# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:21:59 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 4-[(2-azanylpyrimidin-4-yl)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: CN1CCN(CC1)c2ccc(NC(=O)C3=C(Nc4ccnc(N)n4)C=CNC3=O)cc2
#
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
 5Q3  5Q3  4-[(2-azanylpyrimidin-4-yl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide  ligand  55  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5Q3
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
 5Q3  C4   C  CH2   0  -0.306   -5.7159  -1.3423   0.7518
 5Q3  C6   C  CH2   0  -0.315   -6.3608   0.8266  -0.0556
 5Q3  C11  C  CR6   0   0.348   -1.2680   0.9546  -0.0925
 5Q3  C7   C  CH2   0  -0.277   -7.7011   0.2461  -0.4683
 5Q3  C8   C  CR6   0   0.352   -4.0052   0.1977  -0.0492
 5Q3  C9   C  CR16  0  -0.319   -2.9807  -0.7405  -0.2277
 5Q3  C10  C  CR16  0  -0.297   -1.6446  -0.3815  -0.2481
 5Q3  C12  C  CR16  0  -0.343   -2.2795   1.8963   0.0777
 5Q3  C13  C  CR16  0  -0.346   -3.6159   1.5319   0.1068
 5Q3  N2   N  NT    0  -0.412   -8.0768  -0.8628   0.3826
 5Q3  C3   C  CH2   0  -0.283   -7.0611  -1.8924   0.3228
 5Q3  C1   C  CH3   0  -0.519   -9.3826  -1.3781   0.0413
 5Q3  N5   N  NT    0  -0.515   -5.3419  -0.2022  -0.0733
 5Q3  C15  C  C     0   0.610    1.1910   0.7542   0.0628
 5Q3  O16  O  O     0  -0.526    1.1994  -0.4613   0.2904
 5Q3  C17  C  CR6   0  -0.452    2.4477   1.5443   0.0040
 5Q3  C18  C  CR6   0   0.531    3.6989   0.8965   0.0551
 5Q3  C19  C  CR16  0  -0.462    4.8905   1.6706   0.0813
 5Q3  C20  C  CR16  0   0.070    4.8025   3.0172   0.0109
 5Q3  N21  N  NR16  0  -0.663    3.6137   3.6314  -0.0952
 5Q3  C23  C  CR6   0   0.584    2.4013   2.9825  -0.0992
 5Q3  O24  O  O     0  -0.525    1.3794   3.6753  -0.1954
 5Q3  N25  N  NH1   0  -0.772    3.7649  -0.4554   0.1381
 5Q3  C26  C  CR6   0   0.499    4.8215  -1.3119  -0.0963
 5Q3  C27  C  CR16  0  -0.437    5.8986  -1.0282  -0.9393
 5Q3  C28  C  CR16  0  -0.022    6.8249  -2.0440  -1.0792
 5Q3  N29  N  N     0  -0.466    6.7320  -3.2214  -0.4824
 5Q3  C30  C  CR6   0   0.552    5.6458  -3.3977   0.2795
 5Q3  N31  N  N     0  -0.495    4.6920  -2.4895   0.4959
 5Q3  N32  N  NH2   0  -0.820    5.5165  -4.5812   0.9047
 5Q3  H1   H  HCH2  0   0.214   -5.7622  -1.0544   1.8126
 5Q3  H2   H  HCH2  0   0.254   -4.9734  -2.1323   0.6639
 5Q3  H3   H  HCH2  0   0.251   -6.1012   1.6123  -0.7668
 5Q3  H4   H  HCH2  0   0.211   -6.4531   1.2959   0.9362
 5Q3  H5   H  HCH2  0   0.240   -8.4585   1.0301  -0.3957
 5Q3  H6   H  HCH2  0   0.192   -7.6470  -0.0561  -1.5291
 5Q3  H7   H  HCR6  0   0.260   -3.2233  -1.7840  -0.3821
 5Q3  H8   H  HCR6  0   0.270   -0.9084  -1.1524  -0.4059
