# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:35:37 2021
#   Inital geometry file: a 121 line input string
#   Ligand name: ~{N}2-[4-methoxy-3-(2,3,4,7-tetrahydro-1~{H}-azepin-5-yl)phenyl]-~{N}4,6-dimethyl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(C)nc(Nc2ccc(OC)c(c2)C3=CCNCCC3)n1
#
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
 F80  F80  ~{N}2-[4-methoxy-3-(2,3,4,7-tetrahydro-1~{H}-azepin-5-yl)phenyl]-~{N}4,6-dimethyl-pyrimidine-2,4-diamine  ligand  50  25  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_F80
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
 F80  C2   C  CH3   0  -0.723  11.7003  19.1822  26.5254
 F80  C1   C  CR6   0   0.284  10.2431  18.9714  26.7894
 F80  N1   N  N     0  -0.527   9.8626  17.7167  27.0528
 F80  C3   C  CR16  0  -0.486   9.3516  20.0202  26.7636
 F80  C5   C  CR6   0   0.583   8.0017  19.7126  27.0284
 F80  N2   N  NH1   0  -0.658   7.0558  20.6614  27.0193
 F80  C4   C  CH3   0  -0.517   5.6621  20.4057  27.2817
 F80  N3   N  N     0  -0.533   7.6186  18.4634  27.2951
 F80  C20  C  CR6   0   0.572   8.5652  17.5340  27.2934
 F80  N5   N  NH1   0  -0.776   8.2259  16.2404  27.5572
 F80  C6   C  CR6   0   0.366   7.0093  15.6498  27.8917
 F80  C8   C  CR16  0  -0.324   5.7986  16.3159  28.0566
 F80  C9   C  CR16  0  -0.373   4.6563  15.6063  28.4092
 F80  C11  C  CR6   0   0.316   4.6765  14.2298  28.5985
 F80  O1   O  O2    0  -0.464   3.5948  13.5093  28.9662
 F80  C10  C  CH3   0  -0.436   2.3811  14.1909  29.1966
 F80  C7   C  CR16  0  -0.405   7.0201  14.2657  28.0861
 F80  C19  C  CR6   0  -0.031   5.8878  13.5373  28.4242
 F80  C12  C  C     0   0.118   6.0191  12.0707  28.6060
 F80  C17  C  C1    0  -0.262   5.2092  11.2141  27.9814
 F80  C16  C  CH2   0  -0.352   5.3303   9.7174  28.0797
 F80  N4   N  NH1   0  -0.589   6.5873   9.2085  27.5474
 F80  C15  C  CH2   0  -0.293   7.6911   9.2768  28.4870
 F80  C14  C  CH2   0  -0.420   8.1748  10.6935  28.7631
 F80  C13  C  CH2   0  -0.537   7.1557  11.5840  29.4780
 F80  H1   H  HCH3  0   0.252  12.2902  18.8880  27.3945
 F80  H2   H  HCH3  0   0.252  12.0297  18.5624  25.6905
 F80  H3   H  HCH3  0   0.244  11.9243  20.2214  26.2930
 F80  H4   H  HCR6  0   0.261   9.6683  21.0312  26.5478
 F80  H5   H  HNH1  0   0.402   7.3396  21.6069  26.8314
 F80  H6   H  HCH3  0   0.254   5.1200  21.3419  27.1806
 F80  H7   H  HCH3  0   0.234   5.2408  19.6886  26.5759
 F80  H8   H  HCH3  0   0.233   5.4977  20.0221  28.2902
 F80  H9   H  HNH1  0   0.400   9.0142  15.6126  27.5222
 F80  H10  H  HCR6  0   0.301   5.7370  17.3828  27.9202
 F80  H11  H  HCR6  0   0.274   3.7424  16.1697  28.5415
 F80  H12  H  HCH3  0   0.256   1.6566  13.4384  29.4994
 F80  H13  H  HCH3  0   0.224   2.4711  14.9331  29.9949
 F80  H14  H  HCH3  0   0.224   2.0117  14.6908  28.2968
 F80  H15  H  HCR6  0   0.262   7.9549  13.7296  27.9575
 F80  H16  H  H     0   0.238   4.4182  11.5981  27.3477
