# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:13:59 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2~{R},6~{S})-2,6-dimethyl-4-[6-[5-(1-methylcyclopropyl)oxy-1~{H}-indazol-3-yl]pyrimidin-4-yl]morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(C[C@@H](C)O1)c2cc(ncn2)c3n[nH]c4ccc(OC5(C)CC5)cc34
#
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
 A1N  A1N  (2~{R},6~{S})-2,6-dimethyl-4-[6-[5-(1-methylcyclopropyl)oxy-1~{H}-indazol-3-yl]pyrimidin-4-yl]morpholine  ligand  53  28  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A1N
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
 A1N  C1   C  CH3   0  -0.697   5.0484  -1.6678   1.3611
 A1N  N1   N  NT    0  -0.503   3.8597   0.2323  -0.8222
 A1N  O1   O  O2    0  -0.496   6.4786  -0.1508   0.0381
 A1N  C2   C  CH1   0   0.032   5.6006  -1.2632  -0.0005
 A1N  N2   N  N     0  -0.468  -0.0955   0.9862  -0.0640
 A1N  O2   O  O2    0  -0.492  -5.3332   0.6636   0.2692
 A1N  C3   C  CH2   0  -0.344   4.4906  -1.0527  -1.0295
 A1N  N3   N  N     0  -0.478   2.1347   1.6963  -0.4227
 A1N  C4   C  CH2   0  -0.339   4.8146   1.3153  -0.9422
 A1N  N4   N  N     0  -0.251  -0.4334  -2.5901  -0.0696
 A1N  C5   C  CH1   0   0.021   5.9142   1.1503   0.1004
 A1N  N5   N  NR15  0  -0.529  -1.5669  -3.2551   0.0445
 A1N  C6   C  CH3   0  -0.688   5.4543   1.5543   1.4953
 A1N  C7   C  CR6   0   0.581   2.5518   0.4280  -0.5598
 A1N  C8   C  CR16  0  -0.430   1.6238  -0.6249  -0.4365
 A1N  C9   C  CR6   0   0.232   0.3083  -0.2878  -0.1912
 A1N  C10  C  CR16  0   0.054   0.8535   1.8936  -0.1871
 A1N  C11  C  CR5   0   0.171  -0.7313  -1.3053  -0.0635
 A1N  C12  C  CR56  0   0.388  -2.6439  -2.4328   0.1259
 A1N  C13  C  CR16  0  -0.278  -4.0127  -2.6969   0.2418
 A1N  C14  C  CR16  0  -0.352  -4.8543  -1.6150   0.2830
 A1N  C15  C  CR6   0   0.392  -4.3665  -0.2859   0.2158
 A1N  C16  C  CT    0   0.236  -4.9729   2.0172   0.1660
 A1N  C17  C  CH3   0  -0.689  -4.6692   2.4719  -1.2373
 A1N  C18  C  CH2   0  -0.515  -5.7362   2.9125   1.0803
 A1N  C19  C  CH2   0  -0.511  -4.2813   2.6306   1.3420
 A1N  C20  C  CR16  0  -0.474  -3.0168  -0.0275   0.1103
 A1N  C21  C  CR56  0  -0.054  -2.1420  -1.1257   0.0619
 A1N  H1   H  HCH3  0   0.227   4.2286  -1.0345   1.6995
 A1N  H2   H  HCH3  0   0.239   4.6664  -2.6881   1.3032
 A1N  H3   H  HCH3  0   0.241   5.8295  -1.6461   2.1211
 A1N  H4   H  HCH1  0   0.239   6.2217  -2.0872  -0.3625
 A1N  H5   H  HCH2  0   0.272   3.7781  -1.8705  -0.9666
 A1N  H6   H  HCH2  0   0.262   4.9127  -1.0718  -2.0398
 A1N  H7   H  HCH2  0   0.253   5.2490   1.2862  -1.9479
 A1N  H8   H  HCH2  0   0.279   4.3152   2.2720  -0.8211
 A1N  H10  H  HCH1  0   0.238   6.7333   1.8171  -0.1843
