# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:50:03 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: N-cyclopropyl-4-{8-[(thiophen-2-ylmethyl)amino]imidazo[1,2-a]pyrazin-3-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC1CC1)c2ccc(cc2)c3cnc4n3ccnc4NCc5sccc5
#
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
 O23  O23  N-cyclopropyl-4-{8-[(thiophen-2-ylmethyl)amino]imidazo[1,2-a]pyrazin-3-yl}benzamide  ligand  47  28  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O23
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
 O23  O    O  O     0  -0.479  -6.3587  -1.5248   1.2660
 O23  C    C  C     0   0.530  -5.9427  -0.6696   0.4988
 O23  N    N  NH1   0  -0.656  -6.7326   0.2815  -0.0347
 O23  C1   C  CH1   0  -0.080  -8.1281   0.3556   0.2478
 O23  C3   C  CH2   0  -0.483  -8.5705   0.8610   1.5833
 O23  C2   C  CH2   0  -0.511  -8.7354   1.7157   0.3645
 O23  C4   C  CR6   0  -0.045  -4.5047  -0.6259   0.0930
 O23  C9   C  CR16  0  -0.253  -3.7728  -1.8105   0.1143
 O23  C8   C  CR16  0  -0.291  -2.4359  -1.8183  -0.2392
 O23  C7   C  CR6   0   0.057  -1.7903  -0.6377  -0.6138
 O23  C6   C  CR16  0  -0.299  -2.5234   0.5498  -0.6254
 O23  C5   C  CR16  0  -0.274  -3.8628   0.5545  -0.2739
 O23  C10  C  CR5   0   0.278  -0.3914  -0.6833  -1.0212
 O23  N2   N  N     0  -0.528   0.5629   0.2395  -0.6810
 O23  C13  C  CR16  0  -0.090   0.5389   1.3396   0.1514
 O23  C14  C  CR16  0  -0.154   1.6951   2.0245   0.2942
 O23  N3   N  N     0  -0.463   2.8651   1.7060  -0.3174
 O23  C15  C  CR6   0   0.451   2.8911   0.6555  -1.0954
 O23  C12  C  CR56  0   0.419   1.7214  -0.1466  -1.2943
 O23  N1   N  N     0  -0.451   1.5641  -1.2496  -1.9978
 O23  C11  C  CR15  0  -0.231   0.2706  -1.5876  -1.8289
 O23  N4   N  NH1   0  -0.646   4.0149   0.3057  -1.7435
 O23  C16  C  CH2   0  -0.376   5.2694   0.9883  -1.5337
 O23  C17  C  CR5   0  -0.146   6.0057   0.5493  -0.3041
 O23  S    S  S2    0   0.213   5.4314   0.8873   1.2880
 O23  C20  C  CR15  0  -0.472   6.7670   0.0850   2.0062
 O23  C19  C  CR15  0  -0.185   7.6153  -0.4181   1.0692
 O23  C18  C  CR15  0  -0.235   7.1753  -0.1497  -0.2561
 O23  H1   H  HNH1  0   0.407  -6.3817   0.8343  -0.8003
 O23  H2   H  HCH1  0   0.268  -8.7346  -0.4187  -0.2124
 O23  H3   H  HCH2  0   0.256  -9.4493   0.4090   2.0239
 O23  H4   H  HCH2  0   0.257  -7.8020   1.1390   2.2929
 O23  H5   H  HCH2  0   0.258  -8.0780   2.5695   0.2572
 O23  H6   H  HCH2  0   0.260  -9.7275   1.8590  -0.0421
 O23  H7   H  HCR6  0   0.265  -4.2505  -2.7351   0.4091
 O23  H8   H  HCR6  0   0.262  -1.8808  -2.7471  -0.2111
 O23  H9   H  HCR6  0   0.276  -2.0609   1.4791  -0.9312
 O23  H10  H  HCR6  0   0.265  -4.3937   1.4980  -0.2764
 O23  H11  H  HCR6  0   0.310  -0.3804   1.5877   0.6554
 O23  H12  H  HCR6  0   0.270   1.7142   2.8890   0.9442
 O23  H13  H  HCR5  0   0.272  -0.1614  -2.4540  -2.3072
 O23  H14  H  HNH1  0   0.404   4.0294  -0.5865  -2.2110
 O23  H15  H  HCH2  0   0.284   5.9024   0.7906  -2.3979
 O23  H16  H  HCH2  0   0.270   5.0835   2.0623  -1.5125
 O23  H17  H  HCR5  0   0.291   6.8538   0.0232   3.0803
 O23  H18  H  HCR5  0   0.264   8.5190  -0.9601   1.3085
 O23  H19  H  HCR5  0   0.262   7.7076  -0.4606  -1.1451

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
 O23  C3   C1   single    1.495  0.020  1.495