 F80  H17  H  HCH2  0   0.243   4.5195   9.2646  27.5086
 F80  H18  H  HCH2  0   0.205   5.1747   9.4077  29.1286
 F80  H19  H  HNH1  0   0.352   6.4508   8.2387  27.2944
 F80  H21  H  HCH2  0   0.183   7.4362   8.8094  29.4541
 F80  H22  H  HCH2  0   0.230   8.5197   8.6989  28.0713
 F80  H23  H  HCH2  0   0.230   9.0660  10.6180  29.3918
 F80  H24  H  HCH2  0   0.220   8.4891  11.1665  27.8284
 F80  H25  H  HCH2  0   0.249   7.6729  12.4400  29.9129
 F80  H26  H  HCH2  0   0.245   6.7423  11.0297  30.3292

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
 F80  N2   C4   single    1.441  0.020  1.441
 F80  N2   C5   single    1.340  0.020  1.340
 F80  C3   C5   aromatic  1.410  0.020  1.410
 F80  C3   C1   aromatic  1.377  0.020  1.377
 F80  C5   N3   aromatic  1.334  0.020  1.334
 F80  C2   C1   single    1.496  0.020  1.496
 F80  C1   N1   aromatic  1.337  0.020  1.337
 F80  N3   C20  aromatic  1.327  0.020  1.327
 F80  N4   C16  single    1.457  0.020  1.457
 F80  N4   C15  single    1.451  0.020  1.451
 F80  N1   C20  aromatic  1.332  0.020  1.332
 F80  C16  C17  single    1.505  0.020  1.505
 F80  C20  N5   single    1.363  0.020  1.363
 F80  C17  C12  double    1.334  0.020  1.334
 F80  N5   C6   single    1.393  0.020  1.393
 F80  C7   C6   aromatic  1.398  0.020  1.398
 F80  C7   C19  aromatic  1.388  0.020  1.388
 F80  C6   C8   aromatic  1.392  0.020  1.392
 F80  C15  C14  single    1.522  0.020  1.522
 F80  C12  C19  single    1.484  0.020  1.484
 F80  C12  C13  single    1.513  0.020  1.513
 F80  C19  C11  aromatic  1.406  0.020  1.406
 F80  C8   C9   aromatic  1.390  0.020  1.390
 F80  C14  C13  single    1.531  0.020  1.531
 F80  C11  C9   aromatic  1.390  0.020  1.390
 F80  C11  O1   single    1.351  0.020  1.351
 F80  O1   C10  single    1.411  0.020  1.411
 F80  C2   H1   single    0.970  0.020  1.090
 F80  C2   H2   single    0.970  0.020  1.090
 F80  C2   H3   single    0.970  0.020  1.090
 F80  C3   H4   single    0.930  0.020  1.080
 F80  N2   H5   single    0.860  0.020  1.020
 F80  C4   H6   single    0.970  0.020  1.090
 F80  C4   H7   single    0.970  0.020  1.090
 F80  C4   H8   single    0.970  0.020  1.090
 F80  N5   H9   single    0.860  0.020  1.020
 F80  C8   H10  single    0.930  0.020  1.080
 F80  C9   H11  single    0.930  0.020  1.080
 F80  C10  H12  single    0.970  0.020  1.090
 F80  C10  H13  single    0.970  0.020  1.090
 F80  C10  H14  single    0.970  0.020  1.090
 F80  C7   H15  single    0.930  0.020  1.080
 F80  C17  H16  single    0.930  0.020  1.080
 F80  C16  H17  single    0.970  0.020  1.090
 F80  C16  H18  single    0.970  0.020  1.090
 F80  N4   H19  single    0.890  0.020  1.040
 F80  C15  H21  single    0.970  0.020  1.090
 F80  C15  H22  single    0.970  0.020  1.090
 F80  C14  H23  single    0.970  0.020  1.090
 F80  C14  H24  single    0.970  0.020  1.090
 F80  C13  H25  single    0.970  0.020  1.090
 F80  C13  H26  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
