# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:57:26 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-tert-butyl-5-[3-(4-cyclopropylpyrimidin-2-yl)-1H-indol-5-yl]-1,3,4-oxadiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)Nc1oc(nn1)c2ccc3[nH]cc(c4nccc(n4)C5CC5)c3c2
#
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
 38W  38W  N-tert-butyl-5-[3-(4-cyclopropylpyrimidin-2-yl)-1H-indol-5-yl]-1,3,4-oxadiazol-2-amine  ligand  50  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_38W
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
 38W  C01  C  CH3   0  -0.671   8.0705  -0.5267   0.0486
 38W  C02  C  CT    0   0.073   6.7141  -1.2236  -0.0190
 38W  C03  C  CH3   0  -0.646   6.5660  -1.9496  -1.3573
 38W  C04  C  CH3   0  -0.648   6.5984  -2.2098   1.1422
 38W  N05  N  NH1   0  -0.703   5.7095  -0.1590   0.1173
 38W  C06  C  CR5   0   0.707   4.3872  -0.3618   0.1025
 38W  N07  N  N     0  -0.382   3.6996  -1.4618   0.1324
 38W  N08  N  N     0  -0.319   2.3780  -1.0804   0.1418
 38W  C09  C  CR5   0   0.471   2.3418   0.2006   0.1099
 38W  O10  O  O     0  -0.452   3.5935   0.7237   0.0853
 38W  C11  C  CR6   0  -0.013   1.1926   1.0889   0.0949
 38W  C12  C  CR16  0  -0.312   1.3680   2.4872   0.1190
 38W  C13  C  CR16  0  -0.283   0.2838   3.3381   0.1058
 38W  C14  C  CR56  0   0.361  -0.9847   2.7688   0.0673
 38W  N15  N  NR15  0  -0.679  -2.2129   3.3651   0.0444
 38W  C16  C  CR15  0  -0.020  -3.1800   2.4196   0.0061
 38W  C17  C  CR5   0  -0.080  -2.6126   1.1678   0.0028
 38W  C18  C  CR6   0   0.304  -3.3517  -0.0808  -0.0344
 38W  N19  N  N     0  -0.444  -2.6579  -1.2159  -0.0266
 38W  C20  C  CR16  0  -0.015  -3.3653  -2.3407  -0.0593
 38W  C21  C  CR16  0  -0.420  -4.7423  -2.3597  -0.1008
 38W  C22  C  CR6   0   0.388  -5.3864  -1.1192  -0.1075
 38W  N23  N  N     0  -0.471  -4.6835   0.0052  -0.0736
 38W  C24  C  CH1   0  -0.374  -6.8523  -0.9759  -0.1523
 38W  C25  C  CH2   0  -0.476  -7.6956  -1.9586  -0.9261
 38W  C26  C  CH2   0  -0.476  -7.7414  -1.9665   0.5581
 38W  C27  C  CR56  0   0.095  -1.1891   1.3710   0.0427
 38W  C28  C  CR16  0  -0.426  -0.0791   0.5295   0.0571
 38W  H1   H  HCH3  0   0.238   8.1895   0.1987  -0.7593
 38W  H2   H  HCH3  0   0.241   8.1967  -0.0050   0.9989
 38W  H3   H  HCH3  0   0.243   8.8720  -1.2589  -0.0427
 38W  H4   H  HCH3  0   0.239   5.6012  -2.4510  -1.4340
 38W  H5   H  HCH3  0   0.230   6.6583  -1.2528  -2.1919
 38W  H6   H  HCH3  0   0.230   7.3430  -2.7082  -1.4634
 38W  H7   H  HCH3  0   0.231   7.4043  -2.9413   1.0794
 38W  H8   H  HCH3  0   0.230   6.6822  -1.6930   2.0991
 38W  H9   H  HCH3  0   0.244   5.6529  -2.7496   1.1251
 38W  H10  H  HNH1  0   0.405   6.0087   0.7724  -0.1283
 38W  H11  H  HCR6  0   0.259   2.3623   2.9113   0.1502