 A1N  H11  H  HCH3  0   0.238   6.2305   1.3517   2.2337
 A1N  H12  H  HCH3  0   0.235   5.2522   2.6263   1.5125
 A1N  H13  H  HCH3  0   0.228   4.5450   1.0445   1.8103
 A1N  H14  H  HCR6  0   0.272   1.9011  -1.6625  -0.5367
 A1N  H15  H  HCR6  0   0.248   0.5446   2.9295  -0.0830
 A1N  H16  H  HCR6  0   0.275  -4.3975  -3.7066   0.2950
 A1N  H17  H  HCR6  0   0.269  -5.9226  -1.7678   0.3699
 A1N  H18  H  HCH3  0   0.239  -3.8277   1.9311  -1.6719
 A1N  H19  H  HCH3  0   0.241  -5.5342   2.3301  -1.8868
 A1N  H20  H  HCH3  0   0.238  -4.4151   3.5313  -1.2448
 A1N  H21  H  HCH2  0   0.256  -6.0196   3.8891   0.7085
 A1N  H22  H  HCH2  0   0.262  -6.4598   2.4591   1.7465
 A1N  H23  H  HCH2  0   0.266  -4.0424   1.9918   2.1835
 A1N  H24  H  HCH2  0   0.257  -3.5543   3.4117   1.1571
 A1N  H25  H  HCR6  0   0.285  -2.6180   0.9735   0.0690
 A1N  H9   H  HNR5  0   0.422  -1.5553  -4.2622   0.0631

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
 A1N  C17  C16  single    1.506  0.020  1.506
 A1N  C18  C16  single    1.490  0.020  1.490
 A1N  C18  C19  single    1.505  0.020  1.505
 A1N  C16  C19  single    1.496  0.020  1.496
 A1N  C16  O2   single    1.405  0.020  1.405
 A1N  O2   C15  single    1.356  0.020  1.356
 A1N  C15  C20  aromatic  1.378  0.020  1.378
 A1N  C15  C14  aromatic  1.417  0.020  1.417
 A1N  C20  C21  aromatic  1.405  0.020  1.405
 A1N  C14  C13  aromatic  1.371  0.020  1.371
 A1N  C10  N2   aromatic  1.319  0.020  1.319
 A1N  C10  N3   aromatic  1.318  0.020  1.318
 A1N  N2   C9   aromatic  1.342  0.020  1.342
 A1N  C21  C12  aromatic  1.402  0.020  1.402
 A1N  C21  C11  aromatic  1.428  0.020  1.428
 A1N  C13  C12  aromatic  1.399  0.020  1.399
 A1N  N3   C7   aromatic  1.342  0.020  1.342
 A1N  C12  N5   aromatic  1.357  0.020  1.357
 A1N  C9   C11  single    1.460  0.020  1.460
 A1N  C9   C8   aromatic  1.380  0.020  1.380
 A1N  C11  N4   aromatic  1.319  0.020  1.319
 A1N  C7   C8   aromatic  1.409  0.020  1.409
 A1N  C7   N1   single    1.348  0.020  1.348
 A1N  N5   N4   aromatic  1.319  0.020  1.319
 A1N  C3   N1   single    1.446  0.020  1.446
 A1N  C3   C2   single    1.528  0.020  1.528
 A1N  N1   C4   single    1.449  0.020  1.449
 A1N  C1   C2   single    1.524  0.020  1.524
 A1N  C2   O1   single    1.418  0.020  1.418
 A1N  C4   C5   single    1.524  0.020  1.524
 A1N  O1   C5   single    1.420  0.020  1.420
 A1N  C5   C6   single    1.523  0.020  1.523
 A1N  C1   H1   single    0.970  0.020  1.090
 A1N  C1   H2   single    0.970  0.020  1.090
 A1N  C1   H3   single    0.970  0.020  1.090
 A1N  C2   H4   single    0.970  0.020  1.090
 A1N  C3   H5   single    0.970  0.020  1.090