 5Q3  H9   H  HCR6  0   0.261   -2.0249   2.9422   0.2057
 5Q3  H10  H  HCR6  0   0.269   -4.3475   2.3116   0.2653
 5Q3  H12  H  HCH2  0   0.193   -6.9713  -2.3184  -0.6921
 5Q3  H13  H  HCH2  0   0.240   -7.3371  -2.7108   0.9921
 5Q3  H14  H  HCH3  0   0.192   -9.4390  -1.7681  -0.9870
 5Q3  H15  H  HCH3  0   0.234   -9.6543  -2.1888   0.7192
 5Q3  H16  H  HCH3  0   0.234  -10.1334  -0.5930   0.1415
 5Q3  H17  H  HNH1  0   0.435    0.1712   2.4435  -0.2317
 5Q3  H18  H  HCR6  0   0.312    5.8580   1.2169   0.2163
 5Q3  H19  H  HCR6  0   0.328    5.6702   3.6586   0.0465
 5Q3  H20  H  HNR6  0   0.430    3.5842   4.6401  -0.1563
 5Q3  H21  H  HNH1  0   0.430    2.8668  -0.8954   0.3546
 5Q3  H22  H  HCR6  0   0.292    5.9946  -0.1096  -1.4954
 5Q3  H23  H  HCR6  0   0.273    7.6854  -1.8976  -1.7230
 5Q3  H24  H  HNH2  0   0.398    6.1149  -5.3432   0.6381
 5Q3  H25  H  HNH2  0   0.397    4.6468  -4.8076   1.3540
 5Q3  N14  N  NH1   0  -0.780    0.0472   1.4338  -0.1370

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
 5Q3  N32  C30  single    1.345  0.020  1.345
 5Q3  N29  C30  aromatic  1.338  0.020  1.338
 5Q3  N29  C28  aromatic  1.323  0.020  1.323
 5Q3  C30  N31  aromatic  1.335  0.020  1.335
 5Q3  C28  C27  aromatic  1.382  0.020  1.382
 5Q3  N31  C26  aromatic  1.324  0.020  1.324
 5Q3  C27  C26  aromatic  1.397  0.020  1.397
 5Q3  C26  N25  single    1.380  0.020  1.380
 5Q3  C19  C20  double    1.351  0.020  1.351
 5Q3  C19  C18  single    1.421  0.020  1.421
 5Q3  C20  N21  single    1.342  0.020  1.342
 5Q3  N25  C18  single    1.356  0.020  1.356
 5Q3  C18  C17  double    1.410  0.020  1.410
 5Q3  N21  C23  single    1.375  0.020  1.375
 5Q3  C17  C23  single    1.443  0.020  1.443
 5Q3  C17  C15  single    1.486  0.020  1.486
 5Q3  C23  O24  double    1.238  0.020  1.238
 5Q3  O16  C15  double    1.237  0.020  1.237
 5Q3  C15  N14  single    1.345  0.020  1.345
 5Q3  N14  C11  single    1.400  0.020  1.400
 5Q3  C11  C12  aromatic  1.393  0.020  1.393
 5Q3  C11  C10  aromatic  1.397  0.020  1.397
 5Q3  C12  C13  aromatic  1.386  0.020  1.386
 5Q3  C10  C9   aromatic  1.384  0.020  1.384
 5Q3  C13  C8   aromatic  1.399  0.020  1.399
 5Q3  C9   C8   aromatic  1.401  0.020  1.401
 5Q3  C8   N5   single    1.395  0.020  1.395
 5Q3  N5   C6   single    1.448  0.020  1.448
 5Q3  N5   C4   single    1.456  0.020  1.456
 5Q3  C6   C7   single    1.518  0.020  1.518
 5Q3  C4   C3   single    1.515  0.020  1.515
 5Q3  C7   N2   single    1.447  0.020  1.447
 5Q3  N2   C3   single    1.448  0.020  1.448
 5Q3  N2   C1   single    1.445  0.020  1.445
 5Q3  C4   H1   single    0.970  0.020  1.090
 5Q3  C4   H2   single    0.970  0.020  1.090