 O23  C3   C2   single    1.498  0.020  1.498
 O23  C1   C2   single    1.494  0.020  1.494
 O23  C1   N    single    1.426  0.020  1.426
 O23  N    C    single    1.347  0.020  1.347
 O23  O    C    double    1.222  0.020  1.222
 O23  C    C4   single    1.495  0.020  1.495
 O23  C4   C9   aromatic  1.393  0.020  1.393
 O23  C4   C5   aromatic  1.393  0.020  1.393
 O23  C9   C8   aromatic  1.383  0.020  1.383
 O23  C5   C6   aromatic  1.385  0.020  1.385
 O23  C8   C7   aromatic  1.397  0.020  1.397
 O23  C6   C7   aromatic  1.396  0.020  1.396
 O23  C7   C10  single    1.458  0.020  1.458
 O23  C10  N2   aromatic  1.370  0.020  1.370
 O23  C10  C11  aromatic  1.381  0.020  1.381
 O23  C13  N2   aromatic  1.380  0.020  1.380
 O23  C13  C14  aromatic  1.351  0.020  1.351
 O23  N2   C12  aromatic  1.367  0.020  1.367
 O23  C11  N1   aromatic  1.348  0.020  1.348
 O23  C14  N3   aromatic  1.358  0.020  1.358
 O23  C12  N1   aromatic  1.318  0.020  1.318
 O23  C12  C15  aromatic  1.432  0.020  1.432
 O23  N3   C15  aromatic  1.307  0.020  1.307
 O23  C15  N4   single    1.344  0.020  1.344
 O23  N4   C16  single    1.444  0.020  1.444
 O23  C16  C17  single    1.499  0.020  1.499
 O23  C17  C18  aromatic  1.363  0.020  1.363
 O23  C17  S    aromatic  1.726  0.020  1.726
 O23  C18  C19  aromatic  1.422  0.020  1.422
 O23  S    C20  aromatic  1.716  0.020  1.716
 O23  C19  C20  aromatic  1.360  0.020  1.360
 O23  N    H1   single    0.860  0.020  1.020
 O23  C1   H2   single    0.970  0.020  1.090
 O23  C3   H3   single    0.970  0.020  1.090
 O23  C3   H4   single    0.970  0.020  1.090
 O23  C2   H5   single    0.970  0.020  1.090
 O23  C2   H6   single    0.970  0.020  1.090
 O23  C9   H7   single    0.930  0.020  1.080
 O23  C8   H8   single    0.930  0.020  1.080
 O23  C6   H9   single    0.930  0.020  1.080
 O23  C5   H10  single    0.930  0.020  1.080
 O23  C13  H11  single    0.930  0.020  1.080
 O23  C14  H12  single    0.930  0.020  1.080
 O23  C11  H13  single    0.930  0.020  1.080
 O23  N4   H14  single    0.860  0.020  1.020
 O23  C16  H15  single    0.970  0.020  1.090
 O23  C16  H16  single    0.970  0.020  1.090
 O23  C20  H17  single    0.930  0.020  1.080
 O23  C19  H18  single    0.930  0.020  1.080
 O23  C18  H19  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
 O23  C4   C    N    115.85  3.000
 O23  C4   C    O    121.22  3.000
 O23  N    C    O    122.92  3.000
 O23  H1   N    C1   117.58  3.000
 O23  H1   N    C    118.97  3.000
 O23  C1   N    C    122.17  3.000
 O23  H2   C1   C2   117.07  3.000
 O23  H2   C1   C3   117.03  3.000
 O23  C2   C1   C3    60.14  3.000
 O23  H2   C1   N    115.19  3.000
 O23  C2   C1   N    117.43  3.000
 O23  C3   C1   N    118.97  3.000
 O23  H4   C3   H3   114.65  3.000
 O23  H4   C3   C2   117.72  3.000
 O23  H3   C3   C2   118.71  3.000
 O23  H4   C3   C1   117.54  3.000
 O23  H3   C3   C1   117.58  3.000
 O23  C2   C3   C1    59.91  3.000
 O23  H6   C2   H5   114.52  3.000
 O23  H6   C2   C3   118.85  3.000
 O23  H5   C2   C3   117.63  3.000
 O23  H6   C2   C1   117.65  3.000
 O23  H5   C2   C1   117.59  3.000
 O23  C3   C2   C1    59.95  3.000
 O23  C5   C4   C9   118.87  3.000
 O23  C5   C4   C    122.66  3.000
 O23  C9   C4   C    118.46  3.000
 O23  H7   C9   C8   119.46  3.000
