# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 07:22:53 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 9-phenyl-4H-imidazo[1,2-a]indeno[1,2-e]pyrazin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N=C2C(=Cc3c(cccc23)c4ccccc4)n5ccnc15
#
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
 2K9  2K9  9-phenyl-4H-imidazo[1,2-a]indeno[1,2-e]pyrazin-4-one  ligand  34  23  .  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_2K9
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
 2K9  O1   O  O     0  -0.374  -4.8756  -1.3324  -0.0836
 2K9  C9   C  CR6   0   0.426  -3.7818  -0.8227  -0.0483
 2K9  C5   C  CR56  0   0.317  -3.6163   0.6364   0.0268
 2K9  N3   N  N     0  -0.422  -4.5557   1.5455   0.0690
 2K9  C10  C  CR15  0  -0.201  -3.9077   2.7367   0.1323
 2K9  C6   C  CR15  0  -0.092  -2.5487   2.5546   0.1279
 2K9  N1   N  N     0  -0.572  -2.3765   1.2069   0.0607
 2K9  C1   C  CR56  0   0.404  -1.2553   0.4084   0.0209
 2K9  N2   N  N     0  -0.419  -2.6303  -1.6271  -0.0760
 2K9  C2   C  CR56  0   0.146  -1.4981  -1.0378  -0.0465
 2K9  C4   C  CR56  0   0.075  -0.1693  -1.6599  -0.0610
 2K9  C8   C  CR16  0  -0.299   0.1930  -2.9819  -0.0829
 2K9  C12  C  CR16  0  -0.247   1.5625  -3.2786  -0.0634
 2K9  C14  C  CR16  0  -0.298   2.4983  -2.2650  -0.0327
 2K9  C11  C  CR6   0   0.075   2.1320  -0.9021  -0.0222
 2K9  C7   C  CR56  0   0.087   0.7781  -0.6224  -0.0235
 2K9  C3   C  CR15  0  -0.338   0.0613   0.6634   0.0445
 2K9  C13  C  CR6   0   0.055   3.1654   0.1495  -0.0183
 2K9  C16  C  CR16  0  -0.314   3.0860   1.2322  -0.8952
 2K9  C18  C  CR16  0  -0.242   4.0627   2.2175  -0.8897
 2K9  C19  C  CR16  0  -0.259   5.1344   2.1325  -0.0110
 2K9  C17  C  CR16  0  -0.241   5.2271   1.0536   0.8590
 2K9  C15  C  CR16  0  -0.297   4.2514   0.0680   0.8541
 2K9  H1   H  HCR5  0   0.274  -4.4391   3.6739   0.1768
 2K9  H2   H  HCR5  0   0.319  -1.7253   3.2471   0.1661
 2K9  H3   H  HCR6  0   0.274  -0.5493  -3.7687  -0.1100
 2K9  H4   H  HCR6  0   0.275   1.8897  -4.3091  -0.0808
 2K9  H5   H  HCR6  0   0.271   3.5507  -2.5202  -0.0376
 2K9  H6   H  HCR5  0   0.304   0.5272   1.6352   0.1172
 2K9  H7   H  HCR6  0   0.267   2.2720   1.2927  -1.6071
 2K9  H9   H  HCR6  0   0.262   3.9895   3.0478  -1.5797
 2K9  H10  H  HCR6  0   0.262   5.8962   2.9008  -0.0069
 2K9  H11  H  HCR6  0   0.262   6.0594   0.9801   1.5466
 2K9  H13  H  HCR6  0   0.260   4.3255  -0.7620   1.5460

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
 2K9  O1   C9   double    1.207  0.020  1.207
 2K9  N3   C10  aromatic  1.358  0.020  1.358
 2K9  N3   C5   aromatic  1.308  0.020  1.308
 2K9  C9   C5   single    1.470  0.020  1.470
 2K9  C9   N2   single    1.405  0.020  1.405
 2K9  C10  C6   aromatic  1.371  0.020  1.371
 2K9  C5   N1   aromatic  1.365  0.020  1.365
 2K9  N2   C2   double    1.277  0.020  1.277
 2K9  N1   C6   aromatic  1.360  0.020  1.360
 2K9  N1   C1   single    1.377  0.020  1.377
 2K9  C2   C1   single    1.468  0.020  1.468
