# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 20:40:33 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-cyclopropyl-N-[(2R)-1-oxo-1-(piperidin-1-yl)propan-2-yl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1c[nH]c2ncc(nc12)C3CC3)C(=O)N4CCCCC4
#
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
 19S  19S  2-cyclopropyl-N-[(2R)-1-oxo-1-(piperidin-1-yl)propan-2-yl]-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide  ligand  48  25  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_19S
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
 19S  N1   N  NT    0  -0.455   4.5669  -0.0415   0.2362
 19S  C2   C  CH2   0  -0.306   5.7744   0.6268  -0.2340
 19S  C3   C  CH2   0  -0.423   6.2989  -0.0350  -1.5014
 19S  C4   C  CH2   0  -0.435   6.5392  -1.5218  -1.2670
 19S  C5   C  CH2   0  -0.412   5.2826  -2.1850  -0.7160
 19S  C6   C  CH2   0  -0.309   4.7693  -1.4549   0.5203
 19S  N7   N  N     0  -0.361  -4.7193   1.6394  -0.7753
 19S  C8   C  CR6   0   0.268  -4.6486  -0.6642  -0.0938
 19S  C9   C  CR16  0  -0.127  -5.3287   0.4923  -0.5319
 19S  N10  N  N     0  -0.411  -3.3369  -0.6656   0.1029
 19S  C11  C  CR56  0   0.122  -2.7029   0.4790  -0.1378
 19S  C12  C  CR56  0   0.476  -3.4180   1.6124  -0.5748
 19S  N13  N  NR15  0  -0.667  -2.5298   2.6321  -0.7424
 19S  C14  C  CR15  0  -0.013  -1.2907   2.1903  -0.4297
 19S  C15  C  CR5   0  -0.171  -1.3268   0.8672  -0.0460
 19S  N17  N  NH1   0  -0.674   1.0047   0.5952   0.4343
 19S  O18  O  O     0  -0.444  -0.3804  -1.1722   0.6419
 19S  C19  C  CH1   0  -0.203   2.1851  -0.1077   0.8712
 19S  C20  C  CH1   0  -0.352  -5.3587  -1.9356   0.1650
 19S  C21  C  CH2   0  -0.453  -6.7469  -1.9585   0.7495
 19S  C22  C  CH2   0  -0.454  -6.5385  -2.3601  -0.6693
 19S  C23  C  C     0   0.565   3.3989   0.6191   0.2881
 19S  C24  C  CH3   0  -0.640   2.2924  -0.1369   2.3999
 19S  O25  O  O     0  -0.472   3.2834   1.7930  -0.0503
 19S  H1   H  HCH2  0   0.276   5.5662   1.6802  -0.3949
 19S  H2   H  HCH2  0   0.223   6.5294   0.5563   0.5561
 19S  H3   H  HCH2  0   0.222   5.5738   0.1063  -2.3086
 19S  H4   H  HCH2  0   0.233   7.2212   0.4635  -1.8068
 19S  H5   H  HCH2  0   0.235   6.8536  -2.0117  -2.1905
 19S  H6   H  HCH2  0   0.209   7.3580  -1.6455  -0.5496
 19S  H7   H  HCH2  0   0.219   4.4972  -2.1895  -1.4778
 19S  H8   H  HCH2  0   0.235   5.4781  -3.2262  -0.4518
 19S  H9   H  HCH2  0   0.231   5.4984  -1.5410   1.3330
 19S  H10  H  HCH2  0   0.255   3.8536  -1.9198   0.8717
 19S  H12  H  HNR5  0   0.385  -2.7542   3.5644  -1.0534
 19S  H13  H  HCR5  0   0.269  -0.4534   2.8656  -0.5078
 19S  H14  H  HNH1  0   0.378   1.1221   1.5791   0.2488
 19S  H15  H  HCH1  0   0.265   2.1214  -1.1290   0.4944
 19S  H16  H  HCH1  0   0.254  -4.6935  -2.7273   0.4884
 19S  H17  H  HCH2  0   0.253  -6.9596  -2.7283   1.4799
 19S  H18  H  HCH2  0   0.243  -7.2279  -1.0094   0.9513
 19S  H19  H  HCH2  0   0.240  -6.8764  -1.6876  -1.4483
 19S  H20  H  HCH2  0   0.254  -6.6098  -3.4087  -0.9270
