  0.020  1.090
 5Q4  C33  H28  single    0.970  0.020  1.090

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
 5Q4  H2   C4   H1   107.26  3.000
 5Q4  H2   C4   N5   110.38  3.000
 5Q4  H1   C4   N5   110.66  3.000
 5Q4  H2   C4   C3   108.61  3.000
 5Q4  H1   C4   C3   109.32  3.000
 5Q4  N5   C4   C3   110.53  3.000
 5Q4  H4   C6   H3   107.46  3.000
 5Q4  H4   C6   N5   111.90  3.000
 5Q4  H3   C6   N5   109.66  3.000
 5Q4  H4   C6   C7   109.52  3.000
 5Q4  H3   C6   C7   107.96  3.000
 5Q4  N5   C6   C7   110.22  3.000
 5Q4  N14  C11  C12  116.82  3.000
 5Q4  C12  C11  C10  117.60  3.000
 5Q4  N14  C11  C10  125.55  3.000
 5Q4  H6   C7   H5   107.09  3.000
 5Q4  H6   C7   N2   111.69  3.000
 5Q4  H5   C7   N2   109.21  3.000
 5Q4  H6   C7   C6   108.79  3.000
 5Q4  H5   C7   C6   108.75  3.000
 5Q4  N2   C7   C6   111.19  3.000
 5Q4  N5   C8   C13  122.77  3.000
 5Q4  N5   C8   C9   120.51  3.000
 5Q4  C13  C8   C9   116.68  3.000
 5Q4  H7   C9   C10  117.70  3.000
 5Q4  H7   C9   C8   119.93  3.000
 5Q4  C10  C9   C8   122.35  3.000
 5Q4  H8   C10  C9   118.54  3.000
 5Q4  H8   C10  C11  120.99  3.000
 5Q4  C9   C10  C11  120.45  3.000
 5Q4  H9   C12  C13  118.59  3.000
 5Q4  H9   C12  C11  119.65  3.000
 5Q4  C13  C12  C11  121.76  3.000
 5Q4  H10  C13  C12  117.82  3.000
 5Q4  H10  C13  C8   121.03  3.000
 5Q4  C12  C13  C8   121.15  3.000
 5Q4  C1   N2   C3   111.82  3.000
 5Q4  C1   N2   C7   111.79  3.000
 5Q4  C3   N2   C7   109.99  3.000
 5Q4  H13  C3   H12  107.08  3.000
 5Q4  H13  C3   N2   109.21  3.000
 5Q4  H12  C3   N2   111.75  3.000
 5Q4  H13  C3   C4   108.85  3.000
 5Q4  H12  C3   C4   109.16  3.000
 5Q4  N2   C3   C4   110.70  3.000
 5Q4  H16  C1   H15  107.88  3.000
 5Q4  H16  C1   H14  107.75  3.000
 5Q4  H15  C1   H14  107.70  3.000
 5Q4  H16  C1   N2   110.07  3.000
 5Q4  H15  C1   N2   110.02  3.000
 5Q4  H14  C1   N2   113.25  3.000
 5Q4  C8   N5   C6   118.13  3.000
 5Q4  C6   N5   C4   111.58  3.000
 5Q4  C8   N5   C4   117.65  3.000
 5Q4  C17  C15  O16  121.80  3.000
 5Q4  O16  C15  N14  121.76  3.000
 5Q4  C17  C15  N14  116.45  3.000
 5Q4  C23  C17  C18  119.43  3.000
 5Q4  C23  C17  C15  120.62  3.000
 5Q4  C18  C17  C15  119.95  3.000
 5Q4  N25  C18  C19  119.61  3.000
 5Q4  N25  C18  C17  121.23  3.000
 5Q4  C19  C18  C17  119.15  3.000
 5Q4  H18  C19  C20  119.34  3.000
 5Q4  H18  C19  C18  121.33  3.000
 5Q4  C20  C19  C18  119.32  3.000
 5Q4  H19  C20  N21  116.15  3.000
 5Q4  H19  C20  C19  122.49  3.000
