# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 19:02:11 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-{(1S)-1-[5-fluoro-2-(1H-pyrazol-1-yl)phenyl]ethoxy}-5-(3-methyl-1H-pyrazol-4-yl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Oc1cc(cnc1N)c2c[nH]nc2C)c3cc(F)ccc3n4cccn4
#
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
 VOJ  VOJ  3-{(1S)-1-[5-fluoro-2-(1H-pyrazol-1-yl)phenyl]ethoxy}-5-(3-methyl-1H-pyrazol-4-yl)pyridin-2-amine  ligand  47  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VOJ
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
 VOJ  N3   N  N     0  -0.437  -14.2024  22.2099  -0.9872
 VOJ  C4   C  CR15  0  -0.012  -14.7916  20.6320   3.6350
 VOJ  N2   N  N     0  -0.286  -15.2061  18.4762   3.2844
 VOJ  C7   C  CR6   0   0.292  -14.5943  23.8467   0.6969
 VOJ  C6   C  CR16  0  -0.356  -14.7691  22.8556   1.6291
 VOJ  C9   C  CR16  0  -0.173  -14.3484  21.2544  -0.0673
 VOJ  C13  C  CR16  0  -0.471  -17.3529  25.4682   1.7287
 VOJ  C20  C  CR15  0  -0.030  -14.0750  24.1789   6.0764
 VOJ  C8   C  CR6   0   0.346  -14.3222  23.4772  -0.6440
 VOJ  N5   N  NR5   0  -0.376  -15.6694  25.0369   4.9936
 VOJ  C18  C  CR15  0   0.026  -15.4116  25.9170   5.9842
 VOJ  C16  C  CR16  0  -0.233  -18.0015  25.0017   4.3838
 VOJ  C19  C  CR15  0  -0.500  -14.3742  25.3940   6.7160
 VOJ  C2   C  CR5   0   0.224  -15.0937  19.0668   2.1070
 VOJ  C3   C  CR5   0  -0.155  -14.8248  20.4536   2.2633
 VOJ  N1   N  NR15  0  -0.441  -15.0191  19.4343   4.1838
 VOJ  C5   C  CR6   0   0.014  -14.6472  21.5019   1.2601
 VOJ  N4   N  NH2   0  -0.827  -14.1213  24.4365  -1.5982
 VOJ  O1   O  O2    0  -0.492  -14.6669  25.1785   0.9260
 VOJ  C10  C  CH1   0  -0.035  -14.9017  25.6387   2.2455
 VOJ  C11  C  CH3   0  -0.661  -14.5991  27.1273   2.2591
 VOJ  C12  C  CR6   0   0.082  -16.3337  25.3842   2.6696
 VOJ  C14  C  CR6   0   0.568  -18.6647  25.3236   2.1322
 VOJ  C15  C  CR16  0  -0.433  -19.0172  25.0979   3.4481
 VOJ  C17  C  CR6   0   0.261  -16.6751  25.1411   3.9995
 VOJ  N6   N  N     0  -0.296  -14.8648  23.9711   5.0404
 VOJ  F1   F  F     0  -0.308  -19.6315  25.4087   1.2092
 VOJ  H1   H  HCR5  0   0.297  -14.6331  21.5139   4.2371
 VOJ  H3   H  HCR6  0   0.294  -14.9976  23.0982   2.6587
 VOJ  H4   H  HCR6  0   0.249  -14.2057  20.2440  -0.4284
 VOJ  H5   H  HCR6  0   0.287  -17.1333  25.6534   0.6850
 VOJ  H6   H  HCR5  0   0.269  -13.3203  23.4522   6.3355
 VOJ  H7   H  HCR5  0   0.302  -15.9710  26.8329   6.0845
 VOJ  H8   H  HCR6  0   0.288  -18.2399  24.8066   5.4209