 38W  H12  H  HCR6  0   0.272   0.4201   4.4113   0.1245
 38W  H13  H  HNR5  0   0.421  -2.3821   4.3579   0.0552
 38W  H14  H  HCR5  0   0.295  -4.2220   2.6940  -0.0166
 38W  H15  H  HCR6  0   0.270  -2.8020  -3.2673  -0.0518
 38W  H16  H  HCR6  0   0.272  -5.2840  -3.2951  -0.1267
 38W  H17  H  HCH1  0   0.272  -7.1839   0.0552  -0.1556
 38W  H18  H  HCH2  0   0.270  -8.5393  -1.5537  -1.4692
 38W  H19  H  HCH2  0   0.261  -7.1862  -2.7692  -1.4322
 38W  H20  H  HCH2  0   0.261  -7.2646  -2.7825   1.0870
 38W  H21  H  HCH2  0   0.270  -8.6166  -1.5660   1.0520
 38W  H22  H  HCR6  0   0.255  -0.2071  -0.5433   0.0370

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
 38W  C13  C12  aromatic  1.378  0.020  1.378
 38W  C13  C14  aromatic  1.391  0.020  1.391
 38W  C12  C11  aromatic  1.410  0.020  1.410
 38W  N08  N07  aromatic  1.376  0.020  1.376
 38W  N08  C09  aromatic  1.282  0.020  1.282
 38W  N15  C14  aromatic  1.365  0.020  1.365
 38W  N15  C16  aromatic  1.353  0.020  1.353
 38W  C14  C27  aromatic  1.413  0.020  1.413
 38W  N07  C06  aromatic  1.298  0.020  1.298
 38W  C11  C09  single    1.453  0.020  1.453
 38W  C11  C28  aromatic  1.390  0.020  1.390
 38W  C09  O10  aromatic  1.357  0.020  1.357
 38W  C16  C17  aromatic  1.374  0.020  1.374
 38W  C27  C28  aromatic  1.393  0.020  1.393
 38W  C27  C17  aromatic  1.438  0.020  1.438
 38W  C06  O10  aromatic  1.345  0.020  1.345
 38W  C06  N05  single    1.338  0.020  1.338
 38W  C17  C18  single    1.451  0.020  1.451
 38W  N05  C02  single    1.470  0.020  1.470
 38W  C18  N19  aromatic  1.330  0.020  1.330
 38W  C18  N23  aromatic  1.335  0.020  1.335
 38W  N19  C20  aromatic  1.329  0.020  1.329
 38W  C02  C03  single    1.530  0.020  1.530
 38W  C02  C04  single    1.528  0.020  1.528
 38W  C02  C01  single    1.527  0.020  1.527
 38W  N23  C22  aromatic  1.326  0.020  1.326
 38W  C20  C21  aromatic  1.378  0.020  1.378
 38W  C22  C21  aromatic  1.398  0.020  1.398
 38W  C22  C24  single    1.474  0.020  1.474
 38W  C26  C25  single    1.485  0.020  1.485
 38W  C26  C24  single    1.509  0.020  1.509
 38W  C25  C24  single    1.508  0.020  1.508
 38W  C01  H1   single    0.970  0.020  1.090
 38W  C01  H2   single    0.970  0.020  1.090
 38W  C01  H3   single    0.970  0.020  1.090
 38W  C03  H4   single    0.970  0.020  1.090
 38W  C03  H5   single    0.970  0.020  1.090
 38W  C03  H6   single    0.970  0.020  1.090
 38W  C04  H7   single    0.970  0.020  1.090
 38W  C04  H8   single    0.970  0.020  1.090
 38W  C04  H9   single    0.970  0.020  1.090
 38W  N05  H10  single    0.890  0.020  1.040
 38W  C12  H11  single    0.930  0.020  1.080
 38W  C13  H12  single    0.930  0.020  1.080
 38W  N15  H13  single    0.860  0.020  1.020