 5Q4  N21  C20  C19  121.36  3.000
 5Q4  H22  N21  C23  116.57  3.000
 5Q4  H22  N21  C20  119.22  3.000
 5Q4  C23  N21  C20  124.21  3.000
 5Q4  O24  C23  N21  117.32  3.000
 5Q4  O24  C23  C17  126.22  3.000
 5Q4  N21  C23  C17  116.47  3.000
 5Q4  H20  N25  C26  119.50  3.000
 5Q4  H20  N25  C18  113.94  3.000
 5Q4  C26  N25  C18  126.55  3.000
 5Q4  C31  C26  C27  119.73  3.000
 5Q4  C27  C26  N25  121.64  3.000
 5Q4  C31  C26  N25  118.58  3.000
 5Q4  H21  C27  C28  119.94  3.000
 5Q4  H21  C27  C26  119.30  3.000
 5Q4  C28  C27  C26  120.77  3.000
 5Q4  H23  C28  C29  120.63  3.000
 5Q4  H23  C28  C27  120.01  3.000
 5Q4  C29  C28  C27  119.35  3.000
 5Q4  H24  C29  C30  119.03  3.000
 5Q4  H24  C29  C28  120.28  3.000
 5Q4  C30  C29  C28  120.69  3.000
 5Q4  H25  C30  C31  120.77  3.000
 5Q4  H25  C30  C29  119.16  3.000
 5Q4  C31  C30  C29  120.07  3.000
 5Q4  O32  C31  C30  124.66  3.000
 5Q4  C30  C31  C26  119.37  3.000
 5Q4  O32  C31  C26  115.97  3.000
 5Q4  C33  O32  C31  118.55  3.000
 5Q4  H28  C33  H27  108.88  3.000
 5Q4  H28  C33  H26  108.85  3.000
 5Q4  H27  C33  H26  108.87  3.000
 5Q4  H28  C33  O32  106.36  3.000
 5Q4  H27  C33  O32  111.87  3.000
 5Q4  H26  C33  O32  111.90  3.000
 5Q4  H17  N14  C15  114.01  3.000
 5Q4  H17  N14  C11  117.04  3.000
 5Q4  C15  N14  C11  128.91  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
 5Q4  CONST_01  C8   C13  C12  C11     0.00   0.0  0
 5Q4  CONST_02  C8   C9   C10  C11     0.00   0.0  0
 5Q4  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 5Q4  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 5Q4  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 5Q4  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 5Q4  CONST_07  C29  C30  C31  C26     0.00   0.0  0
 5Q4  CONST_08  C29  C28  C27  C26     0.00   0.0  0
 5Q4  CONST_09  C30  C31  C26  C27     0.00   0.0  0
 5Q4  CONST_10  C30  C29  C28  C27     0.00   0.0  0
 5Q4  CONST_11  C31  C30  C29  C28     0.00   0.0  0
 5Q4  CONST_12  C31  C26  C27  C28     0.00   0.0  0
 5Q4  CONST_13  N5   C8   C9   C10   180.00   0.0  0
 5Q4  CONST_14  N5   C8   C13  C12   180.00   0.0  0
 5Q4  CONST_15  C20  N21  C23  C17     0.00   0.0  0
 5Q4  CONST_16  N14  C11  C10  C9    180.00   0.0  0
 5Q4  CONST_17  N14  C11  C12  C13   180.00   0.0  0
 5Q4  CONST_18  C30  C31  C26  N25   180.00   0.0  0
 5Q4  CONST_19  C28  C27  C26  N25   180.00   0.0  0
 5Q4  CONST_20  O32  C31  C26  C27   180.00   0.0  0
 5Q4  CONST_21  O32  C31  C30  C29   180.00   0.0  0