 VOJ  H9   H  HCR5  0   0.270  -13.9004  25.8252   7.5813
 VOJ  H10  H  HCH3  0   0.258  -15.6599  17.2840   1.0917
 VOJ  H11  H  HCH3  0   0.245  -15.9614  18.7557   0.1675
 VOJ  H12  H  HCH3  0   0.247  -14.3242  18.1361   0.3269
 VOJ  H13  H  HNH2  0   0.382  -14.1850  24.1086  -2.5487
 VOJ  H14  H  HNH2  0   0.387  -14.5544  25.3338  -1.4548
 VOJ  H15  H  HCH1  0   0.258  -14.2117  25.1352   2.9290
 VOJ  H16  H  HCH3  0   0.243  -14.7608  27.5263   3.2597
 VOJ  H17  H  HCH3  0   0.254  -13.5597  27.3091   1.9873
 VOJ  H18  H  HCH3  0   0.243  -15.2467  27.6691   1.5694
 VOJ  H19  H  HCR6  0   0.291  -20.0539  24.9876   3.7354
 VOJ  H2   H  HNR5  0   0.419  -15.0590  19.2165   5.1661
 VOJ  C1   C  CH3   0  -0.771  -15.2682  18.2728   0.8576

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
 VOJ  N4   C8   single    1.368  0.020  1.368
 VOJ  N3   C8   aromatic  1.318  0.020  1.318
 VOJ  N3   C9   aromatic  1.334  0.020  1.334
 VOJ  C8   C7   aromatic  1.417  0.020  1.417
 VOJ  C9   C5   aromatic  1.383  0.020  1.383
 VOJ  C7   O1   single    1.353  0.020  1.353
 VOJ  C7   C6   aromatic  1.372  0.020  1.372
 VOJ  O1   C10  single    1.417  0.020  1.417
 VOJ  C1   C2   single    1.491  0.020  1.491
 VOJ  F1   C14  single    1.339  0.020  1.339
 VOJ  C5   C6   aromatic  1.408  0.020  1.408
 VOJ  C5   C3   single    1.462  0.020  1.462
 VOJ  C13  C14  aromatic  1.380  0.020  1.380
 VOJ  C13  C12  aromatic  1.390  0.020  1.390
 VOJ  C14  C15  aromatic  1.381  0.020  1.381
 VOJ  C2   C3   aromatic  1.421  0.020  1.421
 VOJ  C2   N2   aromatic  1.322  0.020  1.322
 VOJ  C11  C10  single    1.519  0.020  1.519
 VOJ  C10  C12  single    1.515  0.020  1.515
 VOJ  C3   C4   aromatic  1.384  0.020  1.384
 VOJ  C12  C17  aromatic  1.394  0.020  1.394
 VOJ  C15  C16  aromatic  1.384  0.020  1.384
 VOJ  N2   N1   aromatic  1.327  0.020  1.327
 VOJ  C4   N1   aromatic  1.337  0.020  1.337
 VOJ  C17  C16  aromatic  1.388  0.020  1.388
 VOJ  C17  N5   single    1.418  0.020  1.418
 VOJ  N5   C18  aromatic  1.350  0.020  1.350
 VOJ  N5   N6   aromatic  1.336  0.020  1.336
 VOJ  C18  C19  aromatic  1.373  0.020  1.373
 VOJ  N6   C20  aromatic  1.319  0.020  1.319
 VOJ  C19  C20  aromatic  1.405  0.020  1.405
 VOJ  C4   H1   single    0.930  0.020  1.080
 VOJ  C6   H3   single    0.930  0.020  1.080
 VOJ  C9   H4   single    0.930  0.020  1.080
 VOJ  C13  H5   single    0.930  0.020  1.080
 VOJ  C20  H6   single    0.930  0.020  1.080
 VOJ  C18  H7   single    0.930  0.020  1.080