 A1N  C3   H6   single    0.970  0.020  1.090
 A1N  C4   H7   single    0.970  0.020  1.090
 A1N  C4   H8   single    0.970  0.020  1.090
 A1N  C5   H10  single    0.970  0.020  1.090
 A1N  C6   H11  single    0.970  0.020  1.090
 A1N  C6   H12  single    0.970  0.020  1.090
 A1N  C6   H13  single    0.970  0.020  1.090
 A1N  C8   H14  single    0.930  0.020  1.080
 A1N  C10  H15  single    0.930  0.020  1.080
 A1N  C13  H16  single    0.930  0.020  1.080
 A1N  C14  H17  single    0.930  0.020  1.080
 A1N  C17  H18  single    0.970  0.020  1.090
 A1N  C17  H19  single    0.970  0.020  1.090
 A1N  C17  H20  single    0.970  0.020  1.090
 A1N  C18  H21  single    0.970  0.020  1.090
 A1N  C18  H22  single    0.970  0.020  1.090
 A1N  C19  H23  single    0.970  0.020  1.090
 A1N  C19  H24  single    0.970  0.020  1.090
 A1N  C20  H25  single    0.930  0.020  1.080
 A1N  N5   H9   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
 A1N  H3   C1   H2   107.85  3.000
 A1N  H3   C1   H1   108.11  3.000
 A1N  H2   C1   H1   107.25  3.000
 A1N  H3   C1   C2   110.98  3.000
 A1N  H2   C1   C2   109.13  3.000
 A1N  H1   C1   C2   113.31  3.000
 A1N  C7   N1   C4   123.16  3.000
 A1N  C4   N1   C3   111.39  3.000
 A1N  C7   N1   C3   125.44  3.000
 A1N  C5   O1   C2   118.31  3.000
 A1N  H4   C2   C3   107.06  3.000
 A1N  H4   C2   O1   104.40  3.000
 A1N  C3   C2   O1   111.11  3.000
 A1N  H4   C2   C1   107.55  3.000
 A1N  O1   C2   C1   114.10  3.000
 A1N  C3   C2   C1   112.02  3.000
 A1N  C10  N2   C9   115.32  3.000
 A1N  C16  O2   C15  119.27  3.000
 A1N  H6   C3   H5   107.04  3.000
 A1N  H6   C3   C2   109.80  3.000
 A1N  H5   C3   C2   109.49  3.000
 A1N  H6   C3   N1   108.41  3.000
 A1N  H5   C3   N1   111.99  3.000
 A1N  C2   C3   N1   110.04  3.000
 A1N  C10  N3   C7   117.52  3.000
 A1N  H8   C4   H7   107.93  3.000
 A1N  H8   C4   C5   110.54  3.000
 A1N  H7   C4   C5   109.81  3.000
 A1N  H8   C4   N1   110.26  3.000
 A1N  H7   C4   N1   108.51  3.000
 A1N  C5   C4   N1   109.75  3.000
 A1N  C11  N4   N5   107.25  3.000
 A1N  H10  C5   C6   107.63  3.000
 A1N  H10  C5   C4   107.23  3.000
 A1N  C6   C5   C4   112.32  3.000
 A1N  H10  C5   O1   104.45  3.000
 A1N  C6   C5   O1   113.78  3.000
 A1N  C4   C5   O1   110.85  3.000
 A1N  H9   N5   C12  127.85  3.000
 A1N  H9   N5   N4   119.72  3.000
 A1N  C12  N5   N4   112.43  3.000
 A1N  H13  C6   H12  107.51  3.000
 A1N  H13  C6   H11  108.15  3.000
 A1N  H12  C6   H11  107.69  3.000
 A1N  H13  C6   C5   113.13  3.000
 A1N  H12  C6   C5   109.32  3.000
 A1N  H11  C6   C5   110.85  3.000
 A1N  C8   C7   N3   119.51  3.000
 A1N  C8   C7   N1   123.20  3.000
 A1N  N3   C7   N1   117.29  3.000
 A1N  H14  C8   C9   119.77  3.000