 38W  C16  H14  single    0.930  0.020  1.080
 38W  C20  H15  single    0.930  0.020  1.080
 38W  C21  H16  single    0.930  0.020  1.080
 38W  C24  H17  single    0.970  0.020  1.090
 38W  C25  H18  single    0.970  0.020  1.090
 38W  C25  H19  single    0.970  0.020  1.090
 38W  C26  H20  single    0.970  0.020  1.090
 38W  C26  H21  single    0.970  0.020  1.090
 38W  C28  H22  single    0.930  0.020  1.080

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
 38W  H3   C01  H2   108.01  3.000
 38W  H3   C01  H1   107.71  3.000
 38W  H2   C01  H1   108.31  3.000
 38W  H3   C01  C02  110.07  3.000
 38W  H2   C01  C02  111.07  3.000
 38W  H1   C01  C02  111.55  3.000
 38W  N05  C02  C04  110.20  3.000
 38W  C04  C02  C03  110.56  3.000
 38W  N05  C02  C03  111.02  3.000
 38W  C04  C02  C01  109.17  3.000
 38W  C03  C02  C01  109.96  3.000
 38W  N05  C02  C01  105.81  3.000
 38W  H6   C03  H5   108.02  3.000
 38W  H6   C03  H4   107.68  3.000
 38W  H5   C03  H4   108.35  3.000
 38W  H6   C03  C02  110.25  3.000
 38W  H5   C03  C02  110.97  3.000
 38W  H4   C03  C02  111.44  3.000
 38W  H9   C04  H8   108.39  3.000
 38W  H9   C04  H7   107.96  3.000
 38W  H8   C04  H7   108.16  3.000
 38W  H9   C04  C02  111.95  3.000
 38W  H8   C04  C02  110.80  3.000
 38W  H7   C04  C02  109.47  3.000
 38W  H10  N05  C06  115.49  3.000
 38W  H10  N05  C02  116.33  3.000
 38W  C06  N05  C02  124.38  3.000
 38W  O10  C06  N07  111.82  3.000
 38W  O10  C06  N05  117.46  3.000
 38W  N07  C06  N05  130.69  3.000
 38W  N08  N07  C06  105.92  3.000
 38W  C09  N08  N07  107.70  3.000
 38W  C11  C09  O10  119.60  3.000
 38W  O10  C09  N08  111.07  3.000
 38W  C11  C09  N08  129.32  3.000
 38W  C09  O10  C06  103.48  3.000
 38W  C28  C11  C12  120.91  3.000
 38W  C28  C11  C09  118.56  3.000
 38W  C12  C11  C09  120.53  3.000
 38W  H11  C12  C13  118.78  3.000
 38W  H11  C12  C11  120.27  3.000
 38W  C13  C12  C11  120.95  3.000
 38W  H12  C13  C14  121.42  3.000
 38W  H12  C13  C12  120.87  3.000
 38W  C14  C13  C12  117.71  3.000
 38W  C27  C14  N15  107.56  3.000
 38W  C27  C14  C13  122.50  3.000
 38W  N15  C14  C13  129.94  3.000
 38W  H13  N15  C16  124.68  3.000
 38W  H13  N15  C14  125.55  3.000
 38W  C16  N15  C14  109.77  3.000
 38W  H14  C16  C17  129.13  3.000
 38W  H14  C16  N15  120.91  3.000
 38W  C17  C16  N15  109.96  3.000
 38W  C27  C17  C18  128.76  3.000
 38W  C18  C17  C16  124.98  3.000
 38W  C27  C17  C16  106.25  3.000
 38W  N23  C18  N19  125.12  3.000
 38W  N23  C18  C17  116.95  3.000
 38W  N19  C18  C17  117.92  3.000
 38W  C20  N19  C18  116.38  3.000
 38W  H15  C20  C21  120.50  3.000
 38W  H15  C20  N19  116.52  3.000
 38W  C21  C20  N19  122.98  3.000
 38W  H16  C21  C22  122.47  3.000
 38W  H16  C21  C20  120.89  3.000
 38W  C22  C21  C20  116.64  3.000