 2K9  C2   C4   single    1.467  0.020  1.467
 2K9  C1   C3   double    1.341  0.020  1.341
 2K9  C4   C8   aromatic  1.371  0.020  1.371
 2K9  C4   C7   aromatic  1.406  0.020  1.406
 2K9  C8   C12  aromatic  1.401  0.020  1.401
 2K9  C3   C7   single    1.474  0.020  1.474
 2K9  C7   C11  aromatic  1.383  0.020  1.383
 2K9  C12  C14  aromatic  1.380  0.020  1.380
 2K9  C11  C14  aromatic  1.411  0.020  1.411
 2K9  C11  C13  single    1.474  0.020  1.474
 2K9  C13  C15  aromatic  1.395  0.020  1.395
 2K9  C13  C16  aromatic  1.395  0.020  1.395
 2K9  C15  C17  aromatic  1.387  0.020  1.387
 2K9  C16  C18  aromatic  1.387  0.020  1.387
 2K9  C17  C19  aromatic  1.389  0.020  1.389
 2K9  C18  C19  aromatic  1.388  0.020  1.388
 2K9  C10  H1   single    0.930  0.020  1.080
 2K9  C6   H2   single    0.930  0.020  1.080
 2K9  C8   H3   single    0.930  0.020  1.080
 2K9  C12  H4   single    0.930  0.020  1.080
 2K9  C14  H5   single    0.930  0.020  1.080
 2K9  C3   H6   single    0.930  0.020  1.080
 2K9  C16  H7   single    0.930  0.020  1.080
 2K9  C18  H9   single    0.930  0.020  1.080
 2K9  C19  H10  single    0.930  0.020  1.080
 2K9  C17  H11  single    0.930  0.020  1.080
 2K9  C15  H13  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
 2K9  N2   C9   C5   118.48  3.000
 2K9  N2   C9   O1   120.02  3.000
 2K9  C5   C9   O1   121.49  3.000
 2K9  N1   C5   N3   111.17  3.000
 2K9  N1   C5   C9   121.21  3.000
 2K9  N3   C5   C9   127.63  3.000
 2K9  C10  N3   C5   105.58  3.000
 2K9  H1   C10  C6   127.16  3.000
 2K9  H1   C10  N3   121.96  3.000
 2K9  C6   C10  N3   110.88  3.000
 2K9  H2   C6   N1   122.83  3.000
 2K9  H2   C6   C10  132.26  3.000
 2K9  N1   C6   C10  104.90  3.000
 2K9  C1   N1   C6   132.76  3.000
 2K9  C1   N1   C5   119.76  3.000
 2K9  C6   N1   C5   107.47  3.000
 2K9  C3   C1   C2   110.51  3.000
 2K9  C3   C1   N1   133.51  3.000
 2K9  C2   C1   N1   115.97  3.000
 2K9  C2   N2   C9   117.53  3.000
 2K9  C4   C2   N2   127.38  3.000
 2K9  C4   C2   C1   105.57  3.000
 2K9  N2   C2   C1   127.04  3.000
 2K9  C7   C4   C8   122.29  3.000
 2K9  C7   C4   C2   107.29  3.000
 2K9  C8   C4   C2   130.42  3.000
 2K9  H3   C8   C12  121.12  3.000
 2K9  H3   C8   C4   121.36  3.000
 2K9  C12  C8   C4   117.53  3.000
 2K9  H4   C12  C14  119.68  3.000
 2K9  H4   C12  C8   119.81  3.000
 2K9  C14  C12  C8   120.50  3.000
 2K9  H5   C14  C11  118.67  3.000
 2K9  H5   C14  C12  119.07  3.000
 2K9  C11  C14  C12  122.24  3.000
 2K9  C13  C11  C7   122.83  3.000
 2K9  C13  C11  C14  120.46  3.000
 2K9  C7   C11  C14  116.71  3.000
 2K9  C3   C7   C11  130.76  3.000
 2K9  C11  C7   C4   120.72  3.000
 2K9  C3   C7   C4   108.51  3.000
 2K9  H6   C3   C7   125.33  3.000
 2K9  H6   C3   C1   126.56  3.000
 2K9  C7   C3   C1   108.10  3.000
 2K9  C15  C13  C16  118.85  3.000
 2K9  C16  C13  C11  120.79  3.000
 2K9  C15  C13  C11  120.36  3.000
 2K9  H7   C16  C18  119.47  3.000
 2K9  H7   C16  C13  119.94  3.000
 2K9  C18  C16  C13  120.56  3.000
 2K9  H9   C18  C19  120.18  3.000
