# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:54:54 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2S)-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}-3-(pyridin-3-yl)propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2cnc3n2ccnc3N[C@H](CO)Cc4cccnc4
#
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
 9K1  9K1  (2S)-2-{[3-(4-methylphenyl)imidazo[1,2-a]pyrazin-8-yl]amino}-3-(pyridin-3-yl)propan-1-ol  ligand  48  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9K1
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
 9K1  C1   C  CR56  0   0.402  -0.0056  -1.0136   0.5118
 9K1  C3   C  CR16  0  -0.095  -0.9724  -0.4290  -1.5868
 9K1  C12  C  CH1   0  -0.119   3.6142  -1.8002   0.1141
 9K1  C13  C  CH2   0  -0.156   4.3085  -3.0255   0.6811
 9K1  C15  C  CH2   0  -0.510   4.3654  -0.4964   0.4502
 9K1  C16  C  CR16  0  -0.299  -3.5873   1.2431  -0.5670
 9K1  C17  C  CR16  0  -0.287  -4.8562   1.7250  -0.8487
 9K1  C18  C  CR6   0   0.090  -5.9875   1.1844  -0.2426
 9K1  C19  C  CR16  0  -0.281  -5.8050   0.1348   0.6563
 9K1  C20  C  CR16  0  -0.292  -4.5422  -0.3629   0.9318
 9K1  C21  C  CH3   0  -0.722  -7.3552   1.7320  -0.5250
 9K1  C22  C  CR6   0   0.035   3.6483   0.6978  -0.0998
 9K1  C23  C  CR16  0  -0.086   3.8555   1.1192  -1.4099
 9K1  C25  C  CR16  0  -0.073   2.2499   2.7225  -1.2820
 9K1  C26  C  CR16  0  -0.312   1.9648   2.3991   0.0349
 9K1  C27  C  CR16  0  -0.200   2.6808   1.3742   0.6333
 9K1  N2   N  N     0  -0.525  -1.0656  -0.5516  -0.2156
 9K1  C4   C  CR16  0  -0.150   0.2137  -0.7508  -2.1500
 9K1  N5   N  N     0  -0.448   1.3078  -1.1827  -1.4718
 9K1  C6   C  CR6   0   0.454   1.2153  -1.3143  -0.1744
 9K1  N7   N  N     0  -0.457  -0.2876  -1.0996   1.7959
 9K1  C8   C  CR15  0  -0.238  -1.5673  -0.6864   1.8977
 9K1  C9   C  CR5   0   0.271  -2.0890  -0.3304   0.6693
 9K1  C10  C  CR6   0   0.044  -3.4101   0.1840   0.3245
 9K1  N11  N  NH1   0  -0.660   2.2457  -1.7479   0.5767
 9K1  O14  O  OH1   0  -0.673   4.3038  -2.9425   2.0880
 9K1  N24  N  N     0  -0.406   3.1859   2.1032  -1.9932
 9K1  H28  H  HCR6  0   0.305  -1.8383  -0.0999  -2.1366
 9K1  H32  H  HCH1  0   0.272   3.5920  -1.9178  -0.9702
 9K1  H33  H  HCH2  0   0.219   3.7827  -3.9197   0.3264
 9K1  H34  H  HCH2  0   0.206   5.3283  -3.0666   0.2781
 9K1  H37  H  HCH2  0   0.256   4.4702  -0.4014   1.5330
 9K1  H36  H  HCH2  0   0.253   5.3741  -0.5644   0.0352
 9K1  H38  H  HCR6  0   0.262  -2.7323   1.7185  -1.0312
 9K1  H39  H  HCR6  0   0.253  -4.9635   2.5453  -1.5481