 VOJ  C16  H8   single    0.930  0.020  1.080
 VOJ  C19  H9   single    0.930  0.020  1.080
 VOJ  C1   H10  single    0.970  0.020  1.090
 VOJ  C1   H11  single    0.970  0.020  1.090
 VOJ  C1   H12  single    0.970  0.020  1.090
 VOJ  N4   H13  single    0.890  0.020  1.040
 VOJ  N4   H14  single    0.890  0.020  1.040
 VOJ  C10  H15  single    0.970  0.020  1.090
 VOJ  C11  H16  single    0.970  0.020  1.090
 VOJ  C11  H17  single    0.970  0.020  1.090
 VOJ  C11  H18  single    0.970  0.020  1.090
 VOJ  C15  H19  single    0.930  0.020  1.080
 VOJ  N1   H2   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
 VOJ  C8   N3   C9   119.93  3.000
 VOJ  H1   C4   N1   121.86  3.000
 VOJ  H1   C4   C3   131.44  3.000
 VOJ  N1   C4   C3   106.70  3.000
 VOJ  N1   N2   C2   105.61  3.000
 VOJ  O1   C7   C8   115.28  3.000
 VOJ  O1   C7   C6   126.10  3.000
 VOJ  C8   C7   C6   118.63  3.000
 VOJ  H3   C6   C5   118.88  3.000
 VOJ  H3   C6   C7   120.76  3.000
 VOJ  C5   C6   C7   120.35  3.000
 VOJ  H4   C9   C5   121.05  3.000
 VOJ  H4   C9   N3   115.09  3.000
 VOJ  C5   C9   N3   123.86  3.000
 VOJ  H5   C13  C14  119.51  3.000
 VOJ  H5   C13  C12  120.96  3.000
 VOJ  C14  C13  C12  119.53  3.000
 VOJ  H6   C20  N6   120.07  3.000
 VOJ  H6   C20  C19  128.45  3.000
 VOJ  N6   C20  C19  111.48  3.000
 VOJ  N4   C8   C7   120.36  3.000
 VOJ  C7   C8   N3   120.95  3.000
 VOJ  N4   C8   N3   118.63  3.000
 VOJ  N6   N5   C17  120.68  3.000
 VOJ  N6   N5   C18  112.29  3.000
 VOJ  C17  N5   C18  127.01  3.000
 VOJ  H7   C18  C19  131.77  3.000
 VOJ  H7   C18  N5   121.55  3.000
 VOJ  C19  C18  N5   106.68  3.000
 VOJ  H8   C16  C17  119.61  3.000
 VOJ  H8   C16  C15  119.91  3.000
 VOJ  C17  C16  C15  120.47  3.000
 VOJ  H9   C19  C18  127.47  3.000
 VOJ  H9   C19  C20  128.19  3.000
 VOJ  C18  C19  C20  104.34  3.000
 VOJ  C3   C2   C1   129.35  3.000
 VOJ  C3   C2   N2   110.73  3.000
 VOJ  C1   C2   N2   119.91  3.000
 VOJ  C5   C3   C2   130.33  3.000
 VOJ  C2   C3   C4   103.85  3.000
 VOJ  C5   C3   C4   125.80  3.000
 VOJ  H2   N1   N2   119.95  3.000
 VOJ  H2   N1   C4   126.94  3.000
 VOJ  N2   N1   C4   113.11  3.000
 VOJ  C3   C5   C9   123.82  3.000
 VOJ  C3   C5   C6   119.93  3.000
 VOJ  C9   C5   C6   116.25  3.000
 VOJ  H14  N4   H13  113.41  3.000
 VOJ  H14  N4   C8   117.55  3.000
 VOJ  H13  N4   C8   114.87  3.000
 VOJ  C10  O1   C7   119.08  3.000
 VOJ  H15  C10  C12  110.12  3.000
 VOJ  H15  C10  C11  108.65  3.000
 VOJ  C12  C10  C11  110.51  3.000