 O23  H7   C9   C4   119.95  3.000
 O23  C8   C9   C4   120.59  3.000
 O23  H8   C8   C7   119.68  3.000
 O23  H8   C8   C9   119.60  3.000
 O23  C7   C8   C9   120.71  3.000
 O23  C10  C7   C6   121.90  3.000
 O23  C10  C7   C8   119.48  3.000
 O23  C6   C7   C8   118.60  3.000
 O23  H9   C6   C5   118.84  3.000
 O23  H9   C6   C7   120.57  3.000
 O23  C5   C6   C7   120.58  3.000
 O23  H10  C5   C6   118.46  3.000
 O23  H10  C5   C4   120.88  3.000
 O23  C6   C5   C4   120.65  3.000
 O23  C11  C10  N2   104.61  3.000
 O23  C11  C10  C7   130.07  3.000
 O23  N2   C10  C7   125.30  3.000
 O23  C12  N2   C13  120.72  3.000
 O23  C12  N2   C10  106.78  3.000
 O23  C13  N2   C10  132.42  3.000
 O23  H11  C13  C14  124.33  3.000
 O23  H11  C13  N2   118.73  3.000
 O23  C14  C13  N2   116.93  3.000
 O23  H12  C14  N3   116.28  3.000
 O23  H12  C14  C13  118.92  3.000
 O23  N3   C14  C13  124.80  3.000
 O23  C15  N3   C14  118.27  3.000
 O23  N4   C15  C12  118.05  3.000
 O23  N4   C15  N3   120.86  3.000
 O23  C12  C15  N3   121.09  3.000
 O23  N1   C12  C15  129.83  3.000
 O23  C15  C12  N2   118.15  3.000
 O23  N1   C12  N2   112.02  3.000
 O23  C11  N1   C12  104.93  3.000
 O23  H13  C11  N1   121.99  3.000
 O23  H13  C11  C10  126.33  3.000
 O23  N1   C11  C10  111.66  3.000
 O23  H14  N4   C16  118.28  3.000
 O23  H14  N4   C15  117.81  3.000
 O23  C16  N4   C15  122.25  3.000
 O23  H16  C16  H15  107.06  3.000
 O23  H16  C16  C17  110.88  3.000
 O23  H15  C16  C17  108.19  3.000
 O23  H16  C16  N4   108.70  3.000
 O23  H15  C16  N4   107.69  3.000
 O23  C17  C16  N4   114.06  3.000
 O23  C18  C17  S    110.69  3.000
 O23  S    C17  C16  122.40  3.000
 O23  C18  C17  C16  126.90  3.000
 O23  C20  S    C17   92.04  3.000
 O23  H17  C20  C19  127.88  3.000
 O23  H17  C20  S    120.40  3.000
 O23  C19  C20  S    111.71  3.000
 O23  H18  C19  C18  124.04  3.000
 O23  H18  C19  C20  123.67  3.000
 O23  C18  C19  C20  112.28  3.000
 O23  H19  C18  C19  124.01  3.000
 O23  H19  C18  C17  122.72  3.000
 O23  C19  C18  C17  113.27  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
 O23  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 O23  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 O23  CONST_03  C6   C5   C4   C9      0.00   0.0  0
 O23  CONST_04  C6   C7   C8   C9      0.00   0.0  0
 O23  CONST_05  C10  C7   C8   C9    180.00   0.0  0
 O23  CONST_06  C5   C4   C9   C8      0.00   0.0  0
 O23  CONST_07  C5   C6   C7   C8      0.00   0.0  0
 O23  CONST_10  C13  N2   C10  C7      0.00   0.0  0
 O23  CONST_11  C12  N2   C10  C7    180.00   0.0  0
 O23  CONST_12  N1   C11  C10  C7    180.00   0.0  0
 O23  CONST_15  C10  C7   C6   C5    180.00   0.0  0
 O23  CONST_16  C14  C13  N2   C10   180.00   0.0  0
 O23  CONST_17  N1   C12  N2   C10     0.00   0.0  0
 O23  CONST_18  C15  C12  N2   C10   180.00   0.0  0
 O23  CONST_19  C12  N1   C11  C10     0.00   0.0  0
 O23  CONST_20  N1   C11  C10  N2      0.00   0.0  0
 O23  CONST_21  N3   C14  C13  N2      0.00   0.0  0
 O23  CONST_22  C11  N1   C12  N2      0.00   0.0  0
 O23  CONST_23  N3   C15  C12  N2      0.00   0.0  0
 O23  CONST_24  C11  C10  N2   C13   180.00   0.0  0
 O23  CONST_25  N1   C12  N2   C13   180.00   0.0  0
 O23  CONST_26  C15  C12  N2   C13     0.00   0.0  0
 O23  CONST_27  C15  N3   C14  C13     0.00   0.0  0