 5Q3  C6   H3   single    0.970  0.020  1.090
 5Q3  C6   H4   single    0.970  0.020  1.090
 5Q3  C7   H5   single    0.970  0.020  1.090
 5Q3  C7   H6   single    0.970  0.020  1.090
 5Q3  C9   H7   single    0.930  0.020  1.080
 5Q3  C10  H8   single    0.930  0.020  1.080
 5Q3  C12  H9   single    0.930  0.020  1.080
 5Q3  C13  H10  single    0.930  0.020  1.080
 5Q3  C3   H12  single    0.970  0.020  1.090
 5Q3  C3   H13  single    0.970  0.020  1.090
 5Q3  C1   H14  single    0.970  0.020  1.090
 5Q3  C1   H15  single    0.970  0.020  1.090
 5Q3  C1   H16  single    0.970  0.020  1.090
 5Q3  N14  H17  single    0.860  0.020  1.020
 5Q3  C19  H18  single    0.930  0.020  1.080
 5Q3  C20  H19  single    0.930  0.020  1.080
 5Q3  N21  H20  single    0.860  0.020  1.020
 5Q3  N25  H21  single    0.860  0.020  1.020
 5Q3  C27  H22  single    0.930  0.020  1.080
 5Q3  C28  H23  single    0.930  0.020  1.080
 5Q3  N32  H24  single    0.890  0.020  1.040
 5Q3  N32  H25  single    0.890  0.020  1.040

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
 5Q3  H2   C4   H1   107.26  3.000
 5Q3  H2   C4   N5   110.33  3.000
 5Q3  H1   C4   N5   110.63  3.000
 5Q3  H2   C4   C3   108.63  3.000
 5Q3  H1   C4   C3   109.31  3.000
 5Q3  N5   C4   C3   110.60  3.000
 5Q3  H4   C6   H3   107.46  3.000
 5Q3  H4   C6   N5   111.89  3.000
 5Q3  H3   C6   N5   109.65  3.000
 5Q3  H4   C6   C7   109.50  3.000
 5Q3  H3   C6   C7   107.96  3.000
 5Q3  N5   C6   C7   110.26  3.000
 5Q3  N14  C11  C12  117.04  3.000
 5Q3  C12  C11  C10  117.69  3.000
 5Q3  N14  C11  C10  125.24  3.000
 5Q3  H6   C7   H5   107.11  3.000
 5Q3  H6   C7   N2   111.58  3.000
 5Q3  H5   C7   N2   109.32  3.000
 5Q3  H6   C7   C6   108.82  3.000
 5Q3  H5   C7   C6   108.64  3.000
 5Q3  N2   C7   C6   111.25  3.000
 5Q3  N5   C8   C13  122.82  3.000
 5Q3  N5   C8   C9   120.43  3.000
 5Q3  C13  C8   C9   116.72  3.000
 5Q3  H7   C9   C10  117.68  3.000
 5Q3  H7   C9   C8   120.00  3.000
 5Q3  C10  C9   C8   122.30  3.000
 5Q3  H8   C10  C9   118.45  3.000
 5Q3  H8   C10  C11  121.09  3.000
 5Q3  C9   C10  C11  120.46  3.000
 5Q3  H9   C12  C13  118.54  3.000
 5Q3  H9   C12  C11  119.76  3.000
 5Q3  C13  C12  C11  121.69  3.000
 5Q3  H10  C13  C12  117.79  3.000
 5Q3  H10  C13  C8   121.07  3.000
 5Q3  C12  C13  C8   121.13  3.000
 5Q3  C1   N2   C3   111.77  3.000
 5Q3  C1   N2   C7   111.65  3.000
 5Q3  C3   N2   C7   109.79  3.000
 5Q3  H13  C3   H12  107.13  3.000
 5Q3  H13  C3   N2   109.28  3.000
 5Q3  H12  C3   N2   111.67  3.000
 5Q3  H13  C3   C4   108.83  3.000
 5Q3  H12  C3   C4   109.15  3.000
 5Q3  N2   C3   C4   110.67  3.000
 5Q3  H16  C1   H15  107.84  3.000
