# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:12:53 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (2R)-2-[(2-amino-7-fluoropyrido[3,2-d]pyrimidin-4-yl)amino]-2-methylhexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@](C)(CO)Nc1nc(N)nc2cc(F)cnc12
#
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
 U57  U57  (2R)-2-[(2-amino-7-fluoropyrido[3,2-d]pyrimidin-4-yl)amino]-2-methylhexan-1-ol  ligand  41  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U57
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
 U57  C11  C  CH2   0  -0.415  139.1905  18.2286  22.4342
 U57  C12  C  CH2   0  -0.416  138.1919  18.6576  21.3657
 U57  C13  C  CH2   0  -0.124  140.5819  14.6891  23.2549
 U57  C15  C  CH3   0  -0.660  137.8909  20.1490  21.4071
 U57  C16  C  CH3   0  -0.693  141.7521  16.8846  23.4977
 U57  C01  C  CR66  0   0.270  137.0180  15.9965  27.0911
 U57  C02  C  CR66  0   0.059  138.2618  16.4550  26.6228
 U57  C03  C  CR6   0   0.548  138.6354  16.0303  25.2884
 U57  C07  C  CR6   0   0.522  136.6600  14.8866  25.1572
 U57  C09  C  CT    0   0.071  140.3895  16.1914  23.4930
 U57  C10  C  CH2   0  -0.415  139.5044  16.7401  22.3611
 U57  C18  C  CR16  0  -0.229  138.7244  17.6260  28.5242
 U57  C19  C  CR6   0   0.454  137.4988  17.2204  29.0700
 U57  C20  C  CR16  0  -0.388  136.6393  16.4124  28.3848
 U57  F21  F  F     0  -0.298  137.1832  17.6498  30.2950
 U57  N04  N  N     0  -0.532  136.2117  15.2042  26.3597
 U57  N05  N  N     0  -0.519  137.8268  15.2637  24.5907
 U57  N06  N  NH1   0  -0.663  139.8006  16.4490  24.8064
 U57  N08  N  NH2   0  -0.821  135.8726  14.1185  24.3830
 U57  N17  N  N     0  -0.410  139.0816  17.2407  27.3242
 U57  H1   H  HCH2  0   0.216  140.1057  18.8170  22.3219
 U57  H2   H  HCH2  0   0.214  138.7860  18.4780  23.4203
 U57  H3   H  HCH2  0   0.211  137.2636  18.0921  21.4922
 U57  H4   H  HCH2  0   0.211  138.5781  18.3885  20.3776
 U57  H5   H  HCH2  0   0.213  139.6074  14.2147  23.1045
 U57  H6   H  HCH2  0   0.199  141.1419  14.5819  22.3156
 U57  H7   H  HCH3  0   0.225  137.1601  20.4326  20.6491
 U57  H8   H  HCH3  0   0.215  137.4892  20.4423  22.3789
 U57  H9   H  HCH3  0   0.215  138.7935  20.7376  21.2338
 U57  H10  H  HCH3  0   0.247  142.4207  16.4399  24.2351
 U57  H11  H  HCH3  0   0.241  142.2191  16.7933  22.5174
 U57  H12  H  HCH3  0   0.243  141.6608  17.9467  23.7269
 U57  H13  H  HCH2  0   0.234  138.5682  16.1779  22.3465
 U57  H14  H  HCH2  0   0.225  140.0079  16.5214  21.4139
 U57  H15  H  HCR6  0   0.281  139.3963  18.2650  29.0859
 U57  H16  H  HCR6  0   0.290  135.6942  16.0971  28.8085
 U57  H17  H  HNH1  0   0.403  140.3370  17.0145  25.4485
 U57  H18  H  HNH2  0   0.395  136.2394  13.7339  23.5306
 U57  H19  H  HNH2  0   0.394  135.0574  13.6878  24.7824
 U57  H20  H  HOH1  0   0.453  141.3368  13.1726  24.1875
 U57  O14  O  OH1   0  -0.666  141.2697  14.1189  24.3411

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
 U57  C12  C15  single    1.522  0.020  1.522
 U57  C12  C11  single    1.524  0.020  1.524
 U57  C10  C11  single    1.523  0.020  1.523
 U57  C10  C09  single    1.538  0.020  1.538
 U57  C13  C09  single    1.533  0.020  1.533
 U57  C13  O14  single    1.406  0.020  1.406
 U57  C16  C09  single    1.529  0.020  1.529
 U57  C09  N06  single    1.462  0.020  1.462
 U57  N08  C07  single    1.345  0.020  1.345