 9K1  H40  H  HCR6  0   0.252  -6.6653  -0.3113   1.1410
 9K1  H41  H  HCR6  0   0.253  -4.4341  -1.1935   1.6180
 9K1  H42  H  HCH3  0   0.246  -8.1130   0.9497  -0.4996
 9K1  H44  H  HCH3  0   0.251  -7.6369   2.4783   0.2210
 9K1  H43  H  HCH3  0   0.245  -7.3994   2.2163  -1.4999
 9K1  H45  H  HCR6  0   0.250   4.6078   0.6236  -2.0180
 9K1  H46  H  HCR6  0   0.258   1.7056   3.5168  -1.7808
 9K1  H47  H  HCR6  0   0.265   1.1994   2.9368   0.5774
 9K1  H48  H  HCR6  0   0.265   2.4803   1.0961   1.6614
 9K1  H29  H  HCR6  0   0.264   0.3194  -0.6657  -3.2235
 9K1  H30  H  HCR5  0   0.266  -2.0779  -0.6336   2.8479
 9K1  H31  H  HNH1  0   0.392   2.1002  -1.7542   1.5752
 9K1  H35  H  HOH1  0   0.461   4.6347  -3.7716   2.4441

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
 9K1  O14  C13  single    1.409  0.020  1.409
 9K1  C13  C12  single    1.518  0.020  1.518
 9K1  C12  C15  single    1.542  0.020  1.542
 9K1  C12  N11  single    1.446  0.020  1.446
 9K1  N5   C4   aromatic  1.358  0.020  1.358
 9K1  N5   C6   aromatic  1.307  0.020  1.307
 9K1  C15  C22  single    1.498  0.020  1.498
 9K1  C23  C22  aromatic  1.392  0.020  1.392
 9K1  C23  N24  aromatic  1.325  0.020  1.325
 9K1  C4   C3   aromatic  1.352  0.020  1.352
 9K1  N11  C6   single    1.347  0.020  1.347
 9K1  C6   C1   aromatic  1.432  0.020  1.432
 9K1  C22  C27  aromatic  1.390  0.020  1.390
 9K1  N24  C25  aromatic  1.329  0.020  1.329
 9K1  C3   N2   aromatic  1.380  0.020  1.380
 9K1  C1   N2   aromatic  1.366  0.020  1.366
 9K1  C1   N7   aromatic  1.317  0.020  1.317
 9K1  C27  C26  aromatic  1.386  0.020  1.386
 9K1  C25  C26  aromatic  1.386  0.020  1.386
 9K1  N2   C9   aromatic  1.371  0.020  1.371
 9K1  N7   C8   aromatic  1.349  0.020  1.349
 9K1  C9   C8   aromatic  1.381  0.020  1.381
 9K1  C9   C10  single    1.459  0.020  1.459
 9K1  C20  C10  aromatic  1.396  0.020  1.396
 9K1  C20  C19  aromatic  1.385  0.020  1.385
 9K1  C10  C16  aromatic  1.396  0.020  1.396
 9K1  C19  C18  aromatic  1.394  0.020  1.394
 9K1  C16  C17  aromatic  1.386  0.020  1.386
 9K1  C18  C17  aromatic  1.393  0.020  1.393
 9K1  C18  C21  single    1.500  0.020  1.500
 9K1  C3   H28  single    0.930  0.020  1.080
 9K1  C12  H32  single    0.970  0.020  1.090
 9K1  C13  H33  single    0.970  0.020  1.090
 9K1  C13  H34  single    0.970  0.020  1.090
 9K1  C15  H37  single    0.970  0.020  1.090
 9K1  C15  H36  single    0.970  0.020  1.090
 9K1  C16  H38  single    0.930  0.020  1.080
 9K1  C17  H39  single    0.930  0.020  1.080
 9K1  C19  H40  single    0.930  0.020  1.080