 2K9  H9   C18  C16  119.66  3.000
 2K9  C19  C18  C16  120.16  3.000
 2K9  H10  C19  C17  120.15  3.000
 2K9  H10  C19  C18  120.16  3.000
 2K9  C17  C19  C18  119.70  3.000
 2K9  H11  C17  C15  119.67  3.000
 2K9  H11  C17  C19  120.13  3.000
 2K9  C15  C17  C19  120.19  3.000
 2K9  H13  C15  C17  119.62  3.000
 2K9  H13  C15  C13  119.83  3.000
 2K9  C17  C15  C13  120.54  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
 2K9  CONST_01  C6   C10  N3   C5     0.00  0.0  0
 2K9  CONST_02  C10  C6   N1   C5     0.00  0.0  0
 2K9  CONST_03  N1   C6   C10  N3     0.00  0.0  0
 2K9  CONST_04  C6   N1   C5   N3     0.00  0.0  0
 2K9  CONST_05  N1   C5   N3   C10    0.00  0.0  0
 2K9  CONST_06  C14  C12  C8   C4     0.00  0.0  0
 2K9  CONST_07  C14  C11  C7   C4     0.00  0.0  0
 2K9  CONST_08  C13  C11  C7   C4   180.00  0.0  0
 2K9  CONST_09  C11  C7   C4   C8     0.00  0.0  0
 2K9  CONST_10  C11  C14  C12  C8     0.00  0.0  0
 2K9  CONST_11  C7   C4   C8   C12    0.00  0.0  0
 2K9  CONST_12  C7   C11  C14  C12    0.00  0.0  0
 2K9  CONST_13  C13  C11  C14  C12  180.00  0.0  0
 2K9  CONST_16  C17  C15  C13  C11  180.00  0.0  0
 2K9  CONST_17  C18  C16  C13  C11  180.00  0.0  0
 2K9  CONST_20  C19  C17  C15  C13    0.00  0.0  0
 2K9  CONST_21  C19  C18  C16  C13    0.00  0.0  0
 2K9  CONST_22  C17  C15  C13  C16    0.00  0.0  0
 2K9  CONST_23  C17  C19  C18  C16    0.00  0.0  0
 2K9  CONST_24  C15  C13  C16  C18    0.00  0.0  0
 2K9  CONST_25  C15  C17  C19  C18    0.00  0.0  0
 2K9  CONST_26  C13  C11  C7   C3     0.00  0.0  0
 2K9  CONST_27  H1   C10  N3   C5   180.00  0.0  0
 2K9  CONST_28  H2   C6   N1   C5   180.00  0.0  0
 2K9  CONST_29  H3   C8   C4   C2     0.00  0.0  0
 2K9  CONST_30  H4   C12  C8   C4   180.00  0.0  0
 2K9  CONST_31  H5   C14  C12  C8   180.00  0.0  0
 2K9  CONST_32  H13  C15  C13  C11    0.00  0.0  0
 2K9  CONST_33  H7   C16  C13  C11    0.00  0.0  0
 2K9  CONST_34  H11  C17  C15  C13  180.00  0.0  0
 2K9  CONST_35  H9   C18  C16  C13  180.00  0.0  0
 2K9  CONST_36  H10  C19  C18  C16  180.00  0.0  0

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
 2K9  plan-1  C11  0.020
 2K9  plan-1  C13  0.020
 2K9  plan-1  C16  0.020
 2K9  plan-1  C18  0.020
 2K9  plan-1  C19  0.020
 2K9  plan-1  C17  0.020
 2K9  plan-1  C15  0.020
 2K9  plan-1  H7   0.020
 2K9  plan-1  H9   0.020
 2K9  plan-1  H10  0.020
 2K9  plan-1  H11  0.020
 2K9  plan-1  H13  0.020
 2K9  plan-2  O1   0.020
 2K9  plan-2  C9   0.020
 2K9  plan-2  C5   0.020
 2K9  plan-2  N3   0.020
 2K9  plan-2  C10  0.020
 2K9  plan-2  C6   0.020
 2K9  plan-2  N1   0.020
 2K9  plan-2  C1   0.020
 2K9  plan-2  N2   0.020
 2K9  plan-2  C2   0.020
 2K9  plan-2  C4   0.020
 2K9  plan-2  C8   0.020
 2K9  plan-2  C12  0.020
 2K9  plan-2  C14  0.020
 2K9  plan-2  C11  0.020
 2K9  plan-2  C7   0.020
 2K9  plan-2  C3   0.020
 2K9  plan-2  C13  0.020
 2K9  plan-2  H1   0.020
 2K9  plan-2  H2   0.020
 2K9  plan-2  H3   0.020
 2K9  plan-2  H4   0.020
 2K9  plan-2  H5   0.020
 2K9  plan-2  H6   0.020

