# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 00:27:51 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 1-oxidanyl-3-(trifluoromethyl)pyrido[1,2-a]benzimidazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(c(C#N)c2nc3ccccc3n12)C(F)(F)F
#
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
 JRF  JRF  "1-Hydroxy-3-(trifluoromethyl)pyrido[1,2-a]benzimidazole-4-carbonitrile"
  ligand  26  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JRF
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
 JRF  C08   C  CR56  0   0.589  185.6628  172.3303  182.5780
 JRF  C09   C  CR6   0  -0.147  184.2838  172.6579  182.5974
 JRF  C10   C  CR56  0   0.343  187.7030  172.2181  181.6892
 JRF  C11   C  CR6   0  -0.020  183.7021  173.1612  181.4549
 JRF  C12   C  CR6   0   0.662  185.7823  173.0035  180.2652
 JRF  C13   C  CR56  0   0.154  187.6608  171.7745  183.0228
 JRF  C14   C  CT    0   1.083  182.2432  173.5404  181.4666
 JRF  C15   C  CR16  0  -0.539  184.4467  173.3226  180.2841
 JRF  C16   C  CR16  0  -0.297  188.8944  172.2888  180.9717
 JRF  C17   C  CSP   0  -0.001  183.5903  172.4588  183.8182
 JRF  C18   C  CR16  0  -0.339  188.8301  171.3458  183.6531
 JRF  C19   C  CR16  0  -0.268  190.0394  171.8607  181.6158
 JRF  C20   C  CR16  0  -0.252  190.0072  171.3883  182.9357
 JRF  F01   F  F     0  -0.303  181.4914  172.5440  181.9377
 JRF  F02   F  F     0  -0.304  182.0367  174.6029  182.2484
 JRF  F03   F  F     0  -0.288  181.7945  173.8434  180.2525
 JRF  N05   N  N     0  -0.691  186.3841  172.5580  181.3989
 JRF  N06   N  N     0  -0.469  186.3981  171.8587  183.5403
 JRF  N07   N  NS    0  -0.227  183.0456  172.2919  184.8195
 JRF  O04   O  OH1   0  -0.584  186.4769  173.1654  179.1590
 JRF  H151  H  HCR6  0   0.315  184.0001  173.6706  179.3655
 JRF  H161  H  HCR6  0   0.274  188.9719  172.6779  179.9672
 JRF  H181  H  HCR6  0   0.266  188.8039  170.9985  184.6773
 JRF  H191  H  HCR6  0   0.269  190.9822  171.9024  181.0879
 JRF  H201  H  HCR6  0   0.266  190.9287  171.0645  183.4010
 JRF  H041  H  HOH1  0   0.508  187.1728  172.5078  179.0231

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
 JRF  O04  C12   single    1.316  0.020  1.316
 JRF  F03  C14   single    1.329  0.020  1.329
 JRF  C15  C12   aromatic  1.373  0.020  1.373
 JRF  C15  C11   aromatic  1.397  0.020  1.397
 JRF  C12  N05   aromatic  1.359  0.020  1.359
 JRF  C16  C19   aromatic  1.382  0.020  1.382
 JRF  C16  C10   aromatic  1.393  0.020  1.393
 JRF  C14  C11   single    1.507  0.020  1.507
 JRF  C14  F01   single    1.334  0.020  1.334
 JRF  C14  F02   single    1.335  0.020  1.335
 JRF  N05  C10   aromatic  1.393  0.020  1.393
 JRF  N05  C08   aromatic  1.401  0.020  1.401
 JRF  C11  C09   aromatic  1.377  0.020  1.377
 JRF  C19  C20   aromatic  1.402  0.020  1.402