 A1N  H14  C8   C7   122.78  3.000
 A1N  C9   C8   C7   117.45  3.000
 A1N  C11  C9   C8   121.60  3.000
 A1N  C8   C9   N2   122.37  3.000
 A1N  C11  C9   N2   116.03  3.000
 A1N  H15  C10  N3   115.89  3.000
 A1N  H15  C10  N2   116.28  3.000
 A1N  N3   C10  N2   127.83  3.000
 A1N  C21  C11  C9   128.58  3.000
 A1N  C9   C11  N4   121.16  3.000
 A1N  C21  C11  N4   110.25  3.000
 A1N  C21  C12  C13  122.02  3.000
 A1N  C13  C12  N5   131.83  3.000
 A1N  C21  C12  N5   106.15  3.000
 A1N  H16  C13  C14  121.11  3.000
 A1N  H16  C13  C12  121.89  3.000
 A1N  C14  C13  C12  117.00  3.000
 A1N  H17  C14  C15  118.40  3.000
 A1N  H17  C14  C13  119.78  3.000
 A1N  C15  C14  C13  121.82  3.000
 A1N  C20  C15  C14  121.09  3.000
 A1N  C14  C15  O2   114.17  3.000
 A1N  C20  C15  O2   124.74  3.000
 A1N  C19  C16  C18   60.53  3.000
 A1N  C19  C16  C17  121.03  3.000
 A1N  C18  C16  C17  119.58  3.000
 A1N  C19  C16  O2   117.13  3.000
 A1N  C18  C16  O2   113.74  3.000
 A1N  C17  C16  O2   114.28  3.000
 A1N  H20  C17  H19  107.89  3.000
 A1N  H20  C17  H18  107.43  3.000
 A1N  H19  C17  H18  108.07  3.000
 A1N  H20  C17  C16  110.30  3.000
 A1N  H19  C17  C16  110.83  3.000
 A1N  H18  C17  C16  112.16  3.000
 A1N  H22  C18  H21  114.45  3.000
 A1N  H22  C18  C19  117.42  3.000
 A1N  H21  C18  C19  118.80  3.000
 A1N  H22  C18  C16  117.91  3.000
 A1N  H21  C18  C16  117.73  3.000
 A1N  C19  C18  C16   59.92  3.000
 A1N  H24  C19  H23  114.21  3.000
 A1N  H24  C19  C18  118.96  3.000
 A1N  H23  C19  C18  117.31  3.000
 A1N  H24  C19  C16  118.16  3.000
 A1N  H23  C19  C16  118.09  3.000
 A1N  C18  C19  C16   59.54  3.000
 A1N  H25  C20  C21  119.61  3.000
 A1N  H25  C20  C15  122.62  3.000
 A1N  C21  C20  C15  117.77  3.000
 A1N  C20  C21  C12  120.30  3.000
 A1N  C12  C21  C11  103.92  3.000
 A1N  C20  C21  C11  135.78  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
 A1N  CONST_01  C7   N3   C10  N2      0.00   0.0  0
 A1N  CONST_02  C21  C11  C9   N2      0.00   0.0  0
 A1N  CONST_03  N4   C11  C9   N2    180.00   0.0  0
 A1N  CONST_04  C7   C8   C9   N2      0.00   0.0  0
 A1N  CONST_05  C9   N2   C10  N3      0.00   0.0  0
 A1N  CONST_06  C9   C8   C7   N3      0.00   0.0  0
 A1N  CONST_07  C20  C21  C11  N4    180.00   0.0  0
 A1N  CONST_08  C12  C21  C11  N4      0.00   0.0  0
 A1N  CONST_09  C8   C9   C11  N4      0.00   0.0  0
 A1N  CONST_10  C21  C12  N5   N4      0.00   0.0  0
 A1N  CONST_11  C13  C12  N5   N4    180.00   0.0  0
 A1N  CONST_12  C20  C21  C12  N5    180.00   0.0  0
 A1N  CONST_13  C11  C21  C12  N5      0.00   0.0  0
 A1N  CONST_14  C14  C13  C12  N5    180.00   0.0  0
 A1N  CONST_15  C21  C11  N4   N5      0.00   0.0  0
