# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 15:38:01 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-[(cyclopropanecarbonyl)amino]-4-{[2-methoxy-3-(pyrimidin-2-yl)phenyl]amino}-N-methylpyridazine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1nnc(NC(=O)C2CC2)cc1Nc3cccc(c3OC)c4ncccn4
#
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
 VZJ  VZJ  6-[(cyclopropanecarbonyl)amino]-4-{[2-methoxy-3-(pyrimidin-2-yl)phenyl]amino}-N-methylpyridazine-3-carboxamide  ligand  52  31  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VZJ
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
 VZJ  C13  C  CH3   0  -0.414  15.6582  -2.1787  26.3961
 VZJ  C18  C  CH1   0  -0.427   8.8402  -3.2862  31.2418
 VZJ  C17  C  C     0   0.597  10.2663  -3.2899  30.8354
 VZJ  C16  C  CR16  0  -0.030  18.0984  -5.1095  24.1012
 VZJ  C15  C  CR16  0  -0.341  17.3904  -5.7131  23.0757
 VZJ  C19  C  CH2   0  -0.462   8.2679  -4.5779  31.7750
 VZJ  C20  C  CH2   0  -0.459   7.8697  -4.1030  30.4290
 VZJ  C21  C  CH3   0  -0.514  17.5244   1.4308  31.8685
 VZJ  C11  C  CR6   0   0.275  15.8974  -4.1435  27.6337
 VZJ  C12  C  CR6   0   0.336  16.3713  -5.4334  25.5255
 VZJ  C1   C  CR6   0  -0.000  14.7970  -1.0046  30.9811
 VZJ  N1   N  N     0  -0.269  13.8541  -0.3395  31.6164
 VZJ  N2   N  N     0  -0.326  12.6212  -0.7322  31.6688
 VZJ  C2   C  CR6   0   0.478  12.2812  -1.8579  31.0269
 VZJ  C3   C  CR16  0  -0.398  13.1825  -2.6238  30.3087
 VZJ  C4   C  CR6   0   0.409  14.5150  -2.2133  30.2852
 VZJ  C5   C  C     0   0.576  16.1610  -0.3978  31.0228
 VZJ  N4   N  NH1   0  -0.626  16.2783   0.7147  31.7448
 VZJ  O1   O  O     0  -0.506  17.1096  -0.9041  30.4200
 VZJ  C6   C  CR6   0   0.265  15.3488  -4.0781  28.9203
 VZJ  C7   C  CR16  0  -0.311  14.7353  -5.2003  29.4657
 VZJ  C8   C  CR16  0  -0.253  14.6094  -6.3570  28.7133
 VZJ  C9   C  CR16  0  -0.286  15.1277  -6.4129  27.4309
 VZJ  C10  C  CR6   0  -0.047  15.7953  -5.3177  26.8858
 VZJ  O2   O  O2    0  -0.470  16.5123  -3.0414  27.1387
 VZJ  N6   N  N     0  -0.403  15.6141  -6.0360  24.6139
 VZJ  C14  C  CR16  0  -0.024  16.1262  -6.1739  23.3986
 VZJ  N7   N  N     0  -0.390  17.5998  -4.9700  25.3219
 VZJ  O3   O  O     0  -0.457  10.7917  -4.2314  30.2715
 VZJ  H1   H  HCH3  0   0.244  16.2624  -1.3351  26.0698
 VZJ  H2   H  HCH3  0   0.227  15.2496  -2.6821  25.5160
 VZJ  H3   H  HCH3  0   0.229  14.8302  -1.8080  27.0058
 VZJ  H4   H  HCH1  0   0.289   8.4613  -2.3710  31.6808
 VZJ  H5   H  HCR6  0   0.277  19.1013  -4.7309  23.9380
 VZJ  H6   H  HCR6  0   0.285  17.8029  -5.8228  22.0836
 VZJ  H7   H  HCH2  0   0.268   7.5606  -4.4911  32.5886
 VZJ  H8   H  HCH2  0   0.262   8.9371  -5.4255  31.8429