 JRF  C10  C13   aromatic  1.406  0.020  1.406
 JRF  C08  C09   aromatic  1.418  0.020  1.418
 JRF  C08  N06   aromatic  1.300  0.020  1.300
 JRF  C09  C17   single    1.418  0.020  1.418
 JRF  C20  C18   aromatic  1.379  0.020  1.379
 JRF  C13  N06   aromatic  1.367  0.020  1.367
 JRF  C13  C18   aromatic  1.396  0.020  1.396
 JRF  C17  N07   triple    1.152  0.020  1.152
 JRF  C15  H151  single    0.930  0.020  1.080
 JRF  C16  H161  single    0.930  0.020  1.080
 JRF  C18  H181  single    0.930  0.020  1.080
 JRF  C19  H191  single    0.930  0.020  1.080
 JRF  C20  H201  single    0.930  0.020  1.080
 JRF  O04  H041  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
 JRF  N06   C08  N05  113.01  3.000
 JRF  N06   C08  C09  128.61  3.000
 JRF  N05   C08  C09  118.35  3.000
 JRF  C17   C09  C11  123.98  3.000
 JRF  C17   C09  C08  117.07  3.000
 JRF  C11   C09  C08  118.94  3.000
 JRF  N05   C10  C16  133.67  3.000
 JRF  N05   C10  C13  104.26  3.000
 JRF  C16   C10  C13  122.03  3.000
 JRF  C15   C11  C14  119.56  3.000
 JRF  C14   C11  C09  119.62  3.000
 JRF  C15   C11  C09  120.82  3.000
 JRF  O04   C12  N05  120.52  3.000
 JRF  N05   C12  C15  119.70  3.000
 JRF  O04   C12  C15  119.76  3.000
 JRF  N06   C13  C18  128.44  3.000
 JRF  C18   C13  C10  120.00  3.000
 JRF  N06   C13  C10  111.55  3.000
 JRF  F03   C14  F02  107.54  3.000
 JRF  F02   C14  F01  107.48  3.000
 JRF  F03   C14  F01  107.61  3.000
 JRF  F02   C14  C11  110.75  3.000
 JRF  F01   C14  C11  111.11  3.000
 JRF  F03   C14  C11  112.14  3.000
 JRF  H151  C15  C12  117.76  3.000
 JRF  H151  C15  C11  122.01  3.000
 JRF  C12   C15  C11  120.21  3.000
 JRF  H161  C16  C19  119.05  3.000
 JRF  H161  C16  C10  123.98  3.000
 JRF  C19   C16  C10  116.94  3.000
 JRF  N07   C17  C09  180.00  3.000
 JRF  H181  C18  C20  121.54  3.000
 JRF  H181  C18  C13  120.38  3.000
 JRF  C20   C18  C13  118.08  3.000
 JRF  H191  C19  C20  119.51  3.000
 JRF  H191  C19  C16  118.88  3.000
 JRF  C20   C19  C16  121.61  3.000
 JRF  H201  C20  C19  119.08  3.000
 JRF  H201  C20  C18  119.61  3.000
 JRF  C19   C20  C18  121.31  3.000
 JRF  C12   N05  C10  132.34  3.000
 JRF  C10   N05  C08  105.81  3.000
 JRF  C12   N05  C08  121.84  3.000
 JRF  C13   N06  C08  105.34  3.000
 JRF  H041  O04  C12  114.48  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
 JRF  CONST_01  C15   C12  N05  C08     0.00   0.0  0
 JRF  CONST_02  C16   C10  N05  C08   180.00   0.0  0
 JRF  CONST_03  C13   C10  N05  C08     0.00   0.0  0
 JRF  CONST_04  C15   C11  C09  C08     0.00   0.0  0
 JRF  CONST_05  C10   C13  N06  C08     0.00   0.0  0
 JRF  CONST_06  C18   C13  N06  C08   180.00   0.0  0
 JRF  CONST_07  C12   C15  C11  C09     0.00   0.0  0
 JRF  CONST_08  C12   N05  C08  C09     0.00   0.0  0
