# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 02:45:18 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (4-amino-1,2,5-oxadiazol-3-yl)[(3R)-3-{4-[(3-methoxyphenyl)amino]-6-methylpyridin-2-yl}pyrrolidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Nc2cc(C)nc(c2)[C@@H]3CCN(C3)C(=O)c4nonc4N)c1
#
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
 9W1  9W1  (4-amino-1,2,5-oxadiazol-3-yl)[(3R)-3-{4-[(3-methoxyphenyl)amino]-6-methylpyridin-2-yl}pyrrolidin-1-yl]methanone  ligand  51  29  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9W1
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
 9W1  N1   N  N     0  -0.096  -6.2177  -0.5885  -0.7408
 9W1  N3   N  N     0  -0.190  -7.7764   0.9825  -0.5411
 9W1  C4   C  CR16  0  -0.422   4.9599   0.7450   0.4504
 9W1  C5   C  CR16  0  -0.467   0.8035  -0.4124  -0.3461
 9W1  C6   C  CR16  0  -0.423   2.8427  -1.5313   0.1904
 9W1  C7   C  CR6   0   0.374   4.2023   1.0515  -0.6740
 9W1  C8   C  CR6   0   0.486   2.2017  -0.3893  -0.3033
 9W1  C10  C  CR5   0   0.033  -5.7017   0.3853  -0.0639
 9W1  C13  C  CR5   0   0.374  -6.7085   1.4031   0.0738
 9W1  C15  C  CH2   0  -0.450  -1.9807  -1.5795  -1.3407
 9W1  C17  C  CH2   0  -0.231  -2.0937  -0.4181   0.7380
 9W1  C1   C  CR16  0  -0.231   6.1068   2.1622  -1.6266
 9W1  C2   C  CR16  0  -0.359   4.7833   1.7771  -1.7196
 9W1  C3   C  CR16  0  -0.403   6.8869   1.8336  -0.5235
 9W1  C9   C  CR6   0   0.396   6.3025   1.1199   0.5199
 9W1  C11  C  CR6   0   0.299   0.1245  -1.5276   0.1126
 9W1  C12  C  CR6   0   0.227   2.0763  -2.6006   0.6256
 9W1  C14  C  C     0   0.588  -4.3507   0.4126   0.5487
 9W1  C16  C  CH2   0  -0.282  -3.4499  -1.2878  -1.0773
 9W1  C18  C  CH1   0  -0.411  -1.3773  -1.5900   0.0659
 9W1  C19  C  CH3   0  -0.720   2.7329  -3.8334   1.1711
 9W1  N2   N  N     0  -0.475   0.7429  -2.6016   0.5987
 9W1  N4   N  NT    0  -0.482  -3.4031  -0.4038   0.0901
 9W1  N5   N  NH2   0  -0.840  -6.5899   2.6124   0.6593
 9W1  N6   N  NH1   0  -0.800   2.8540   0.7167  -0.7756
 9W1  O1   O  O     0  -0.494  -4.1662   1.1948   1.4783
 9W1  O2   O  O     0  -0.212  -7.4585  -0.2436  -1.0374
 9W1  O3   O  O2    0  -0.473   6.9467   0.7633   1.6470
 9W1  H2   H  HCR6  0   0.267   0.2623   0.4417  -0.7357
 9W1  H3   H  HCR6  0   0.278   3.9197  -1.6082   0.2185
 9W1  H4   H  HCH2  0   0.265  -1.8389  -2.5213  -1.8686
 9W1  H5   H  HCH2  0   0.250  -1.5366  -0.7833  -1.9425
 9W1  H6   H  HCH2  0   0.267  -2.1889  -0.5546   1.8150
 9W1  H7   H  HCH2  0   0.251  -1.5760   0.5290   0.5635
 9W1  H8   H  HCH3  0   0.260   8.6147   0.7779   2.7743