 U57  N05  C07  aromatic  1.351  0.020  1.351
 U57  N05  C03  aromatic  1.315  0.020  1.315
 U57  N06  C03  single    1.329  0.020  1.329
 U57  C07  N04  aromatic  1.322  0.020  1.322
 U57  C03  C02  aromatic  1.449  0.020  1.449
 U57  N04  C01  aromatic  1.346  0.020  1.346
 U57  C02  C01  aromatic  1.406  0.020  1.406
 U57  C02  N17  aromatic  1.335  0.020  1.335
 U57  C01  C20  aromatic  1.411  0.020  1.411
 U57  N17  C18  aromatic  1.310  0.020  1.310
 U57  C20  C19  aromatic  1.364  0.020  1.364
 U57  C18  C19  aromatic  1.402  0.020  1.402
 U57  C19  F21  single    1.336  0.020  1.336
 U57  C11  H1   single    0.970  0.020  1.090
 U57  C11  H2   single    0.970  0.020  1.090
 U57  C12  H3   single    0.970  0.020  1.090
 U57  C12  H4   single    0.970  0.020  1.090
 U57  C13  H5   single    0.970  0.020  1.090
 U57  C13  H6   single    0.970  0.020  1.090
 U57  C15  H7   single    0.970  0.020  1.090
 U57  C15  H8   single    0.970  0.020  1.090
 U57  C15  H9   single    0.970  0.020  1.090
 U57  C16  H10  single    0.970  0.020  1.090
 U57  C16  H11  single    0.970  0.020  1.090
 U57  C16  H12  single    0.970  0.020  1.090
 U57  C10  H13  single    0.970  0.020  1.090
 U57  C10  H14  single    0.970  0.020  1.090
 U57  C18  H15  single    0.930  0.020  1.080
 U57  C20  H16  single    0.930  0.020  1.080
 U57  N06  H17  single    0.860  0.020  1.020
 U57  N08  H18  single    0.890  0.020  1.040
 U57  N08  H19  single    0.890  0.020  1.040
 U57  O14  H20  single    0.850  0.020  0.980

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
 U57  H2   C11  H1   106.21  3.000
 U57  H2   C11  C10  110.00  3.000
 U57  H1   C11  C10  110.39  3.000
 U57  H2   C11  C12  108.99  3.000
 U57  H1   C11  C12  108.96  3.000
 U57  C10  C11  C12  112.12  3.000
 U57  H4   C12  H3   106.07  3.000
 U57  H4   C12  C15  109.59  3.000
 U57  H3   C12  C15  109.60  3.000
 U57  H4   C12  C11  109.42  3.000
 U57  H3   C12  C11  109.22  3.000
 U57  C15  C12  C11  112.72  3.000
 U57  H6   C13  H5   107.10  3.000
 U57  H6   C13  O14  111.81  3.000
 U57  H5   C13  O14  111.46  3.000
 U57  H6   C13  C09  107.00  3.000
 U57  H5   C13  C09  109.53  3.000
 U57  O14  C13  C09  109.79  3.000
 U57  H9   C15  H8   107.51  3.000
 U57  H9   C15  H7   107.68  3.000
 U57  H8   C15  H7   107.60  3.000
 U57  H9   C15  C12  111.14  3.000
 U57  H8   C15  C12  111.11  3.000
 U57  H7   C15  C12  111.62  3.000
 U57  H12  C16  H11  107.85  3.000
 U57  H12  C16  H10  107.85  3.000
 U57  H11  C16  H10  108.15  3.000
 U57  H12  C16  C09  111.57  3.000
 U57  H11  C16  C09  109.95  3.000
 U57  H10  C16  C09  111.33  3.000
 U57  N04  C01  C20  120.73  3.000
 U57  C20  C01  C02  116.54  3.000
 U57  N04  C01  C02  122.74  3.000
 U57  N17  C02  C03  119.87  3.000
 U57  N17  C02  C01  124.08  3.000
 U57  C03  C02  C01  116.05  3.000
 U57  N06  C03  N05  122.05  3.000
 U57  N06  C03  C02  117.88  3.000
 U57  N05  C03  C02  120.06  3.000
 U57  N08  C07  N05  115.07  3.000
 U57  N05  C07  N04  127.39  3.000
 U57  N08  C07  N04  117.53  3.000
 U57  N06  C09  C10  111.49  3.000
 U57  N06  C09  C16  106.04  3.000
 U57  C10  C09  C16  110.70  3.000
 U57  N06  C09  C13  111.27  3.000
 U57  C16  C09  C13  109.44  3.000
 U57  C10  C09  C13  107.91  3.000
 U57  H14  C10  H13  106.25  3.000
 U57  H14  C10  C09  107.51  3.000
 U57  H13  C10  C09  108.63  3.000