 VZJ  H9   H  HCH2  0   0.267   6.8810  -3.6844  30.2979
 VZJ  H10  H  HCH2  0   0.261   8.2607  -4.6242  29.5652
 VZJ  H11  H  HCH3  0   0.253  17.3602   2.2925  32.5086
 VZJ  H12  H  HCH3  0   0.241  18.3013   0.8122  32.3188
 VZJ  H13  H  HCH3  0   0.241  17.8857   1.7835  30.9019
 VZJ  H14  H  HCR6  0   0.321  12.8570  -3.5046  29.7833
 VZJ  H15  H  HNH1  0   0.415  10.4280  -1.4343  31.6746
 VZJ  H16  H  HNH1  0   0.410  15.4510   1.0696  32.1978
 VZJ  H17  H  HNH1  0   0.422  16.3780  -2.3906  29.5901
 VZJ  H18  H  HCR6  0   0.288  14.3579  -5.1711  30.4797
 VZJ  H19  H  HCR6  0   0.265  14.1224  -7.2238  29.1391
 VZJ  H20  H  HCR6  0   0.261  15.0360  -7.3204  26.8490
 VZJ  H21  H  HCR6  0   0.278  15.5044  -6.6659  22.6592
 VZJ  N5   N  NH1   0  -0.789  15.4894  -2.8829  29.6365
 VZJ  N3   N  NH1   0  -0.735  10.9369  -2.1444  31.1660

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
 VZJ  C15  C14  aromatic  1.384  0.020  1.384
 VZJ  C15  C16  aromatic  1.385  0.020  1.385
 VZJ  C14  N6   aromatic  1.326  0.020  1.326
 VZJ  C16  N7   aromatic  1.326  0.020  1.326
 VZJ  N6   C12  aromatic  1.329  0.020  1.329
 VZJ  C12  N7   aromatic  1.329  0.020  1.329
 VZJ  C12  C10  single    1.482  0.020  1.482
 VZJ  C13  O2   single    1.423  0.020  1.423
 VZJ  C10  C9   aromatic  1.394  0.020  1.394
 VZJ  C10  C11  aromatic  1.396  0.020  1.396
 VZJ  C9   C8   aromatic  1.384  0.020  1.384
 VZJ  O2   C11  single    1.356  0.020  1.356
 VZJ  C11  C6   aromatic  1.400  0.020  1.400
 VZJ  C8   C7   aromatic  1.386  0.020  1.386
 VZJ  C6   C7   aromatic  1.390  0.020  1.390
 VZJ  C6   N5   single    1.400  0.020  1.400
 VZJ  N5   C4   single    1.349  0.020  1.349
 VZJ  O1   C5   double    1.233  0.020  1.233
 VZJ  C4   C3   aromatic  1.395  0.020  1.395
 VZJ  C4   C1   aromatic  1.423  0.020  1.423
 VZJ  C3   C2   aromatic  1.384  0.020  1.384
 VZJ  O3   C17  double    1.217  0.020  1.217
 VZJ  C5   C1   single    1.494  0.020  1.494
 VZJ  C5   N4   single    1.331  0.020  1.331
 VZJ  C1   N1   aromatic  1.317  0.020  1.317
 VZJ  C20  C18  single    1.507  0.020  1.507
 VZJ  C20  C19  single    1.482  0.020  1.482
 VZJ  C21  N4   single    1.443  0.020  1.443
 VZJ  C17  N3   single    1.368  0.020  1.368
 VZJ  C17  C18  single    1.483  0.020  1.483
 VZJ  C2   N3   single    1.382  0.020  1.382
 VZJ  C2   N2   aromatic  1.340  0.020  1.340
 VZJ  N1   N2   aromatic  1.295  0.020  1.295
 VZJ  C18  C19  single    1.510  0.020  1.510
 VZJ  C13  H1   single    0.970  0.020  1.090
 VZJ  C13  H2   single    0.970  0.020  1.090
 VZJ  C13  H3   single    0.970  0.020  1.090
 VZJ  C18  H4   single    0.970  0.020  1.090
 VZJ  C16  H5   single    0.930  0.020  1.080
 VZJ  C15  H6   single    0.930  0.020  1.080