 F80  H3   C2   H2   108.49  3.000
 F80  H3   C2   H1   108.44  3.000
 F80  H2   C2   H1   107.05  3.000
 F80  H3   C2   C1   111.89  3.000
 F80  H2   C2   C1   110.44  3.000
 F80  H1   C2   C1   110.38  3.000
 F80  C3   C1   N1   122.29  3.000
 F80  N1   C1   C2   116.37  3.000
 F80  C3   C1   C2   121.34  3.000
 F80  C20  N1   C1   116.19  3.000
 F80  H4   C3   C5   121.47  3.000
 F80  H4   C3   C1   121.76  3.000
 F80  C5   C3   C1   116.77  3.000
 F80  N3   C5   N2   117.51  3.000
 F80  N3   C5   C3   121.14  3.000
 F80  N2   C5   C3   121.36  3.000
 F80  H5   N2   C4   118.30  3.000
 F80  H5   N2   C5   117.92  3.000
 F80  C4   N2   C5   123.77  3.000
 F80  H8   C4   H7   107.98  3.000
 F80  H8   C4   H6   108.29  3.000
 F80  H7   C4   H6   108.27  3.000
 F80  H8   C4   N2   112.11  3.000
 F80  H7   C4   N2   111.85  3.000
 F80  H6   C4   N2   108.22  3.000
 F80  C20  N3   C5   116.81  3.000
 F80  N5   C20  N3   119.14  3.000
 F80  N5   C20  N1   114.05  3.000
 F80  N3   C20  N1   126.81  3.000
 F80  H9   N5   C6   115.28  3.000
 F80  H9   N5   C20  112.92  3.000
 F80  C6   N5   C20  131.77  3.000
 F80  C7   C6   C8   117.66  3.000
 F80  C8   C6   N5   125.83  3.000
 F80  C7   C6   N5   116.52  3.000
 F80  H10  C8   C9   119.38  3.000
 F80  H10  C8   C6   120.57  3.000
 F80  C9   C8   C6   120.04  3.000
 F80  H11  C9   C11  120.76  3.000
 F80  H11  C9   C8   117.35  3.000
 F80  C11  C9   C8   121.89  3.000
 F80  C19  C11  O1   117.45  3.000
 F80  O1   C11  C9   123.63  3.000
 F80  C19  C11  C9   118.91  3.000
 F80  C10  O1   C11  118.40  3.000
 F80  H14  C10  H13  108.55  3.000
 F80  H14  C10  H12  108.69  3.000
 F80  H13  C10  H12  108.73  3.000
 F80  H14  C10  O1   112.14  3.000
 F80  H13  C10  O1   112.10  3.000
 F80  H12  C10  O1   106.51  3.000
 F80  H15  C7   C19  118.18  3.000
 F80  H15  C7   C6   118.64  3.000
 F80  C19  C7   C6   123.17  3.000
 F80  C12  C19  C7   118.44  3.000
 F80  C12  C19  C11  123.22  3.000
 F80  C7   C19  C11  118.32  3.000
 F80  C13  C12  C17  121.29  3.000
 F80  C13  C12  C19  117.07  3.000
 F80  C17  C12  C19  121.57  3.000
 F80  H16  C17  C16  116.70  3.000
 F80  H16  C17  C12  119.30  3.000
 F80  C16  C17  C12  124.00  3.000
 F80  H18  C16  H17  106.03  3.000
 F80  H18  C16  N4   111.75  3.000
 F80  H17  C16  N4   107.77  3.000
 F80  H18  C16  C17  109.24  3.000
 F80  H17  C16  C17  108.60  3.000
 F80  N4   C16  C17  113.15  3.000
 F80  H19  N4   C15  108.04  3.000
 F80  H19  N4   C16  108.06  3.000
 F80  C15  N4   C16  113.78  3.000
 F80  H22  C15  H21  106.53  3.000
 F80  H22  C15  C14  108.68  3.000
 F80  H21  C15  C14  107.97  3.000
 F80  H22  C15  N4   107.80  3.000
 F80  H21  C15  N4   111.82  3.000
 F80  C14  C15  N4   113.77  3.000
 F80  H24  C14  H23  106.69  3.000
 F80  H24  C14  C13  109.81  3.000
 F80  H23  C14  C13  108.32  3.000
 F80  H24  C14  C15  109.80  3.000
 F80  H23  C14  C15  107.40  3.000
 F80  C13  C14  C15  114.49  3.000