 U57  H14  C10  C11  109.36  3.000
 U57  H13  C10  C11  109.09  3.000
 U57  C09  C10  C11  115.59  3.000
 U57  H15  C18  N17  118.62  3.000
 U57  H15  C18  C19  120.72  3.000
 U57  N17  C18  C19  120.66  3.000
 U57  F21  C19  C20  120.14  3.000
 U57  F21  C19  C18  118.07  3.000
 U57  C20  C19  C18  121.79  3.000
 U57  H16  C20  C19  121.73  3.000
 U57  H16  C20  C01  120.48  3.000
 U57  C19  C20  C01  117.78  3.000
 U57  C07  N04  C01  115.62  3.000
 U57  C07  N05  C03  118.14  3.000
 U57  H17  N06  C09  117.12  3.000
 U57  H17  N06  C03  114.31  3.000
 U57  C09  N06  C03  128.57  3.000
 U57  H19  N08  H18  118.00  3.000
 U57  H19  N08  C07  119.40  3.000
 U57  H18  N08  C07  119.56  3.000
 U57  C18  N17  C02  119.15  3.000
 U57  H20  O14  C13  108.05  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
 U57  CONST_01  N05  C07  N04  C01     0.00   0.0  0
 U57  CONST_02  N05  C03  C02  C01     0.00   0.0  0
 U57  CONST_03  C18  N17  C02  C01     0.00   0.0  0
 U57  CONST_04  C18  C19  C20  C01     0.00   0.0  0
 U57  CONST_05  C07  N05  C03  C02     0.00   0.0  0
 U57  CONST_06  C07  N04  C01  C02     0.00   0.0  0
 U57  CONST_07  C19  C20  C01  C02     0.00   0.0  0
 U57  CONST_08  C19  C18  N17  C02     0.00   0.0  0
 U57  CONST_09  N04  C07  N05  C03     0.00   0.0  0
 U57  CONST_10  N04  C01  C02  C03     0.00   0.0  0
 U57  CONST_11  C20  C01  C02  C03   180.00   0.0  0
 U57  CONST_12  C18  N17  C02  C03   180.00   0.0  0
 U57  CONST_13  C20  C01  N04  C07   180.00   0.0  0
 U57  CONST_14  N04  C01  C20  C19   180.00   0.0  0
 U57  CONST_15  N17  C02  C01  C20     0.00   0.0  0
 U57  CONST_16  N17  C18  C19  C20     0.00   0.0  0
 U57  CONST_17  N17  C02  C01  N04   180.00   0.0  0
 U57  CONST_18  N17  C02  C03  N05   180.00   0.0  0
 U57  CONST_19  N08  C07  N04  C01   180.00   0.0  0
 U57  CONST_20  N06  C03  C02  C01   180.00   0.0  0
 U57  CONST_21  F21  C19  C20  C01   180.00   0.0  0
 U57  CONST_22  N08  C07  N05  C03   180.00   0.0  0
 U57  CONST_23  N06  C03  N05  C07   180.00   0.0  0
 U57  CONST_24  N17  C18  C19  F21   180.00   0.0  0
 U57  CONST_25  N17  C02  C03  N06     0.00   0.0  0
 U57  CONST_26  H16  C20  C01  C02   180.00   0.0  0
 U57  CONST_27  H15  C18  N17  C02   180.00   0.0  0
 U57  CONST_28  C09  N06  C03  C02   180.00   0.0  0
 U57  CONST_29  N05  C03  N06  C09     0.00   0.0  0
 U57  CONST_30  H17  N06  C03  C02     0.00   0.0  0
 U57  CONST_31  H18  N08  C07  N04   180.00   0.0  0
 U57  CONST_32  H19  N08  C07  N04     0.00   0.0  0
 U57  Var_01    C09  C10  C11  C12  -173.87  30.0  2
 U57  Var_02    C10  C11  C12  C15  -178.77  30.0  3
 U57  Var_03    H7   C15  C12  C11  -178.85  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
 U57  chir_01  C09  C13  C16  N06  positiv

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
 U57  plan-1  C01  0.020
 U57  plan-1  C02  0.020
 U57  plan-1  C03  0.020
 U57  plan-1  C07  0.020
 U57  plan-1  C18  0.020
 U57  plan-1  C19  0.020
 U57  plan-1  C20  0.020
 U57  plan-1  F21  0.020
 U57  plan-1  N04  0.020
 U57  plan-1  N05  0.020
 U57  plan-1  N06  0.020
 U57  plan-1  N08  0.020
 U57  plan-1  N17  0.020
 U57  plan-1  H15  0.020
 U57  plan-1  H16  0.020
 U57  plan-2  C03  0.020
 U57  plan-2  C09  0.020
 U57  plan-2  N06  0.020
 U57  plan-2  H17  0.020
 U57  plan-3  C07  0.020
 U57  plan-3  N08  0.020
 U57  plan-3  H18  0.020
 U57  plan-3  H19  0.020