 19S  H21  H  HCH3  0   0.254   1.4124  -0.6174   2.8251
 19S  H22  H  HCH3  0   0.229   3.1698  -0.6888   2.7362
 19S  H23  H  HCH3  0   0.227   2.3587   0.8766   2.7957
 19S  C16  C  C     0   0.529  -0.2074   0.0102   0.3721
 19S  H11  H  HCR6  0   0.236  -6.4011   0.4756  -0.6880

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
 19S  C24  C19  single    1.533  0.020  1.533
 19S  C2   N1   single    1.458  0.020  1.458
 19S  C2   C3   single    1.523  0.020  1.523
 19S  C19  N17  single    1.442  0.020  1.442
 19S  C19  C23  single    1.530  0.020  1.530
 19S  N1   C23  single    1.343  0.020  1.343
 19S  N1   C6   single    1.456  0.020  1.456
 19S  C3   C4   single    1.524  0.020  1.524
 19S  N17  C16  single    1.347  0.020  1.347
 19S  C23  O25  double    1.227  0.020  1.227
 19S  C21  C20  single    1.506  0.020  1.506
 19S  C21  C22  single    1.489  0.020  1.489
 19S  O18  C16  double    1.225  0.020  1.225
 19S  C16  C15  single    1.470  0.020  1.470
 19S  C6   C5   single    1.525  0.020  1.525
 19S  C4   C5   single    1.524  0.020  1.524
 19S  C15  C11  aromatic  1.433  0.020  1.433
 19S  C15  C14  aromatic  1.378  0.020  1.378
 19S  N10  C11  aromatic  1.330  0.020  1.330
 19S  N10  C8   aromatic  1.326  0.020  1.326
 19S  C11  C12  aromatic  1.410  0.020  1.410
 19S  C14  N13  aromatic  1.352  0.020  1.352
 19S  C20  C22  single    1.506  0.020  1.506
 19S  C20  C8   single    1.479  0.020  1.479
 19S  C8   C9   aromatic  1.411  0.020  1.411
 19S  C12  N13  aromatic  1.363  0.020  1.363
 19S  C12  N7   aromatic  1.317  0.020  1.317
 19S  C9   N7   aromatic  1.322  0.020  1.322
 19S  C2   H1   single    0.970  0.020  1.090
 19S  C2   H2   single    0.970  0.020  1.090
 19S  C3   H3   single    0.970  0.020  1.090
 19S  C3   H4   single    0.970  0.020  1.090
 19S  C4   H5   single    0.970  0.020  1.090
 19S  C4   H6   single    0.970  0.020  1.090
 19S  C5   H7   single    0.970  0.020  1.090
 19S  C5   H8   single    0.970  0.020  1.090
 19S  C6   H9   single    0.970  0.020  1.090
 19S  C6   H10  single    0.970  0.020  1.090
 19S  C9   H11  single    0.930  0.020  1.080
 19S  N13  H12  single    0.860  0.020  1.020
 19S  C14  H13  single    0.930  0.020  1.080
 19S  N17  H14  single    0.860  0.020  1.020
 19S  C19  H15  single    0.970  0.020  1.090
 19S  C20  H16  single    0.970  0.020  1.090
 19S  C21  H17  single    0.970  0.020  1.090
 19S  C21  H18  single    0.970  0.020  1.090
 19S  C22  H19  single    0.970  0.020  1.090
 19S  C22  H20  single    0.970  0.020  1.090
 19S  C24  H21  single    0.970  0.020  1.090
 19S  C24  H22  single    0.970  0.020  1.090
 19S  C24  H23  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
 19S  C23  N1   C6   126.23  3.000
 19S  C6   N1   C2   113.13  3.000
 19S  C23  N1   C2   120.49  3.000
 19S  H2   C2   H1   107.55  3.000
 19S  H2   C2   C3   109.58  3.000
 19S  H1   C2   C3   111.37  3.000
 19S  H2   C2   N1   107.98  3.000
 19S  H1   C2   N1   109.49  3.000
 19S  C3   C2   N1   110.76  3.000