 9K1  C20  H41  single    0.930  0.020  1.080
 9K1  C21  H42  single    0.970  0.020  1.090
 9K1  C21  H44  single    0.970  0.020  1.090
 9K1  C21  H43  single    0.970  0.020  1.090
 9K1  C23  H45  single    0.930  0.020  1.080
 9K1  C25  H46  single    0.930  0.020  1.080
 9K1  C26  H47  single    0.930  0.020  1.080
 9K1  C27  H48  single    0.930  0.020  1.080
 9K1  C4   H29  single    0.930  0.020  1.080
 9K1  C8   H30  single    0.930  0.020  1.080
 9K1  N11  H31  single    0.890  0.020  1.040
 9K1  O14  H35  single    0.850  0.020  0.980

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
 9K1  N7   C1   C6   129.47  3.000
 9K1  N7   C1   N2   112.02  3.000
 9K1  C6   C1   N2   118.50  3.000
 9K1  H28  C3   C4   124.43  3.000
 9K1  H28  C3   N2   118.69  3.000
 9K1  C4   C3   N2   116.88  3.000
 9K1  H32  C12  N11  107.62  3.000
 9K1  H32  C12  C15  108.53  3.000
 9K1  N11  C12  C15  111.16  3.000
 9K1  H32  C12  C13  107.07  3.000
 9K1  N11  C12  C13  110.03  3.000
 9K1  C15  C12  C13  112.23  3.000
 9K1  H34  C13  H33  107.24  3.000
 9K1  H34  C13  O14  111.84  3.000
 9K1  H33  C13  O14  111.68  3.000
 9K1  H34  C13  C12  108.55  3.000
 9K1  H33  C13  C12  108.55  3.000
 9K1  O14  C13  C12  108.89  3.000
 9K1  H36  C15  H37  107.06  3.000
 9K1  H36  C15  C22  110.61  3.000
 9K1  H37  C15  C22  109.92  3.000
 9K1  H36  C15  C12  108.32  3.000
 9K1  H37  C15  C12  109.67  3.000
 9K1  C22  C15  C12  111.16  3.000
 9K1  H38  C16  C10  120.44  3.000
 9K1  H38  C16  C17  118.89  3.000
 9K1  C10  C16  C17  120.65  3.000
 9K1  H39  C17  C18  119.63  3.000
 9K1  H39  C17  C16  119.02  3.000
 9K1  C18  C17  C16  121.35  3.000
 9K1  C21  C18  C19  121.04  3.000
 9K1  C21  C18  C17  121.13  3.000
 9K1  C19  C18  C17  117.81  3.000
 9K1  H40  C19  C20  119.14  3.000
 9K1  H40  C19  C18  119.64  3.000
 9K1  C20  C19  C18  121.21  3.000
 9K1  H41  C20  C10  119.68  3.000
 9K1  H41  C20  C19  119.52  3.000
 9K1  C10  C20  C19  120.80  3.000
 9K1  H43  C21  H44  107.28  3.000
 9K1  H43  C21  H42  108.17  3.000
 9K1  H44  C21  H42  107.18  3.000
 9K1  H43  C21  C18  111.58  3.000
 9K1  H44  C21  C18  110.86  3.000
 9K1  H42  C21  C18  111.57  3.000
 9K1  C27  C22  C23  116.93  3.000
 9K1  C27  C22  C15  121.85  3.000
 9K1  C23  C22  C15  121.06  3.000
 9K1  H45  C23  N24  116.23  3.000
 9K1  H45  C23  C22  119.45  3.000
 9K1  N24  C23  C22  124.32  3.000
 9K1  H46  C25  N24  116.66  3.000
 9K1  H46  C25  C26  120.32  3.000
 9K1  N24  C25  C26  123.01  3.000
 9K1  H47  C26  C27  121.11  3.000
 9K1  H47  C26  C25  120.42  3.000