 5Q3  H16  C1   H14  107.78  3.000
 5Q3  H15  C1   H14  107.71  3.000
 5Q3  H16  C1   N2   110.10  3.000
 5Q3  H15  C1   N2   110.08  3.000
 5Q3  H14  C1   N2   113.15  3.000
 5Q3  C8   N5   C6   118.04  3.000
 5Q3  C6   N5   C4   111.63  3.000
 5Q3  C8   N5   C4   117.43  3.000
 5Q3  C17  C15  O16  121.62  3.000
 5Q3  O16  C15  N14  121.98  3.000
 5Q3  C17  C15  N14  116.40  3.000
 5Q3  C23  C17  C18  119.29  3.000
 5Q3  C23  C17  C15  120.39  3.000
 5Q3  C18  C17  C15  120.32  3.000
 5Q3  N25  C18  C19  120.07  3.000
 5Q3  N25  C18  C17  120.23  3.000
 5Q3  C19  C18  C17  119.63  3.000
 5Q3  H18  C19  C20  119.00  3.000
 5Q3  H18  C19  C18  121.73  3.000
 5Q3  C20  C19  C18  119.16  3.000
 5Q3  H19  C20  N21  116.27  3.000
 5Q3  H19  C20  C19  122.55  3.000
 5Q3  N21  C20  C19  121.18  3.000
 5Q3  H20  N21  C23  116.42  3.000
 5Q3  H20  N21  C20  119.16  3.000
 5Q3  C23  N21  C20  124.41  3.000
 5Q3  O24  C23  N21  117.63  3.000
 5Q3  O24  C23  C17  126.14  3.000
 5Q3  N21  C23  C17  116.22  3.000
 5Q3  H21  N25  C26  116.17  3.000
 5Q3  H21  N25  C18  113.51  3.000
 5Q3  C26  N25  C18  130.21  3.000
 5Q3  N31  C26  C27  121.72  3.000
 5Q3  C27  C26  N25  124.52  3.000
 5Q3  N31  C26  N25  113.64  3.000
 5Q3  H22  C27  C28  120.96  3.000
 5Q3  H22  C27  C26  123.57  3.000
 5Q3  C28  C27  C26  115.38  3.000
 5Q3  H23  C28  N29  116.32  3.000
 5Q3  H23  C28  C27  119.52  3.000
 5Q3  N29  C28  C27  124.15  3.000
 5Q3  C30  N29  C28  115.52  3.000
 5Q3  N32  C30  N31  117.05  3.000
 5Q3  N31  C30  N29  125.64  3.000
 5Q3  N32  C30  N29  117.30  3.000
 5Q3  C30  N31  C26  117.56  3.000
 5Q3  H25  N32  H24  117.60  3.000
 5Q3  H25  N32  C30  119.30  3.000
 5Q3  H24  N32  C30  119.13  3.000
 5Q3  H17  N14  C15  114.20  3.000
 5Q3  H17  N14  C11  117.07  3.000
 5Q3  C15  N14  C11  128.37  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
 5Q3  CONST_01  C8   C13  C12  C11     0.00   0.0  0
 5Q3  CONST_02  C8   C9   C10  C11     0.00   0.0  0
 5Q3  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 5Q3  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 5Q3  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 5Q3  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 5Q3  CONST_07  N29  C30  N31  C26     0.00   0.0  0
 5Q3  CONST_08  N29  C28  C27  C26     0.00   0.0  0
 5Q3  CONST_09  C30  N29  C28  C27     0.00   0.0  0
 5Q3  CONST_10  C30  N31  C26  C27     0.00   0.0  0
 5Q3  CONST_11  N31  C30  N29  C28     0.00   0.0  0
 5Q3  CONST_12  N31  C26  C27  C28     0.00   0.0  0
 5Q3  CONST_13  N5   C8   C9   C10   180.00   0.0  0
 5Q3  CONST_14  N5   C8   C13  C12   180.00   0.0  0
 5Q3  CONST_15  C20  N21  C23  C17     0.00   0.0  0
 5Q3  CONST_16  N14  C11  C10  C9    180.00   0.0  0