 19S  H4   C3   H3   107.12  3.000
 19S  H4   C3   C4   110.80  3.000
 19S  H3   C3   C4   110.11  3.000
 19S  H4   C3   C2   108.98  3.000
 19S  H3   C3   C2   109.25  3.000
 19S  C4   C3   C2   110.50  3.000
 19S  H6   C4   H5   106.74  3.000
 19S  H6   C4   C5   109.29  3.000
 19S  H5   C4   C5   110.37  3.000
 19S  H6   C4   C3   109.19  3.000
 19S  H5   C4   C3   110.67  3.000
 19S  C5   C4   C3   110.49  3.000
 19S  H8   C5   H7   107.04  3.000
 19S  H8   C5   C6   108.71  3.000
 19S  H7   C5   C6   108.96  3.000
 19S  H8   C5   C4   110.78  3.000
 19S  H7   C5   C4   110.00  3.000
 19S  C6   C5   C4   111.24  3.000
 19S  H10  C6   H9   106.72  3.000
 19S  H10  C6   C5   109.96  3.000
 19S  H9   C6   C5   109.88  3.000
 19S  H10  C6   N1   111.21  3.000
 19S  H9   C6   N1   108.28  3.000
 19S  C5   C6   N1   110.70  3.000
 19S  C12  N7   C9   114.19  3.000
 19S  C20  C8   N10  116.61  3.000
 19S  C20  C8   C9   121.82  3.000
 19S  N10  C8   C9   121.56  3.000
 19S  H11  C9   C8   120.59  3.000
 19S  H11  C9   N7   116.30  3.000
 19S  C8   C9   N7   123.11  3.000
 19S  C11  N10  C8   116.33  3.000
 19S  C15  C11  C12  106.81  3.000
 19S  C12  C11  N10  120.40  3.000
 19S  C15  C11  N10  132.78  3.000
 19S  N13  C12  C11  108.01  3.000
 19S  N13  C12  N7   127.59  3.000
 19S  C11  C12  N7   124.40  3.000
 19S  H12  N13  C14  125.27  3.000
 19S  H12  N13  C12  125.80  3.000
 19S  C14  N13  C12  108.93  3.000
 19S  H13  C14  C15  129.91  3.000
 19S  H13  C14  N13  119.35  3.000
 19S  C15  C14  N13  110.74  3.000
 19S  C16  C15  C14  128.23  3.000
 19S  C14  C15  C11  105.51  3.000
 19S  C16  C15  C11  126.26  3.000
 19S  H14  N17  C19  115.87  3.000
 19S  H14  N17  C16  121.34  3.000
 19S  C19  N17  C16  122.61  3.000
 19S  H15  C19  C24  109.32  3.000
 19S  H15  C19  C23  111.07  3.000
 19S  C24  C19  C23  109.49  3.000
 19S  H15  C19  N17  107.71  3.000
 19S  C23  C19  N17  107.60  3.000
 19S  C24  C19  N17  111.65  3.000
 19S  H16  C20  C22  116.13  3.000
 19S  H16  C20  C21  116.03  3.000
 19S  C22  C20  C21   59.25  3.000
 19S  H16  C20  C8   112.68  3.000
 19S  C22  C20  C8   121.43  3.000
 19S  C21  C20  C8   121.56  3.000
 19S  H18  C21  H17  114.22  3.000
 19S  H18  C21  C22  118.43  3.000
 19S  H17  C21  C22  118.60  3.000
 19S  H18  C21  C20  117.93  3.000
 19S  H17  C21  C20  116.98  3.000
 19S  C22  C21  C20   60.36  3.000
 19S  H20  C22  H19  114.19  3.000
 19S  H20  C22  C21  118.62  3.000
 19S  H19  C22  C21  118.30  3.000
 19S  H20  C22  C20  117.17  3.000
 19S  H19  C22  C20  117.89  3.000
 19S  C21  C22  C20   60.39  3.000
 19S  O25  C23  C19  119.00  3.000
 19S  O25  C23  N1   122.80  3.000
 19S  C19  C23  N1   118.10  3.000
 19S  H23  C24  H22  108.05  3.000
 19S  H23  C24  H21  108.52  3.000
 19S  H22  C24  H21  107.86  3.000
 19S  H23  C24  C19  110.40  3.000
 19S  H22  C24  C19  111.95  3.000
 19S  H21  C24  C19  109.95  3.000
 19S  O18  C16  N17  122.41  3.000
 19S  O18  C16  C15  121.17  3.000
 19S  N17  C16  C15  116.42  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