 9K1  C27  C26  C25  118.47  3.000
 9K1  H48  C27  C26  120.25  3.000
 9K1  H48  C27  C22  120.29  3.000
 9K1  C26  C27  C22  119.46  3.000
 9K1  C9   N2   C3   132.65  3.000
 9K1  C9   N2   C1   106.86  3.000
 9K1  C3   N2   C1   120.45  3.000
 9K1  H29  C4   N5   116.22  3.000
 9K1  H29  C4   C3   118.70  3.000
 9K1  N5   C4   C3   125.08  3.000
 9K1  C6   N5   C4   118.08  3.000
 9K1  N11  C6   N5   122.12  3.000
 9K1  N11  C6   C1   116.90  3.000
 9K1  N5   C6   C1   120.97  3.000
 9K1  C8   N7   C1   104.87  3.000
 9K1  H30  C8   C9   126.25  3.000
 9K1  H30  C8   N7   122.01  3.000
 9K1  C9   C8   N7   111.73  3.000
 9K1  C10  C9   C8   130.02  3.000
 9K1  C10  C9   N2   125.47  3.000
 9K1  C8   C9   N2   104.51  3.000
 9K1  C9   C10  C20  119.55  3.000
 9K1  C20  C10  C16  118.17  3.000
 9K1  C9   C10  C16  122.24  3.000
 9K1  H31  N11  C6   116.32  3.000
 9K1  H31  N11  C12  116.94  3.000
 9K1  C6   N11  C12  123.88  3.000
 9K1  H35  O14  C13  108.54  3.000
 9K1  C25  N24  C23  117.80  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
 9K1  CONST_01  C4   N5   C6   C1     0.00   0.0  0
 9K1  CONST_02  C4   C3   N2   C1     0.00   0.0  0
 9K1  CONST_03  C8   C9   N2   C1     0.00   0.0  0
 9K1  CONST_04  C10  C9   N2   C1   180.00   0.0  0
 9K1  CONST_05  C9   C8   N7   C1     0.00   0.0  0
 9K1  CONST_06  C6   N5   C4   C3     0.00   0.0  0
 9K1  CONST_07  C6   C1   N2   C3     0.00   0.0  0
 9K1  CONST_08  N7   C1   N2   C3   180.00   0.0  0
 9K1  CONST_09  C8   C9   N2   C3   180.00   0.0  0
 9K1  CONST_10  C10  C9   N2   C3     0.00   0.0  0
 9K1  CONST_13  C19  C20  C10  C16    0.00   0.0  0
 9K1  CONST_14  C19  C18  C17  C16    0.00   0.0  0
 9K1  CONST_15  C9   C10  C16  C17  180.00   0.0  0
 9K1  CONST_16  C20  C10  C16  C17    0.00   0.0  0
 9K1  CONST_17  C20  C19  C18  C17    0.00   0.0  0
 9K1  CONST_18  C10  C20  C19  C18    0.00   0.0  0
 9K1  CONST_19  C10  C16  C17  C18    0.00   0.0  0
 9K1  CONST_20  C9   C10  C20  C19  180.00   0.0  0
 9K1  CONST_23  C25  N24  C23  C22    0.00   0.0  0
 9K1  CONST_24  C25  C26  C27  C22    0.00   0.0  0
 9K1  CONST_25  C26  C27  C22  C23    0.00   0.0  0
 9K1  CONST_26  C26  C25  N24  C23    0.00   0.0  0
 9K1  CONST_27  N24  C23  C22  C27    0.00   0.0  0
 9K1  CONST_28  N24  C25  C26  C27    0.00   0.0  0
 9K1  CONST_29  N5   C4   C3   N2     0.00   0.0  0
 9K1  CONST_30  N5   C6   C1   N2     0.00   0.0  0
 9K1  CONST_31  C8   N7   C1   N2     0.00   0.0  0
 9K1  CONST_32  N7   C8   C9   N2     0.00   0.0  0
 9K1  CONST_33  C9   N2   C3   C4   180.00   0.0  0