 VZJ  C19  H7   single    0.970  0.020  1.090
 VZJ  C19  H8   single    0.970  0.020  1.090
 VZJ  C20  H9   single    0.970  0.020  1.090
 VZJ  C20  H10  single    0.970  0.020  1.090
 VZJ  C21  H11  single    0.970  0.020  1.090
 VZJ  C21  H12  single    0.970  0.020  1.090
 VZJ  C21  H13  single    0.970  0.020  1.090
 VZJ  C3   H14  single    0.930  0.020  1.080
 VZJ  N3   H15  single    0.860  0.020  1.020
 VZJ  N4   H16  single    0.860  0.020  1.020
 VZJ  N5   H17  single    0.860  0.020  1.020
 VZJ  C7   H18  single    0.930  0.020  1.080
 VZJ  C8   H19  single    0.930  0.020  1.080
 VZJ  C9   H20  single    0.930  0.020  1.080
 VZJ  C14  H21  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
 VZJ  H3   C13  H2   108.79  3.000
 VZJ  H3   C13  H1   108.97  3.000
 VZJ  H2   C13  H1   108.85  3.000
 VZJ  H3   C13  O2   111.67  3.000
 VZJ  H2   C13  O2   111.43  3.000
 VZJ  H1   C13  O2   107.06  3.000
 VZJ  H4   C18  C20  116.83  3.000
 VZJ  H4   C18  C19  116.55  3.000
 VZJ  C20  C18  C19   58.84  3.000
 VZJ  H4   C18  C17  116.71  3.000
 VZJ  C19  C18  C17  117.33  3.000
 VZJ  C20  C18  C17  118.05  3.000
 VZJ  O3   C17  N3   123.25  3.000
 VZJ  N3   C17  C18  113.77  3.000
 VZJ  O3   C17  C18  122.97  3.000
 VZJ  H5   C16  N7   116.72  3.000
 VZJ  H5   C16  C15  120.90  3.000
 VZJ  N7   C16  C15  122.37  3.000
 VZJ  H6   C15  C14  121.97  3.000
 VZJ  H6   C15  C16  121.96  3.000
 VZJ  C14  C15  C16  116.07  3.000
 VZJ  H8   C19  H7   114.84  3.000
 VZJ  H8   C19  C20  118.31  3.000
 VZJ  H7   C19  C20  118.80  3.000
 VZJ  H8   C19  C18  117.25  3.000
 VZJ  H7   C19  C18  116.41  3.000
 VZJ  C20  C19  C18   60.46  3.000
 VZJ  H10  C20  H9   114.83  3.000
 VZJ  H10  C20  C19  118.27  3.000
 VZJ  H9   C20  C19  118.67  3.000
 VZJ  H10  C20  C18  117.33  3.000
 VZJ  H9   C20  C18  116.38  3.000
 VZJ  C19  C20  C18   60.70  3.000
 VZJ  H13  C21  H12  108.27  3.000
 VZJ  H13  C21  H11  108.42  3.000
 VZJ  H12  C21  H11  108.33  3.000
 VZJ  H13  C21  N4   111.76  3.000
 VZJ  H12  C21  N4   111.67  3.000
 VZJ  H11  C21  N4   108.29  3.000
 VZJ  O2   C11  C10  121.43  3.000
 VZJ  O2   C11  C6   118.38  3.000
 VZJ  C10  C11  C6   120.19  3.000
 VZJ  N7   C12  N6   125.43  3.000
 VZJ  N7   C12  C10  118.22  3.000
 VZJ  N6   C12  C10  116.32  3.000
 VZJ  C5   C1   C4   122.67  3.000
 VZJ  C5   C1   N1   115.79  3.000
 VZJ  C4   C1   N1   121.53  3.000
 VZJ  N2   N1   C1   123.22  3.000
 VZJ  C2   N2   N1   118.50  3.000
 VZJ  N3   C2   C3   124.84  3.000
 VZJ  N3   C2   N2   111.90  3.000
 VZJ  C3   C2   N2   123.26  3.000
 VZJ  H14  C3   C4   121.45  3.000
 VZJ  H14  C3   C2   120.63  3.000
 VZJ  C4   C3   C2   117.92  3.000
 VZJ  N5   C4   C3   123.53  3.000
 VZJ  C3   C4   C1   115.54  3.000