 19S  CONST_01  C15  C11  C12  N7    180.00   0.0  0
 19S  CONST_02  N10  C11  C12  N7      0.00   0.0  0
 19S  CONST_03  C14  N13  C12  N7    180.00   0.0  0
 19S  CONST_04  N10  C8   C9   N7      0.00   0.0  0
 19S  CONST_05  C15  C11  N10  C8    180.00   0.0  0
 19S  CONST_06  C12  C11  N10  C8      0.00   0.0  0
 19S  CONST_07  C12  N7   C9   C8      0.00   0.0  0
 19S  CONST_08  C11  N10  C8   C9      0.00   0.0  0
 19S  CONST_09  C11  C12  N7   C9      0.00   0.0  0
 19S  CONST_10  N13  C12  N7   C9    180.00   0.0  0
 19S  CONST_11  C14  C15  C11  N10   180.00   0.0  0
 19S  CONST_12  N13  C12  C11  N10   180.00   0.0  0
 19S  CONST_13  N13  C14  C15  C11     0.00   0.0  0
 19S  CONST_14  C14  N13  C12  C11     0.00   0.0  0
 19S  CONST_15  C14  C15  C11  C12     0.00   0.0  0
 19S  CONST_16  C15  C14  N13  C12     0.00   0.0  0
 19S  CONST_17  C15  C11  C12  N13     0.00   0.0  0
 19S  CONST_18  C20  C8   C9   N7    180.00   0.0  0
 19S  CONST_19  C20  C8   N10  C11   180.00   0.0  0
 19S  CONST_20  C16  C15  C11  N10     0.00   0.0  0
 19S  CONST_21  C16  C15  C11  C12   180.00   0.0  0
 19S  CONST_22  C16  C15  C14  N13   180.00   0.0  0
 19S  CONST_23  H12  N13  C12  N7      0.00   0.0  0
 19S  CONST_24  H11  C9   C8   N10   180.00   0.0  0
 19S  CONST_25  H13  C14  C15  C11   180.00   0.0  0
 19S  CONST_26  C19  C23  N1   C2    180.00   0.0  0
 19S  CONST_27  O25  C23  N1   C2      0.00   0.0  0
 19S  CONST_28  C19  C23  N1   C6      0.00   0.0  0
 19S  CONST_29  O25  C23  N1   C6    180.00   0.0  0
 19S  CONST_30  C19  N17  C16  C15   180.00   0.0  0
 19S  CONST_31  H14  N17  C16  C15     0.00   0.0  0
 19S  CONST_32  C19  N17  C16  O18     0.00   0.0  0
 19S  Var_01    C4   C3   C2   N1    -55.96  30.0  1
 19S  Var_02    C4   C5   C6   N1     54.49  30.0  1
 19S  Var_03    C5   C6   N1   C2    -57.70  30.0  1
 19S  Var_04    C5   C4   C3   C2     53.79  30.0  1
 19S  Var_05    C6   N1   C2   C3     58.71  30.0  1
 19S  Var_06    C6   C5   C4   C3    -53.26  30.0  1
 19S  Var_07    C22  C21  C20  C8    110.28  30.0  1
 19S  Var_08    C21  C20  C8   C9    -35.80  30.0  2
 19S  Var_09    N17  C16  C15  C11  -177.63  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
 19S  chir_01  C19  C24  N17  C23  negativ
 19S  chir_02  C20  C21  C22  C8   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
 19S  plan-1  N1   0.020
 19S  plan-1  C2   0.020
 19S  plan-1  C6   0.020
 19S  plan-1  C19  0.020
 19S  plan-1  C23  0.020
 19S  plan-1  O25  0.020
 19S  plan-2  N7   0.020
 19S  plan-2  C8   0.020
 19S  plan-2  C9   0.020
 19S  plan-2  N10  0.020
 19S  plan-2  C11  0.020
 19S  plan-2  C12  0.020
 19S  plan-2  N13  0.020
 19S  plan-2  C14  0.020
 19S  plan-2  C15  0.020
 19S  plan-2  C20  0.020
 19S  plan-2  H12  0.020
 19S  plan-2  H13  0.020
 19S  plan-2  C16  0.020
 19S  plan-2  H11  0.020
 19S  plan-3  C15  0.020
 19S  plan-3  N17  0.020
 19S  plan-3  O18  0.020
 19S  plan-3  C19  0.020
 19S  plan-3  H14  0.020
 19S  plan-3  C16  0.020