 9W1  H9   H  HCH3  0   0.228   8.9400   0.7213   1.0338
 9W1  H10  H  HCH3  0   0.229   8.4127   2.2398   1.7918
 9W1  H11  H  HCR6  0   0.262   6.5537   2.7231  -2.4370
 9W1  H12  H  HCR6  0   0.263   4.1983   2.0325  -2.5942
 9W1  H13  H  HCR6  0   0.277   7.9227   2.1406  -0.4948
 9W1  H14  H  HCH2  0   0.267  -3.9377  -0.8068  -1.9227
 9W1  H15  H  HCH2  0   0.255  -3.9944  -2.2044  -0.8432
 9W1  H16  H  HCH1  0   0.272  -1.6768  -2.5160   0.5632
 9W1  H17  H  HCH3  0   0.251   2.5654  -3.9100   2.2471
 9W1  H18  H  HCH3  0   0.247   2.3123  -4.7297   0.7154
 9W1  H19  H  HCH3  0   0.242   3.8079  -3.8319   1.0003
 9W1  H20  H  HNH2  0   0.405  -5.8790   2.6929   1.3674
 9W1  H21  H  HNH2  0   0.401  -7.4457   3.1044   0.8590
 9W1  H22  H  HNH1  0   0.405   2.2951   1.3447  -1.3316
 9W1  H1   H  HCR6  0   0.281   4.5181   0.2390   1.2986
 9W1  C20  C  CH3   0  -0.437   8.2967   1.1529   1.8049

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
 9W1  C20  O3   single    1.414  0.020  1.414
 9W1  O3   C9   single    1.346  0.020  1.346
 9W1  C9   C3   aromatic  1.393  0.020  1.393
 9W1  C9   C4   aromatic  1.396  0.020  1.396
 9W1  C3   C1   aromatic  1.390  0.020  1.390
 9W1  C4   C7   aromatic  1.390  0.020  1.390
 9W1  C1   C2   aromatic  1.381  0.020  1.381
 9W1  O1   C14  double    1.229  0.020  1.229
 9W1  C7   C2   aromatic  1.399  0.020  1.399
 9W1  C7   N6   single    1.393  0.020  1.393
 9W1  N5   C13  single    1.349  0.020  1.349
 9W1  C16  N4   single    1.465  0.020  1.465
 9W1  C16  C15  single    1.521  0.020  1.521
 9W1  N6   C8   single    1.368  0.020  1.368
 9W1  C14  N4   single    1.332  0.020  1.332
 9W1  C14  C10  single    1.484  0.020  1.484
 9W1  C13  C10  aromatic  1.438  0.020  1.438
 9W1  C13  N3   aromatic  1.302  0.020  1.302
 9W1  N4   C17  single    1.461  0.020  1.461
 9W1  C8   C5   aromatic  1.399  0.020  1.399
 9W1  C8   C6   aromatic  1.400  0.020  1.400
 9W1  C15  C18  single    1.531  0.020  1.531
 9W1  C10  N1   aromatic  1.293  0.020  1.293
 9W1  C5   C11  aromatic  1.384  0.020  1.384
 9W1  N3   O2   aromatic  1.360  0.020  1.360
 9W1  C6   C12  aromatic  1.386  0.020  1.386
 9W1  C11  C18  single    1.504  0.020  1.504
 9W1  C11  N2   aromatic  1.331  0.020  1.331
 9W1  C18  C17  single    1.529  0.020  1.529
 9W1  N1   O2   aromatic  1.322  0.020  1.322
 9W1  C12  N2   aromatic  1.334  0.020  1.334
 9W1  C12  C19  single    1.499  0.020  1.499
 9W1  C4   H1   single    0.930  0.020  1.080
 9W1  C5   H2   single    0.930  0.020  1.080
 9W1  C6   H3   single    0.930  0.020  1.080
 9W1  C15  H4   single    0.970  0.020  1.090