 9K1  CONST_34  N7   C1   C6   N5   180.00   0.0  0
 9K1  CONST_35  C9   N2   C1   C6   180.00   0.0  0
 9K1  CONST_36  C8   N7   C1   C6   180.00   0.0  0
 9K1  CONST_37  C9   N2   C1   N7     0.00   0.0  0
 9K1  CONST_38  C10  C9   C8   N7   180.00   0.0  0
 9K1  CONST_39  N24  C23  C22  C15  180.00   0.0  0
 9K1  CONST_40  C26  C27  C22  C15  180.00   0.0  0
 9K1  CONST_41  C21  C18  C17  C16  180.00   0.0  0
 9K1  CONST_42  C21  C18  C19  C20  180.00   0.0  0
 9K1  CONST_43  N11  C6   C1   N2   180.00   0.0  0
 9K1  CONST_44  N11  C6   N5   C4   180.00   0.0  0
 9K1  CONST_45  N11  C6   C1   N7     0.00   0.0  0
 9K1  CONST_46  H28  C3   N2   C1   180.00   0.0  0
 9K1  CONST_47  H30  C8   N7   C1   180.00   0.0  0
 9K1  CONST_48  H41  C20  C10  C16  180.00   0.0  0
 9K1  CONST_49  H40  C19  C18  C17  180.00   0.0  0
 9K1  CONST_50  H38  C16  C17  C18  180.00   0.0  0
 9K1  CONST_51  H39  C17  C18  C19  180.00   0.0  0
 9K1  CONST_52  H47  C26  C27  C22  180.00   0.0  0
 9K1  CONST_53  H48  C27  C22  C23  180.00   0.0  0
 9K1  CONST_54  H46  C25  N24  C23  180.00   0.0  0
 9K1  CONST_55  H45  C23  N24  C25  180.00   0.0  0
 9K1  CONST_56  H29  C4   C3   N2   180.00   0.0  0
 9K1  CONST_57  C12  N11  C6   C1   180.00   0.0  0
 9K1  CONST_59  H31  N11  C6   C1     0.00   0.0  0
 9K1  Var_01    C23  C22  C15  C12  -85.49  30.0  2
 9K1  Var_02    H42  C21  C18  C17  146.50  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
 9K1  chir_01  C12  C13  C15  N11  positiv

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
 9K1  plan-1  C16  0.020
 9K1  plan-1  C17  0.020
 9K1  plan-1  C18  0.020
 9K1  plan-1  C19  0.020
 9K1  plan-1  C20  0.020
 9K1  plan-1  C21  0.020
 9K1  plan-1  C9   0.020
 9K1  plan-1  C10  0.020
 9K1  plan-1  H38  0.020
 9K1  plan-1  H39  0.020
 9K1  plan-1  H40  0.020
 9K1  plan-1  H41  0.020
 9K1  plan-2  C15  0.020
 9K1  plan-2  C22  0.020
 9K1  plan-2  C23  0.020
 9K1  plan-2  C25  0.020
 9K1  plan-2  C26  0.020
 9K1  plan-2  C27  0.020
 9K1  plan-2  N24  0.020
 9K1  plan-2  H45  0.020
 9K1  plan-2  H46  0.020
 9K1  plan-2  H47  0.020
 9K1  plan-2  H48  0.020
 9K1  plan-3  C1   0.020
 9K1  plan-3  C3   0.020
 9K1  plan-3  N2   0.020
 9K1  plan-3  C4   0.020
 9K1  plan-3  N5   0.020
 9K1  plan-3  C6   0.020
 9K1  plan-3  N7   0.020
 9K1  plan-3  C8   0.020
 9K1  plan-3  C9   0.020
 9K1  plan-3  C10  0.020
 9K1  plan-3  N11  0.020
 9K1  plan-3  H28  0.020
 9K1  plan-3  H29  0.020
 9K1  plan-3  H30  0.020
 9K1  plan-4  C12  0.020
 9K1  plan-4  C6   0.020
 9K1  plan-4  N11  0.020
 9K1  plan-4  H31  0.020