 38W  C24  C22  N23  116.46  3.000
 38W  C24  C22  C21  123.01  3.000
 38W  N23  C22  C21  120.53  3.000
 38W  C22  N23  C18  118.34  3.000
 38W  H17  C24  C26  116.49  3.000
 38W  H17  C24  C25  116.58  3.000
 38W  C26  C24  C25   58.96  3.000
 38W  H17  C24  C22  113.40  3.000
 38W  C25  C24  C22  120.56  3.000
 38W  C26  C24  C22  120.53  3.000
 38W  H19  C25  H18  114.35  3.000
 38W  H19  C25  C26  118.53  3.000
 38W  H18  C25  C26  118.67  3.000
 38W  H19  C25  C24  117.67  3.000
 38W  H18  C25  C24  116.72  3.000
 38W  C26  C25  C24   60.53  3.000
 38W  H21  C26  H20  114.34  3.000
 38W  H21  C26  C25  118.64  3.000
 38W  H20  C26  C25  118.59  3.000
 38W  H21  C26  C24  116.66  3.000
 38W  H20  C26  C24  117.73  3.000
 38W  C25  C26  C24   60.51  3.000
 38W  C28  C27  C17  134.71  3.000
 38W  C17  C27  C14  106.46  3.000
 38W  C28  C27  C14  118.83  3.000
 38W  H22  C28  C27  120.34  3.000
 38W  H22  C28  C11  120.56  3.000
 38W  C27  C28  C11  119.10  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
 38W  CONST_01  C09  N08  N07  C06     0.00   0.0  0
 38W  CONST_02  N08  C09  O10  C06     0.00   0.0  0
 38W  CONST_03  C11  C09  O10  C06   180.00   0.0  0
 38W  CONST_04  C11  C09  N08  N07   180.00   0.0  0
 38W  CONST_05  O10  C09  N08  N07     0.00   0.0  0
 38W  CONST_06  C09  O10  C06  N07     0.00   0.0  0
 38W  CONST_07  O10  C06  N07  N08     0.00   0.0  0
 38W  CONST_08  C12  C11  C09  N08   180.00   0.0  0
 38W  CONST_09  C28  C11  C09  N08     0.00   0.0  0
 38W  CONST_10  C13  C12  C11  C09   180.00   0.0  0
 38W  CONST_11  C27  C28  C11  C09   180.00   0.0  0
 38W  CONST_12  C12  C11  C09  O10     0.00   0.0  0
 38W  CONST_13  C28  C11  C09  O10   180.00   0.0  0
 38W  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 38W  CONST_15  C14  C27  C28  C11     0.00   0.0  0
 38W  CONST_16  C17  C27  C28  C11   180.00   0.0  0
 38W  CONST_17  N15  C14  C13  C12   180.00   0.0  0
 38W  CONST_18  C27  C14  C13  C12     0.00   0.0  0
 38W  CONST_19  C27  C28  C11  C12     0.00   0.0  0
 38W  CONST_20  C28  C11  C12  C13     0.00   0.0  0
 38W  CONST_21  C16  N15  C14  C13   180.00   0.0  0
 38W  CONST_22  C28  C27  C14  C13     0.00   0.0  0
 38W  CONST_23  C17  C27  C14  C13   180.00   0.0  0
 38W  CONST_24  C17  C16  N15  C14     0.00   0.0  0
 38W  CONST_25  C16  C17  C27  C14     0.00   0.0  0
 38W  CONST_26  C18  C17  C27  C14   180.00   0.0  0
 38W  CONST_27  C28  C27  C14  N15   180.00   0.0  0
 38W  CONST_28  C17  C27  C14  N15     0.00   0.0  0
 38W  CONST_29  C27  C17  C16  N15     0.00   0.0  0
 38W  CONST_30  C18  C17  C16  N15   180.00   0.0  0
 38W  CONST_31  C27  C14  N15  C16     0.00   0.0  0
 38W  CONST_32  C28  C27  C17  C16   180.00   0.0  0
 38W  CONST_33  N19  C18  C17  C16   180.00   0.0  0