 9W1  C15  H5   single    0.970  0.020  1.090
 9W1  C17  H6   single    0.970  0.020  1.090
 9W1  C17  H7   single    0.970  0.020  1.090
 9W1  C20  H8   single    0.970  0.020  1.090
 9W1  C20  H9   single    0.970  0.020  1.090
 9W1  C20  H10  single    0.970  0.020  1.090
 9W1  C1   H11  single    0.930  0.020  1.080
 9W1  C2   H12  single    0.930  0.020  1.080
 9W1  C3   H13  single    0.930  0.020  1.080
 9W1  C16  H14  single    0.970  0.020  1.090
 9W1  C16  H15  single    0.970  0.020  1.090
 9W1  C18  H16  single    0.970  0.020  1.090
 9W1  C19  H17  single    0.970  0.020  1.090
 9W1  C19  H18  single    0.970  0.020  1.090
 9W1  C19  H19  single    0.970  0.020  1.090
 9W1  N5   H20  single    0.890  0.020  1.040
 9W1  N5   H21  single    0.890  0.020  1.040
 9W1  N6   H22  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
 9W1  O2   N1   C10  107.19  3.000
 9W1  O2   N3   C13  105.77  3.000
 9W1  H1   C4   C9   118.65  3.000
 9W1  H1   C4   C7   120.97  3.000
 9W1  C9   C4   C7   120.36  3.000
 9W1  H2   C5   C11  120.62  3.000
 9W1  H2   C5   C8   119.81  3.000
 9W1  C11  C5   C8   119.57  3.000
 9W1  H3   C6   C12  119.23  3.000
 9W1  H3   C6   C8   121.60  3.000
 9W1  C12  C6   C8   119.15  3.000
 9W1  N6   C7   C2   118.17  3.000
 9W1  N6   C7   C4   122.25  3.000
 9W1  C2   C7   C4   119.50  3.000
 9W1  N6   C8   C6   124.26  3.000
 9W1  C6   C8   C5   117.07  3.000
 9W1  N6   C8   C5   118.64  3.000
 9W1  C14  C10  C13  125.79  3.000
 9W1  C13  C10  N1   107.68  3.000
 9W1  C14  C10  N1   126.39  3.000
 9W1  N5   C13  C10  127.92  3.000
 9W1  C10  C13  N3   107.47  3.000
 9W1  N5   C13  N3   124.52  3.000
 9W1  H5   C15  H4   108.08  3.000
 9W1  H5   C15  C18  110.55  3.000
 9W1  H4   C15  C18  112.84  3.000
 9W1  H5   C15  C16  110.38  3.000
 9W1  H4   C15  C16  112.07  3.000
 9W1  C18  C15  C16  102.88  3.000
 9W1  H7   C17  H6   107.91  3.000
 9W1  H7   C17  N4   110.19  3.000
 9W1  H6   C17  N4   111.18  3.000
 9W1  H7   C17  C18  111.83  3.000
 9W1  H6   C17  C18  112.29  3.000
 9W1  N4   C17  C18  103.44  3.000
 9W1  H11  C1   C3   119.01  3.000
 9W1  H11  C1   C2   119.32  3.000
 9W1  C3   C1   C2   121.67  3.000
 9W1  H12  C2   C1   120.41  3.000
 9W1  H12  C2   C7   120.10  3.000
 9W1  C1   C2   C7   119.48  3.000
 9W1  H13  C3   C9   121.86  3.000
 9W1  H13  C3   C1   119.45  3.000
 9W1  C9   C3   C1   118.69  3.000
 9W1  O3   C9   C3   124.21  3.000
 9W1  C3   C9   C4   120.27  3.000
 9W1  O3   C9   C4   115.52  3.000
 9W1  N2   C11  C18  116.22  3.000
 9W1  N2   C11  C5   122.90  3.000
 9W1  C18  C11  C5   120.87  3.000