 VZJ  N5   C4   C1   120.92  3.000
 VZJ  O1   C5   N4   122.73  3.000
 VZJ  N4   C5   C1   115.79  3.000
 VZJ  O1   C5   C1   121.48  3.000
 VZJ  H16  N4   C5   117.76  3.000
 VZJ  H16  N4   C21  119.72  3.000
 VZJ  C5   N4   C21  122.51  3.000
 VZJ  C7   C6   N5   122.17  3.000
 VZJ  N5   C6   C11  118.06  3.000
 VZJ  C7   C6   C11  119.71  3.000
 VZJ  H18  C7   C8   119.97  3.000
 VZJ  H18  C7   C6   119.98  3.000
 VZJ  C8   C7   C6   120.05  3.000
 VZJ  H19  C8   C9   120.06  3.000
 VZJ  H19  C8   C7   119.74  3.000
 VZJ  C9   C8   C7   120.18  3.000
 VZJ  H20  C9   C10  119.30  3.000
 VZJ  H20  C9   C8   120.03  3.000
 VZJ  C10  C9   C8   120.66  3.000
 VZJ  C9   C10  C12  118.94  3.000
 VZJ  C9   C10  C11  119.11  3.000
 VZJ  C12  C10  C11  121.95  3.000
 VZJ  C11  O2   C13  114.28  3.000
 VZJ  C14  N6   C12  117.10  3.000
 VZJ  H21  C14  N6   116.79  3.000
 VZJ  H21  C14  C15  121.06  3.000
 VZJ  N6   C14  C15  122.15  3.000
 VZJ  C12  N7   C16  116.88  3.000
 VZJ  H17  N5   C6   118.52  3.000
 VZJ  H17  N5   C4   114.39  3.000
 VZJ  C6   N5   C4   126.67  3.000
 VZJ  H15  N3   C2   113.25  3.000
 VZJ  H15  N3   C17  117.59  3.000
 VZJ  C2   N3   C17  128.78  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
 VZJ  CONST_01  N6   C14  C15  C16     0.00   0.0  0
 VZJ  CONST_02  N6   C12  N7   C16     0.00   0.0  0
 VZJ  CONST_03  C10  C12  N7   C16   180.00   0.0  0
 VZJ  CONST_04  C12  N6   C14  C15     0.00   0.0  0
 VZJ  CONST_05  C12  N7   C16  C15     0.00   0.0  0
 VZJ  CONST_08  C8   C9   C10  C11     0.00   0.0  0
 VZJ  CONST_09  C8   C7   C6   C11     0.00   0.0  0
 VZJ  CONST_10  C8   C9   C10  C12   180.00   0.0  0
 VZJ  CONST_11  C6   C11  C10  C12   180.00   0.0  0
 VZJ  CONST_12  C2   C3   C4   C1      0.00   0.0  0
 VZJ  CONST_13  C2   N2   N1   C1      0.00   0.0  0
 VZJ  CONST_14  C3   C4   C1   N1      0.00   0.0  0
 VZJ  CONST_15  C3   C2   N2   N1      0.00   0.0  0
 VZJ  CONST_16  C4   C3   C2   N2      0.00   0.0  0
 VZJ  CONST_17  C4   C1   N1   N2      0.00   0.0  0
 VZJ  CONST_18  C9   C10  C11  C6      0.00   0.0  0
 VZJ  CONST_19  C9   C8   C7   C6      0.00   0.0  0
 VZJ  CONST_20  C10  C9   C8   C7      0.00   0.0  0
 VZJ  CONST_21  C10  C11  C6   C7      0.00   0.0  0
 VZJ  CONST_24  C14  N6   C12  C10   180.00   0.0  0
 VZJ  CONST_25  N7   C16  C15  C14     0.00   0.0  0
 VZJ  CONST_26  N7   C12  N6   C14     0.00   0.0  0
 VZJ  CONST_27  O2   C11  C10  C12     0.00   0.0  0
 VZJ  CONST_28  N5   C4   C1   N1    180.00   0.0  0
 VZJ  CONST_29  N3   C2   N2   N1    180.00   0.0  0
 VZJ  CONST_30  C5   C1   N1   N2    180.00   0.0  0
 VZJ  CONST_31  N5   C4   C3   C2    180.00   0.0  0
 VZJ  CONST_32  C5   C1   C4   C3    180.00   0.0  0
 VZJ  CONST_33  N3   C2   C3   C4    180.00   0.0  0