 VOJ  H15  C10  O1   109.14  3.000
 VOJ  C12  C10  O1   111.27  3.000
 VOJ  C11  C10  O1   107.07  3.000
 VOJ  H18  C11  H17  109.02  3.000
 VOJ  H18  C11  H16  108.11  3.000
 VOJ  H17  C11  H16  108.03  3.000
 VOJ  H18  C11  C10  111.29  3.000
 VOJ  H17  C11  C10  110.57  3.000
 VOJ  H16  C11  C10  109.73  3.000
 VOJ  C17  C12  C10  121.85  3.000
 VOJ  C17  C12  C13  118.47  3.000
 VOJ  C10  C12  C13  119.57  3.000
 VOJ  F1   C14  C15  118.87  3.000
 VOJ  C15  C14  C13  122.57  3.000
 VOJ  F1   C14  C13  118.56  3.000
 VOJ  H19  C15  C14  120.96  3.000
 VOJ  H19  C15  C16  121.12  3.000
 VOJ  C14  C15  C16  117.91  3.000
 VOJ  C12  C17  C16  121.03  3.000
 VOJ  C16  C17  N5   118.45  3.000
 VOJ  C12  C17  N5   120.52  3.000
 VOJ  N5   N6   C20  105.20  3.000
 VOJ  H12  C1   H11  107.31  3.000
 VOJ  H12  C1   H10  107.57  3.000
 VOJ  H11  C1   H10  108.02  3.000
 VOJ  H12  C1   C2   111.90  3.000
 VOJ  H11  C1   C2   111.65  3.000
 VOJ  H10  C1   C2   110.21  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
 VOJ  CONST_01  C6   C7   C8   N3     0.00   0.0  0
 VOJ  CONST_02  C6   C5   C9   N3     0.00   0.0  0
 VOJ  CONST_03  C3   C5   C9   N3   180.00   0.0  0
 VOJ  CONST_06  N2   C2   C3   C4     0.00   0.0  0
 VOJ  CONST_07  C2   N2   N1   C4     0.00   0.0  0
 VOJ  CONST_08  C5   C3   C2   N2   180.00   0.0  0
 VOJ  CONST_09  C3   C4   N1   N2     0.00   0.0  0
 VOJ  CONST_10  C9   N3   C8   C7     0.00   0.0  0
 VOJ  CONST_11  C9   C5   C6   C7     0.00   0.0  0
 VOJ  CONST_12  C3   C5   C6   C7   180.00   0.0  0
 VOJ  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 VOJ  CONST_16  C16  C17  C12  C13    0.00   0.0  0
 VOJ  CONST_17  N5   C17  C12  C13  180.00   0.0  0
 VOJ  CONST_18  C17  N5   N6   C20  180.00   0.0  0
 VOJ  CONST_19  C18  N5   N6   C20    0.00   0.0  0
 VOJ  CONST_20  N5   C18  C19  C20    0.00   0.0  0
 VOJ  CONST_21  C5   C9   N3   C8     0.00   0.0  0
 VOJ  CONST_22  C5   C6   C7   C8     0.00   0.0  0
 VOJ  CONST_23  C15  C16  C17  N5   180.00   0.0  0
 VOJ  CONST_24  C19  C20  N6   N5     0.00   0.0  0
 VOJ  CONST_27  N6   C20  C19  C18    0.00   0.0  0
 VOJ  CONST_29  C17  N5   C18  C19  180.00   0.0  0
 VOJ  CONST_30  N6   N5   C18  C19    0.00   0.0  0
 VOJ  CONST_31  N1   C4   C3   C2     0.00   0.0  0
 VOJ  CONST_32  N1   N2   C2   C3     0.00   0.0  0
 VOJ  CONST_33  C5   C3   C4   N1   180.00   0.0  0
 VOJ  CONST_34  C15  C14  C13  C12    0.00   0.0  0
 VOJ  CONST_35  C15  C16  C17  C12    0.00   0.0  0
 VOJ  CONST_37  C17  C12  C13  C14    0.00   0.0  0