 38W  CONST_34  N23  C18  C17  C16     0.00   0.0  0
 38W  CONST_35  C20  N19  C18  C17   180.00   0.0  0
 38W  CONST_36  C22  N23  C18  C17   180.00   0.0  0
 38W  CONST_37  C28  C27  C17  C18     0.00   0.0  0
 38W  CONST_38  C21  C20  N19  C18     0.00   0.0  0
 38W  CONST_39  C21  C22  N23  C18     0.00   0.0  0
 38W  CONST_40  C27  C17  C18  N19     0.00   0.0  0
 38W  CONST_41  C22  N23  C18  N19     0.00   0.0  0
 38W  CONST_42  C22  C21  C20  N19     0.00   0.0  0
 38W  CONST_43  N23  C18  N19  C20     0.00   0.0  0
 38W  CONST_44  N23  C22  C21  C20     0.00   0.0  0
 38W  CONST_45  C27  C17  C18  N23   180.00   0.0  0
 38W  CONST_46  C24  C22  N23  C18   180.00   0.0  0
 38W  CONST_47  C24  C22  C21  C20   180.00   0.0  0
 38W  CONST_48  N08  N07  C06  N05   180.00   0.0  0
 38W  CONST_49  C09  O10  C06  N05   180.00   0.0  0
 38W  CONST_50  H11  C12  C11  C09     0.00   0.0  0
 38W  CONST_51  H22  C28  C11  C09     0.00   0.0  0
 38W  CONST_52  H12  C13  C12  C11   180.00   0.0  0
 38W  CONST_53  H13  N15  C14  C13     0.00   0.0  0
 38W  CONST_54  H14  C16  N15  C14   180.00   0.0  0
 38W  CONST_55  H15  C20  N19  C18   180.00   0.0  0
 38W  CONST_56  H16  C21  C20  N19   180.00   0.0  0
 38W  CONST_57  N07  C06  N05  C02     0.00   0.0  0
 38W  CONST_58  O10  C06  N05  C02   180.00   0.0  0
 38W  CONST_59  H10  N05  C06  N07   180.00   0.0  0
 38W  Var_01    C26  C24  C22  C21    35.20  30.0  2
 38W  Var_02    C25  C26  C24  C22  -109.51  30.0  1
 38W  Var_03    C06  N05  C02  C01   179.74  30.0  3
 38W  Var_04    H4   C03  C02  C01  -179.61  30.0  3
 38W  Var_05    H7   C04  C02  C01   -59.09  30.0  3
 38W  Var_06    H1   C01  C02  C03    59.27  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
 38W  chir_01  C24  C22  C26  C25  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
 38W  plan-1  N05  0.020
 38W  plan-1  C06  0.020
 38W  plan-1  N07  0.020
 38W  plan-1  N08  0.020
 38W  plan-1  C09  0.020
 38W  plan-1  O10  0.020
 38W  plan-1  C11  0.020
 38W  plan-2  C17  0.020
 38W  plan-2  C18  0.020
 38W  plan-2  N19  0.020
 38W  plan-2  C20  0.020
 38W  plan-2  C21  0.020
 38W  plan-2  C22  0.020
 38W  plan-2  N23  0.020
 38W  plan-2  C24  0.020
 38W  plan-2  H15  0.020
 38W  plan-2  H16  0.020
 38W  plan-3  C09  0.020
 38W  plan-3  C11  0.020
 38W  plan-3  C12  0.020
 38W  plan-3  C13  0.020
 38W  plan-3  C14  0.020
 38W  plan-3  N15  0.020
 38W  plan-3  C16  0.020
 38W  plan-3  C17  0.020
 38W  plan-3  C18  0.020
 38W  plan-3  C27  0.020
 38W  plan-3  C28  0.020
 38W  plan-3  H11  0.020
 38W  plan-3  H12  0.020
 38W  plan-3  H13  0.020
 38W  plan-3  H14  0.020
 38W  plan-3  H22  0.020
 38W  plan-4  C02  0.020
 38W  plan-4  N05  0.020
 38W  plan-4  C06  0.020
 38W  plan-4  H10  0.020