 5Q3  CONST_17  N14  C11  C12  C13   180.00   0.0  0
 5Q3  CONST_18  C30  N31  C26  N25   180.00   0.0  0
 5Q3  CONST_19  C28  C27  C26  N25   180.00   0.0  0
 5Q3  CONST_20  N32  C30  N31  C26   180.00   0.0  0
 5Q3  CONST_21  N32  C30  N29  C28   180.00   0.0  0
 5Q3  CONST_26  O24  C23  N21  C20   180.00   0.0  0
 5Q3  CONST_27  H10  C13  C12  C11   180.00   0.0  0
 5Q3  CONST_28  H7   C9   C10  C11   180.00   0.0  0
 5Q3  CONST_29  H9   C12  C13  C8    180.00   0.0  0
 5Q3  CONST_30  H8   C10  C9   C8    180.00   0.0  0
 5Q3  CONST_31  H23  C28  C27  C26   180.00   0.0  0
 5Q3  CONST_32  H22  C27  C28  N29   180.00   0.0  0
 5Q3  CONST_33  H20  N21  C23  C17   180.00   0.0  0
 5Q3  CONST_34  C17  C15  N14  C11   180.00   0.0  0
 5Q3  CONST_37  H17  N14  C11  C10   180.00   0.0  0
 5Q3  CONST_39  H24  N32  C30  N29     0.00   0.0  0
 5Q3  CONST_40  H25  N32  C30  N29   180.00   0.0  0
 5Q3  CONST_41  O16  C15  N14  C11     0.00   0.0  0
 5Q3  Var_01    C13  C8   N5   C4   -132.66  30.0  3
 5Q3  Var_02    C7   C6   N5   C4    -55.03  30.0  1
 5Q3  Var_03    C7   N2   C3   C4     58.37  30.0  1
 5Q3  Var_04    C3   C4   N5   C6     55.50  30.0  1
 5Q3  Var_05    C3   N2   C7   C6    -58.43  30.0  1
 5Q3  Var_06    N5   C6   C7   N2     56.70  30.0  1
 5Q3  Var_07    N5   C4   C3   N2    -56.97  30.0  1
 5Q3  Var_08    C18  C17  C15  N14  -173.04  30.0  2
 5Q3  Var_09    H14  C1   N2   C7     61.37  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
 5Q3  plan-1  C11  0.020
 5Q3  plan-1  C8   0.020
 5Q3  plan-1  C9   0.020
 5Q3  plan-1  C10  0.020
 5Q3  plan-1  C12  0.020
 5Q3  plan-1  C13  0.020
 5Q3  plan-1  N5   0.020
 5Q3  plan-1  H7   0.020
 5Q3  plan-1  H8   0.020
 5Q3  plan-1  H9   0.020
 5Q3  plan-1  H10  0.020
 5Q3  plan-1  N14  0.020
 5Q3  plan-2  C11  0.020
 5Q3  plan-2  C15  0.020
 5Q3  plan-2  O16  0.020
 5Q3  plan-2  C17  0.020
 5Q3  plan-2  H17  0.020
 5Q3  plan-2  N14  0.020
 5Q3  plan-3  C15  0.020
 5Q3  plan-3  C17  0.020
 5Q3  plan-3  C18  0.020
 5Q3  plan-3  C19  0.020
 5Q3  plan-3  C20  0.020
 5Q3  plan-3  N21  0.020
 5Q3  plan-3  C23  0.020
 5Q3  plan-3  O24  0.020
 5Q3  plan-3  N25  0.020
 5Q3  plan-3  H18  0.020
 5Q3  plan-3  H19  0.020
 5Q3  plan-3  H20  0.020
 5Q3  plan-4  N25  0.020
 5Q3  plan-4  C26  0.020
 5Q3  plan-4  C27  0.020
 5Q3  plan-4  C28  0.020
 5Q3  plan-4  N29  0.020
 5Q3  plan-4  C30  0.020
 5Q3  plan-4  N31  0.020
 5Q3  plan-4  N32  0.020
 5Q3  plan-4  H22  0.020
 5Q3  plan-4  H23  0.020
 5Q3  plan-5  C18  0.020
 5Q3  plan-5  N25  0.020
 5Q3  plan-5  C26  0.020
 5Q3  plan-5  H21  0.020
 5Q3  plan-6  C30  0.020
 5Q3  plan-6  N32  0.020
 5Q3  plan-6  H24  0.020
 5Q3  plan-6  H25  0.020