 F80  H26  C13  H25  105.43  3.000
 F80  H26  C13  C14  108.63  3.000
 F80  H25  C13  C14  109.09  3.000
 F80  H26  C13  C12  109.07  3.000
 F80  H25  C13  C12  109.49  3.000
 F80  C14  C13  C12  114.72  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
 F80  CONST_01  N3   C5   C3   C1      0.00   0.0  0
 F80  CONST_02  N3   C20  N1   C1      0.00   0.0  0
 F80  CONST_03  C5   C3   C1   N1      0.00   0.0  0
 F80  CONST_04  C5   N3   C20  N1      0.00   0.0  0
 F80  CONST_05  C20  N3   C5   C3      0.00   0.0  0
 F80  CONST_06  C20  N1   C1   C3      0.00   0.0  0
 F80  CONST_07  C11  C19  C7   C6      0.00   0.0  0
 F80  CONST_08  C11  C9   C8   C6      0.00   0.0  0
 F80  CONST_09  C19  C7   C6   C8      0.00   0.0  0
 F80  CONST_10  C19  C11  C9   C8      0.00   0.0  0
 F80  CONST_11  C7   C6   C8   C9      0.00   0.0  0
 F80  CONST_12  C7   C19  C11  C9      0.00   0.0  0
 F80  CONST_13  C12  C19  C7   C6    180.00   0.0  0
 F80  CONST_14  C12  C19  C11  C9    180.00   0.0  0
 F80  CONST_15  C5   C3   C1   C2    180.00   0.0  0
 F80  CONST_16  C20  N1   C1   C2    180.00   0.0  0
 F80  CONST_17  N2   C5   C3   C1    180.00   0.0  0
 F80  CONST_18  N5   C20  N1   C1    180.00   0.0  0
 F80  CONST_19  N5   C20  N3   C5    180.00   0.0  0
 F80  CONST_20  C20  N3   C5   N2    180.00   0.0  0
 F80  CONST_21  C19  C7   C6   N5    180.00   0.0  0
 F80  CONST_22  C9   C8   C6   N5    180.00   0.0  0
 F80  CONST_23  O1   C11  C9   C8    180.00   0.0  0
 F80  CONST_24  C7   C19  C11  O1    180.00   0.0  0
 F80  CONST_25  C12  C19  C11  O1      0.00   0.0  0
 F80  CONST_26  H4   C3   C1   N1    180.00   0.0  0
 F80  CONST_27  H11  C9   C8   C6    180.00   0.0  0
 F80  CONST_28  H15  C7   C6   C8    180.00   0.0  0
 F80  CONST_29  H10  C8   C9   C11   180.00   0.0  0
 F80  CONST_30  C4   N2   C5   C3    180.00   0.0  0
 F80  CONST_31  N3   C5   N2   C4      0.00   0.0  0
 F80  CONST_32  H5   N2   C5   C3      0.00   0.0  0
 F80  Var_01    C6   N5   C20  N1    177.78  30.0  2
 F80  Var_02    C7   C6   N5   C20   179.45  30.0  2
 F80  Var_03    C19  C11  O1   C10   177.61  30.0  1
 F80  Var_04    H1   C2   C1   N1    -60.72  30.0  2
 F80  Var_05    H6   C4   N2   C5   -178.35  30.0  3
 F80  Var_06    H12  C10  O1   C11  -178.76  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
 F80  plan-1  C2   0.020
 F80  plan-1  C1   0.020
 F80  plan-1  N1   0.020
 F80  plan-1  C3   0.020
 F80  plan-1  C5   0.020
 F80  plan-1  N2   0.020
 F80  plan-1  N3   0.020
 F80  plan-1  C20  0.020
 F80  plan-1  N5   0.020
 F80  plan-1  H4   0.020
 F80  plan-2  N5   0.020
 F80  plan-2  C6   0.020
 F80  plan-2  C8   0.020
 F80  plan-2  C9   0.020
 F80  plan-2  C11  0.020
 F80  plan-2  O1   0.020
 F80  plan-2  C7   0.020
 F80  plan-2  C19  0.020
 F80  plan-2  C12  0.020
 F80  plan-2  H10  0.020
 F80  plan-2  H11  0.020
 F80  plan-2  H15  0.020
 F80  plan-3  C5   0.020
 F80  plan-3  N2   0.020
 F80  plan-3  C4   0.020
 F80  plan-3  H5   0.020