 9W1  N2   C12  C19  116.39  3.000
 9W1  C19  C12  C6   120.43  3.000
 9W1  N2   C12  C6   123.17  3.000
 9W1  O1   C14  N4   122.94  3.000
 9W1  N4   C14  C10  119.62  3.000
 9W1  O1   C14  C10  117.44  3.000
 9W1  H15  C16  H14  108.31  3.000
 9W1  H15  C16  N4   110.59  3.000
 9W1  H14  C16  N4   111.51  3.000
 9W1  H15  C16  C15  110.97  3.000
 9W1  H14  C16  C15  112.54  3.000
 9W1  N4   C16  C15  102.88  3.000
 9W1  H16  C18  C11  107.14  3.000
 9W1  H16  C18  C17  108.72  3.000
 9W1  C11  C18  C17  114.99  3.000
 9W1  H16  C18  C15  108.42  3.000
 9W1  C17  C18  C15  102.35  3.000
 9W1  C11  C18  C15  114.96  3.000
 9W1  H19  C19  H18  108.46  3.000
 9W1  H19  C19  H17  107.83  3.000
 9W1  H18  C19  H17  107.17  3.000
 9W1  H19  C19  C12  111.98  3.000
 9W1  H18  C19  C12  110.80  3.000
 9W1  H17  C19  C12  110.43  3.000
 9W1  C12  N2   C11  118.12  3.000
 9W1  C16  N4   C14  128.42  3.000
 9W1  C14  N4   C17  119.39  3.000
 9W1  C16  N4   C17  112.09  3.000
 9W1  H21  N5   H20  114.93  3.000
 9W1  H21  N5   C13  116.70  3.000
 9W1  H20  N5   C13  116.05  3.000
 9W1  H22  N6   C8   115.45  3.000
 9W1  H22  N6   C7   115.29  3.000
 9W1  C8   N6   C7   129.10  3.000
 9W1  N3   O2   N1   111.89  3.000
 9W1  C9   O3   C20  118.51  3.000
 9W1  H10  C20  H9   108.76  3.000
 9W1  H10  C20  H8   108.82  3.000
 9W1  H9   C20  H8   108.71  3.000
 9W1  H10  C20  O3   111.96  3.000
 9W1  H9   C20  O3   111.98  3.000
 9W1  H8   C20  O3   106.49  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
 9W1  CONST_01  N3   C13  C10  N1     0.00   0.0  0
 9W1  CONST_02  C13  N3   O2   N1     0.00   0.0  0
 9W1  CONST_03  C10  N1   O2   N3     0.00   0.0  0
 9W1  CONST_04  C1   C3   C9   C4     0.00   0.0  0
 9W1  CONST_05  C1   C2   C7   C4     0.00   0.0  0
 9W1  CONST_06  C12  C6   C8   C5     0.00   0.0  0
 9W1  CONST_07  C12  N2   C11  C5     0.00   0.0  0
 9W1  CONST_08  C11  C5   C8   C6     0.00   0.0  0
 9W1  CONST_09  C11  N2   C12  C6     0.00   0.0  0
 9W1  CONST_10  C3   C9   C4   C7     0.00   0.0  0
 9W1  CONST_11  C3   C1   C2   C7     0.00   0.0  0
 9W1  CONST_12  N2   C11  C5   C8     0.00   0.0  0
 9W1  CONST_13  N2   C12  C6   C8     0.00   0.0  0
 9W1  CONST_14  O2   N3   C13  C10    0.00   0.0  0
 9W1  CONST_15  O2   N1   C10  C13    0.00   0.0  0
 9W1  CONST_16  C9   C3   C1   C2     0.00   0.0  0
 9W1  CONST_17  C9   C4   C7   C2     0.00   0.0  0
 9W1  CONST_18  C18  C11  C5   C8   180.00   0.0  0
 9W1  CONST_19  C18  C11  N2   C12  180.00   0.0  0
 9W1  CONST_20  N5   C13  C10  N1   180.00   0.0  0
 9W1  CONST_21  C14  C10  C13  N3   180.00   0.0  0