 O23  CONST_28  C12  N2   C13  C14     0.00   0.0  0
 O23  CONST_29  C12  C15  N3   C14     0.00   0.0  0
 O23  CONST_30  N1   C12  C15  N3    180.00   0.0  0
 O23  CONST_31  C11  N1   C12  C15   180.00   0.0  0
 O23  CONST_32  C11  C10  N2   C12     0.00   0.0  0
 O23  CONST_33  C20  C19  C18  C17     0.00   0.0  0
 O23  CONST_34  C19  C20  S    C17     0.00   0.0  0
 O23  CONST_35  C19  C18  C17  S       0.00   0.0  0
 O23  CONST_36  C18  C19  C20  S       0.00   0.0  0
 O23  CONST_37  C18  C17  S    C20     0.00   0.0  0
 O23  CONST_38  C8   C9   C4   C     180.00   0.0  0
 O23  CONST_39  C6   C5   C4   C     180.00   0.0  0
 O23  CONST_40  N4   C15  C12  N2    180.00   0.0  0
 O23  CONST_41  N4   C15  N3   C14   180.00   0.0  0
 O23  CONST_42  N4   C15  C12  N1      0.00   0.0  0
 O23  CONST_43  C19  C18  C17  C16   180.00   0.0  0
 O23  CONST_44  C20  S    C17  C16   180.00   0.0  0
 O23  CONST_45  H8   C8   C9   C4    180.00   0.0  0
 O23  CONST_46  H9   C6   C5   C4    180.00   0.0  0
 O23  CONST_47  H10  C5   C4   C9    180.00   0.0  0
 O23  CONST_48  H7   C9   C8   C7    180.00   0.0  0
 O23  CONST_49  H13  C11  C10  C7      0.00   0.0  0
 O23  CONST_50  H11  C13  N2   C10     0.00   0.0  0
 O23  CONST_51  H12  C14  C13  N2    180.00   0.0  0
 O23  CONST_52  H18  C19  C18  C17   180.00   0.0  0
 O23  CONST_53  H17  C20  S    C17   180.00   0.0  0
 O23  CONST_54  H19  C18  C17  S     180.00   0.0  0
 O23  CONST_55  C4   C    N    C1    180.00   0.0  0
 O23  CONST_56  C16  N4   C15  N3      0.00   0.0  0
 O23  CONST_57  C16  N4   C15  C12   180.00   0.0  0
 O23  CONST_58  H14  N4   C15  N3    180.00   0.0  0
 O23  CONST_59  C1   N    C    O       0.00   0.0  0
 O23  CONST_60  H1   N    C    C4      0.00   0.0  0
 O23  Var_01    C2   C3   C1   N     106.82  30.0  1
 O23  Var_02    H5   C2   C3   C1   -107.53  30.0  1
 O23  Var_03    C9   C4   C    O      26.45  30.0  2
 O23  Var_04    C3   C1   N    C      74.38  30.0  1
 O23  Var_05    C17  C16  N4   C15    80.61  30.0  3
 O23  Var_06    C18  C17  C16  N4    111.15  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
 O23  chir_01  C1  C3  C2  N  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
 O23  plan-1  C16  0.020
 O23  plan-1  C17  0.020
 O23  plan-1  S    0.020
 O23  plan-1  C20  0.020
 O23  plan-1  C19  0.020
 O23  plan-1  C18  0.020
 O23  plan-1  H17  0.020
 O23  plan-1  H18  0.020
 O23  plan-1  H19  0.020
 O23  plan-2  C    0.020
 O23  plan-2  C4   0.020
 O23  plan-2  C9   0.020
 O23  plan-2  C8   0.020
 O23  plan-2  C7   0.020
 O23  plan-2  C6   0.020
 O23  plan-2  C5   0.020
 O23  plan-2  C10  0.020
 O23  plan-2  H7   0.020
 O23  plan-2  H8   0.020
 O23  plan-2  H9   0.020
 O23  plan-2  H10  0.020
 O23  plan-3  C7   0.020
 O23  plan-3  C10  0.020
 O23  plan-3  N2   0.020
 O23  plan-3  C13  0.020
 O23  plan-3  C14  0.020
 O23  plan-3  N3   0.020
 O23  plan-3  C15  0.020
 O23  plan-3  C12  0.020
 O23  plan-3  N1   0.020
 O23  plan-3  C11  0.020
 O23  plan-3  N4   0.020
 O23  plan-3  H11  0.020
 O23  plan-3  H12  0.020
 O23  plan-3  H13  0.020
 O23  plan-4  C15  0.020
 O23  plan-4  N4   0.020
 O23  plan-4  C16  0.020
 O23  plan-4  H14  0.020
 O23  plan-5  O    0.020
 O23  plan-5  C    0.020
 O23  plan-5  N    0.020
 O23  plan-5  C1   0.020
 O23  plan-5  C4   0.020
 O23  plan-5  H1   0.020