 A1N  CONST_16  C9   C11  N4   N5    180.00   0.0  0
 A1N  CONST_17  C11  C9   C8   C7    180.00   0.0  0
 A1N  CONST_18  C10  N2   C9   C8      0.00   0.0  0
 A1N  CONST_19  C21  C11  C9   C8    180.00   0.0  0
 A1N  CONST_20  C10  N3   C7   C8      0.00   0.0  0
 A1N  CONST_21  C20  C21  C11  C9      0.00   0.0  0
 A1N  CONST_22  C12  C21  C11  C9    180.00   0.0  0
 A1N  CONST_23  C11  C9   N2   C10   180.00   0.0  0
 A1N  CONST_24  C15  C20  C21  C11   180.00   0.0  0
 A1N  CONST_25  C13  C12  C21  C11   180.00   0.0  0
 A1N  CONST_26  C12  N5   N4   C11     0.00   0.0  0
 A1N  CONST_27  C15  C20  C21  C12     0.00   0.0  0
 A1N  CONST_28  C15  C14  C13  C12     0.00   0.0  0
 A1N  CONST_29  C20  C15  C14  C13     0.00   0.0  0
 A1N  CONST_30  C20  C21  C12  C13     0.00   0.0  0
 A1N  CONST_31  C21  C20  C15  C14     0.00   0.0  0
 A1N  CONST_32  C21  C12  C13  C14     0.00   0.0  0
 A1N  CONST_33  C10  N3   C7   N1    180.00   0.0  0
 A1N  CONST_34  C9   C8   C7   N1    180.00   0.0  0
 A1N  CONST_35  C21  C20  C15  O2    180.00   0.0  0
 A1N  CONST_36  C13  C14  C15  O2    180.00   0.0  0
 A1N  CONST_37  H14  C8   C7   N1      0.00   0.0  0
 A1N  CONST_38  H16  C13  C12  N5      0.00   0.0  0
 A1N  CONST_39  H15  C10  N3   C7    180.00   0.0  0
 A1N  CONST_40  H25  C20  C21  C11     0.00   0.0  0
 A1N  CONST_41  H9   N5   N4   C11   180.00   0.0  0
 A1N  CONST_42  H17  C14  C13  C12   180.00   0.0  0
 A1N  Var_01    C7   N1   C3   C2   -121.06  30.0  1
 A1N  Var_02    N3   C7   N1   C3   -178.66  30.0  2
 A1N  Var_03    C5   C4   N1   C3    -60.17  30.0  1
 A1N  Var_04    C19  C18  C16  O2    108.89  30.0  1
 A1N  Var_05    C18  C16  O2   C15  -140.18  30.0  3
 A1N  Var_06    C20  C15  O2   C16     2.33  30.0  2
 A1N  Var_07    H23  C19  C18  C16  -108.13  30.0  1
 A1N  Var_08    H18  C17  C16  C18   158.92  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
 A1N  chir_01  C2   C3   C1   O1  positiv
 A1N  chir_02  C5   O1   C6   C4  positiv
 A1N  chir_03  C16  C18  C19  O2  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
 A1N  plan-1  N1   0.020
 A1N  plan-1  N2   0.020
 A1N  plan-1  N3   0.020
 A1N  plan-1  C7   0.020
 A1N  plan-1  C8   0.020
 A1N  plan-1  C9   0.020
 A1N  plan-1  C10  0.020
 A1N  plan-1  C11  0.020
 A1N  plan-1  H14  0.020
 A1N  plan-1  H15  0.020
 A1N  plan-2  O2   0.020
 A1N  plan-2  N4   0.020
 A1N  plan-2  N5   0.020
 A1N  plan-2  C9   0.020
 A1N  plan-2  C11  0.020
 A1N  plan-2  C12  0.020
 A1N  plan-2  C13  0.020
 A1N  plan-2  C14  0.020
 A1N  plan-2  C15  0.020
 A1N  plan-2  C20  0.020
 A1N  plan-2  C21  0.020
 A1N  plan-2  H16  0.020
 A1N  plan-2  H17  0.020
 A1N  plan-2  H25  0.020
 A1N  plan-2  H9   0.020