 9W1  CONST_22  O3   C9   C4   C7   180.00   0.0  0
 9W1  CONST_23  C19  C12  C6   C8   180.00   0.0  0
 9W1  CONST_24  O3   C9   C3   C1   180.00   0.0  0
 9W1  CONST_25  N6   C7   C2   C1   180.00   0.0  0
 9W1  CONST_26  N6   C7   C4   C9   180.00   0.0  0
 9W1  CONST_27  N6   C8   C5   C11  180.00   0.0  0
 9W1  CONST_28  C19  C12  N2   C11  180.00   0.0  0
 9W1  CONST_29  N6   C8   C6   C12  180.00   0.0  0
 9W1  CONST_30  O2   N1   C10  C14  180.00   0.0  0
 9W1  CONST_31  O2   N3   C13  N5   180.00   0.0  0
 9W1  CONST_32  C16  N4   C14  C10    0.00   0.0  0
 9W1  CONST_33  C17  N4   C14  C10  180.00   0.0  0
 9W1  CONST_34  H13  C3   C9   C4   180.00   0.0  0
 9W1  CONST_35  H12  C2   C7   C4   180.00   0.0  0
 9W1  CONST_36  H3   C6   C8   C5   180.00   0.0  0
 9W1  CONST_37  H2   C5   C8   C6   180.00   0.0  0
 9W1  CONST_38  H11  C1   C2   C7   180.00   0.0  0
 9W1  CONST_39  H1   C4   C7   C2   180.00   0.0  0
 9W1  CONST_40  O1   C14  N4   C17    0.00   0.0  0
 9W1  CONST_41  O1   C14  N4   C16  180.00   0.0  0
 9W1  Var_01    C17  N4   C16  C15  -14.46  30.0  1
 9W1  Var_02    C18  C17  N4   C16  -10.85  30.0  1
 9W1  Var_03    N4   C16  C15  C18   33.72  30.0  1
 9W1  Var_04    N4   C14  C10  N1    21.52  30.0  2
 9W1  Var_05    C8   N6   C7   C4   -35.54  30.0  2
 9W1  Var_06    C7   N6   C8   C5   170.25  30.0  2
 9W1  Var_07    C3   C9   O3   C20    1.20  30.0  2
 9W1  Var_08    H17  C19  C12  C6   109.65  30.0  2
 9W1  Var_09    H8   C20  O3   C9   179.34  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
 9W1  chir_01  C18  C15  C11  C17  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
 9W1  plan-1  N1   0.020
 9W1  plan-1  N3   0.020
 9W1  plan-1  C10  0.020
 9W1  plan-1  C13  0.020
 9W1  plan-1  C14  0.020
 9W1  plan-1  N5   0.020
 9W1  plan-1  O2   0.020
 9W1  plan-2  C5   0.020
 9W1  plan-2  C6   0.020
 9W1  plan-2  C8   0.020
 9W1  plan-2  C11  0.020
 9W1  plan-2  C12  0.020
 9W1  plan-2  C18  0.020
 9W1  plan-2  C19  0.020
 9W1  plan-2  N2   0.020
 9W1  plan-2  N6   0.020
 9W1  plan-2  H2   0.020
 9W1  plan-2  H3   0.020
 9W1  plan-3  C4   0.020
 9W1  plan-3  C7   0.020
 9W1  plan-3  C1   0.020
 9W1  plan-3  C2   0.020
 9W1  plan-3  C3   0.020
 9W1  plan-3  C9   0.020
 9W1  plan-3  N6   0.020
 9W1  plan-3  O3   0.020
 9W1  plan-3  H11  0.020
 9W1  plan-3  H12  0.020
 9W1  plan-3  H13  0.020
 9W1  plan-3  H1   0.020
 9W1  plan-4  C13  0.020
 9W1  plan-4  N5   0.020
 9W1  plan-4  H20  0.020
 9W1  plan-4  H21  0.020
 9W1  plan-5  C10  0.020
 9W1  plan-5  C17  0.020
 9W1  plan-5  C14  0.020
 9W1  plan-5  C16  0.020
 9W1  plan-5  N4   0.020
 9W1  plan-5  O1   0.020