 VZJ  CONST_34  C10  C11  C6   N5    180.00   0.0  0
 VZJ  CONST_35  C8   C7   C6   N5    180.00   0.0  0
 VZJ  CONST_36  O2   C11  C6   C7    180.00   0.0  0
 VZJ  CONST_37  O2   C11  C10  C9    180.00   0.0  0
 VZJ  CONST_38  H21  C14  C15  C16   180.00   0.0  0
 VZJ  CONST_39  H20  C9   C10  C11   180.00   0.0  0
 VZJ  CONST_40  H18  C7   C6   C11   180.00   0.0  0
 VZJ  CONST_41  H5   C16  N7   C12   180.00   0.0  0
 VZJ  CONST_42  H14  C3   C4   C1    180.00   0.0  0
 VZJ  CONST_43  H19  C8   C7   C6    180.00   0.0  0
 VZJ  CONST_44  H6   C15  C14  N6    180.00   0.0  0
 VZJ  CONST_45  C2   N3   C17  C18   180.00   0.0  0
 VZJ  CONST_46  C3   C2   N3   C17     0.00   0.0  0
 VZJ  CONST_47  N2   C2   N3   C17   180.00   0.0  0
 VZJ  CONST_48  H15  N3   C2   N2      0.00   0.0  0
 VZJ  CONST_49  C1   C5   N4   C21   180.00   0.0  0
 VZJ  CONST_50  O3   C17  N3   C2      0.00   0.0  0
 VZJ  CONST_51  H16  N4   C5   C1      0.00   0.0  0
 VZJ  CONST_52  O1   C5   N4   C21     0.00   0.0  0
 VZJ  Var_01    C19  C20  C18  C17   106.60  30.0  1
 VZJ  Var_02    C4   N5   C6   C11   131.32  30.0  2
 VZJ  Var_03    C6   N5   C4   C1    179.83  30.0  2
 VZJ  Var_04    H7   C19  C20  C18   105.78  30.0  1
 VZJ  Var_05    C10  C11  O2   C13    87.94  30.0  2
 VZJ  Var_06    O3   C17  C18  C19    38.35  30.0  2
 VZJ  Var_07    O1   C5   C1   N1   -177.11  30.0  2
 VZJ  Var_08    H1   C13  O2   C11   179.22  30.0  3
 VZJ  Var_09    H11  C21  N4   C5   -179.71  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VZJ  chir_01  C18  C20  C17  C19  both

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
 VZJ  plan-1  C16  0.020
 VZJ  plan-1  C15  0.020
 VZJ  plan-1  C12  0.020
 VZJ  plan-1  C10  0.020
 VZJ  plan-1  N6   0.020
 VZJ  plan-1  C14  0.020
 VZJ  plan-1  N7   0.020
 VZJ  plan-1  H5   0.020
 VZJ  plan-1  H6   0.020
 VZJ  plan-1  H21  0.020
 VZJ  plan-2  C1   0.020
 VZJ  plan-2  N1   0.020
 VZJ  plan-2  N2   0.020
 VZJ  plan-2  C2   0.020
 VZJ  plan-2  C3   0.020
 VZJ  plan-2  C4   0.020
 VZJ  plan-2  C5   0.020
 VZJ  plan-2  H14  0.020
 VZJ  plan-2  N5   0.020
 VZJ  plan-2  N3   0.020
 VZJ  plan-3  C11  0.020
 VZJ  plan-3  C12  0.020
 VZJ  plan-3  C6   0.020
 VZJ  plan-3  C7   0.020
 VZJ  plan-3  C8   0.020
 VZJ  plan-3  C9   0.020
 VZJ  plan-3  C10  0.020
 VZJ  plan-3  O2   0.020
 VZJ  plan-3  H18  0.020
 VZJ  plan-3  H19  0.020
 VZJ  plan-3  H20  0.020
 VZJ  plan-3  N5   0.020
 VZJ  plan-4  C21  0.020
 VZJ  plan-4  C1   0.020
 VZJ  plan-4  C5   0.020
 VZJ  plan-4  N4   0.020
 VZJ  plan-4  O1   0.020
 VZJ  plan-4  H16  0.020
 VZJ  plan-5  C18  0.020
 VZJ  plan-5  C17  0.020
 VZJ  plan-5  C2   0.020
 VZJ  plan-5  O3   0.020
 VZJ  plan-5  H15  0.020
 VZJ  plan-5  N3   0.020