 VOJ  CONST_38  C17  C16  C15  C14    0.00   0.0  0
 VOJ  CONST_39  O1   C7   C8   N3   180.00   0.0  0
 VOJ  CONST_40  C1   C2   C3   C4   180.00   0.0  0
 VOJ  CONST_41  N4   C8   C7   C6   180.00   0.0  0
 VOJ  CONST_42  N4   C8   N3   C9   180.00   0.0  0
 VOJ  CONST_43  C10  C12  C17  N5     0.00   0.0  0
 VOJ  CONST_44  F1   C14  C15  C16  180.00   0.0  0
 VOJ  CONST_45  C10  C12  C17  C16  180.00   0.0  0
 VOJ  CONST_46  C5   C3   C2   C1     0.00   0.0  0
 VOJ  CONST_47  N1   N2   C2   C1   180.00   0.0  0
 VOJ  CONST_48  O1   C7   C6   C5   180.00   0.0  0
 VOJ  CONST_49  C14  C13  C12  C10  180.00   0.0  0
 VOJ  CONST_50  F1   C14  C13  C12  180.00   0.0  0
 VOJ  CONST_51  H1   C4   N1   N2   180.00   0.0  0
 VOJ  CONST_52  H4   C9   C5   C6   180.00   0.0  0
 VOJ  CONST_53  H3   C6   C5   C9   180.00   0.0  0
 VOJ  CONST_54  H19  C15  C14  C13  180.00   0.0  0
 VOJ  CONST_55  H7   C18  C19  C20  180.00   0.0  0
 VOJ  CONST_56  H8   C16  C17  N5     0.00   0.0  0
 VOJ  CONST_57  H9   C19  C18  N5   180.00   0.0  0
 VOJ  CONST_58  H6   C20  N6   N5   180.00   0.0  0
 VOJ  CONST_59  H2   N1   N2   C2   180.00   0.0  0
 VOJ  CONST_60  H5   C13  C14  C15  180.00   0.0  0
 VOJ  Var_01    H10  C1   C2   N2    10.44  30.0  2

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
 VOJ  chir_01  C10  O1  C11  C12  negativ

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
 VOJ  plan-1  C20  0.020
 VOJ  plan-1  N5   0.020
 VOJ  plan-1  C18  0.020
 VOJ  plan-1  C19  0.020
 VOJ  plan-1  C17  0.020
 VOJ  plan-1  N6   0.020
 VOJ  plan-1  H6   0.020
 VOJ  plan-1  H7   0.020
 VOJ  plan-1  H9   0.020
 VOJ  plan-2  C4   0.020
 VOJ  plan-2  N2   0.020
 VOJ  plan-2  C2   0.020
 VOJ  plan-2  C3   0.020
 VOJ  plan-2  N1   0.020
 VOJ  plan-2  C5   0.020
 VOJ  plan-2  H1   0.020
 VOJ  plan-2  H2   0.020
 VOJ  plan-2  C1   0.020
 VOJ  plan-3  N3   0.020
 VOJ  plan-3  C7   0.020
 VOJ  plan-3  C6   0.020
 VOJ  plan-3  C9   0.020
 VOJ  plan-3  C8   0.020
 VOJ  plan-3  C3   0.020
 VOJ  plan-3  C5   0.020
 VOJ  plan-3  N4   0.020
 VOJ  plan-3  O1   0.020
 VOJ  plan-3  H3   0.020
 VOJ  plan-3  H4   0.020
 VOJ  plan-4  C13  0.020
 VOJ  plan-4  N5   0.020
 VOJ  plan-4  C16  0.020
 VOJ  plan-4  C10  0.020
 VOJ  plan-4  C12  0.020
 VOJ  plan-4  C14  0.020
 VOJ  plan-4  C15  0.020
 VOJ  plan-4  C17  0.020
 VOJ  plan-4  F1   0.020
 VOJ  plan-4  H5   0.020
 VOJ  plan-4  H8   0.020
 VOJ  plan-4  H19  0.020
 VOJ  plan-5  C8   0.020
 VOJ  plan-5  N4   0.020
 VOJ  plan-5  H13  0.020
 VOJ  plan-5  H14  0.020