 5Q4  CONST_22  C26  N25  C18  C17   180.00   0.0  0
 5Q4  CONST_25  C26  N25  C18  C19     0.00   0.0  0
 5Q4  CONST_26  O24  C23  N21  C20   180.00   0.0  0
 5Q4  CONST_27  H10  C13  C12  C11   180.00   0.0  0
 5Q4  CONST_28  H7   C9   C10  C11   180.00   0.0  0
 5Q4  CONST_29  H9   C12  C13  C8    180.00   0.0  0
 5Q4  CONST_30  H8   C10  C9   C8    180.00   0.0  0
 5Q4  CONST_31  H25  C30  C31  C26   180.00   0.0  0
 5Q4  CONST_32  H23  C28  C27  C26   180.00   0.0  0
 5Q4  CONST_33  H24  C29  C28  C27   180.00   0.0  0
 5Q4  CONST_34  H21  C27  C28  C29   180.00   0.0  0
 5Q4  CONST_35  H22  N21  C23  C17   180.00   0.0  0
 5Q4  CONST_36  C17  C15  N14  C11   180.00   0.0  0
 5Q4  CONST_41  O16  C15  N14  C11     0.00   0.0  0
 5Q4  Var_01    C13  C8   N5   C4   -133.26  30.0  2
 5Q4  Var_02    C7   C6   N5   C4    -55.41  30.0  1
 5Q4  Var_03    C7   N2   C3   C4     58.08  30.0  1
 5Q4  Var_04    C3   C4   N5   C6     55.77  30.0  1
 5Q4  Var_05    C3   N2   C7   C6    -58.18  30.0  1
 5Q4  Var_06    N5   C6   C7   N2     56.73  30.0  1
 5Q4  Var_07    N5   C4   C3   N2    -56.85  30.0  1
 5Q4  Var_08    C18  C17  C15  N14   178.57  30.0  1
 5Q4  Var_09    H14  C1   N2   C7     61.78  30.0  3
 5Q4  Var_10    H26  C33  O32  C31   -63.49  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
 5Q4  plan-1  C11  0.020
 5Q4  plan-1  C8   0.020
 5Q4  plan-1  C9   0.020
 5Q4  plan-1  C10  0.020
 5Q4  plan-1  C12  0.020
 5Q4  plan-1  C13  0.020
 5Q4  plan-1  N5   0.020
 5Q4  plan-1  H7   0.020
 5Q4  plan-1  H8   0.020
 5Q4  plan-1  H9   0.020
 5Q4  plan-1  H10  0.020
 5Q4  plan-1  N14  0.020
 5Q4  plan-2  C15  0.020
 5Q4  plan-2  C17  0.020
 5Q4  plan-2  C18  0.020
 5Q4  plan-2  C19  0.020
 5Q4  plan-2  C20  0.020
 5Q4  plan-2  N21  0.020
 5Q4  plan-2  C23  0.020
 5Q4  plan-2  O24  0.020
 5Q4  plan-2  N25  0.020
 5Q4  plan-2  H18  0.020
 5Q4  plan-2  H19  0.020
 5Q4  plan-2  H22  0.020
 5Q4  plan-3  N25  0.020
 5Q4  plan-3  C26  0.020
 5Q4  plan-3  C27  0.020
 5Q4  plan-3  C28  0.020
 5Q4  plan-3  C29  0.020
 5Q4  plan-3  C30  0.020
 5Q4  plan-3  C31  0.020
 5Q4  plan-3  O32  0.020
 5Q4  plan-3  H21  0.020
 5Q4  plan-3  H23  0.020
 5Q4  plan-3  H24  0.020
 5Q4  plan-3  H25  0.020
 5Q4  plan-4  C18  0.020
 5Q4  plan-4  N25  0.020
 5Q4  plan-4  C26  0.020
 5Q4  plan-4  H20  0.020
 5Q4  plan-5  C11  0.020
 5Q4  plan-5  C15  0.020
 5Q4  plan-5  O16  0.020
 5Q4  plan-5  C17  0.020
 5Q4  plan-5  H17  0.020
 5Q4  plan-5  N14  0.020