 JRF  CONST_09  C10   N05  C08  C09   180.00   0.0  0
 JRF  CONST_10  C13   N06  C08  C09   180.00   0.0  0
 JRF  CONST_11  C20   C19  C16  C10     0.00   0.0  0
 JRF  CONST_12  C15   C12  N05  C10   180.00   0.0  0
 JRF  CONST_13  N06   C08  N05  C10     0.00   0.0  0
 JRF  CONST_14  C20   C18  C13  C10     0.00   0.0  0
 JRF  CONST_15  N05   C12  C15  C11     0.00   0.0  0
 JRF  CONST_16  N05   C08  C09  C11     0.00   0.0  0
 JRF  CONST_17  N06   C08  C09  C11   180.00   0.0  0
 JRF  CONST_18  C16   C10  N05  C12     0.00   0.0  0
 JRF  CONST_19  C13   C10  N05  C12   180.00   0.0  0
 JRF  CONST_20  N06   C08  N05  C12   180.00   0.0  0
 JRF  CONST_21  C19   C16  C10  C13     0.00   0.0  0
 JRF  CONST_22  N05   C08  N06  C13     0.00   0.0  0
 JRF  CONST_23  C19   C20  C18  C13     0.00   0.0  0
 JRF  CONST_24  C18   C20  C19  C16     0.00   0.0  0
 JRF  CONST_25  N06   C13  C10  C16   180.00   0.0  0
 JRF  CONST_26  C18   C13  C10  C16     0.00   0.0  0
 JRF  CONST_27  N05   C10  C13  C18   180.00   0.0  0
 JRF  CONST_28  N05   C10  C16  C19   180.00   0.0  0
 JRF  CONST_29  N06   C13  C18  C20   180.00   0.0  0
 JRF  CONST_30  N06   C13  C10  N05     0.00   0.0  0
 JRF  CONST_31  O04   C12  N05  C08   180.00   0.0  0
 JRF  CONST_32  C14   C11  C09  C08   180.00   0.0  0
 JRF  CONST_33  O04   C12  N05  C10     0.00   0.0  0
 JRF  CONST_34  O04   C12  C15  C11   180.00   0.0  0
 JRF  CONST_35  C14   C11  C15  C12   180.00   0.0  0
 JRF  CONST_36  C17   C09  C11  C15   180.00   0.0  0
 JRF  CONST_37  N05   C08  C09  C17   180.00   0.0  0
 JRF  CONST_38  N06   C08  C09  C17     0.00   0.0  0
 JRF  CONST_39  H151  C15  C11  C09   180.00   0.0  0
 JRF  CONST_40  H191  C19  C16  C10   180.00   0.0  0
 JRF  CONST_41  H181  C18  C13  C10   180.00   0.0  0
 JRF  CONST_42  H161  C16  C10  C13   180.00   0.0  0
 JRF  CONST_43  H201  C20  C18  C13   180.00   0.0  0
 JRF  CONST_44  H201  C20  C19  C16   180.00   0.0  0
 JRF  CONST_45  H191  C19  C20  C18   180.00   0.0  0
 JRF  CONST_46  H181  C18  C20  C19   180.00   0.0  0
 JRF  CONST_47  H161  C16  C19  C20   180.00   0.0  0
 JRF  CONST_48  H151  C15  C12  N05   180.00   0.0  0
 JRF  CONST_49  H161  C16  C10  N05     0.00   0.0  0
 JRF  CONST_50  H181  C18  C13  N06     0.00   0.0  0
 JRF  Var_01    N07   C17  C09  C08     5.67  30.0  2
 JRF  Var_02    F03   C14  C11  C09  -171.88  30.0  2
 JRF  Var_03    F01   C14  C11  C09   -51.40  30.0  2
 JRF  Var_04    F02   C14  C11  C09    67.98  30.0  2
 JRF  Var_05    N07   C17  C09  C11  -173.41  30.0  2
 JRF  Var_06    C17   C09  C11  C14     0.28  30.0  1
 JRF  Var_07    F03   C14  C11  C15     8.00  30.0  2
 JRF  Var_08    F01   C14  C11  C15   128.48  30.0  2
 JRF  Var_09    F02   C14  C11  C15  -112.14  30.0  2
 JRF  Var_10    H151  C15  C11  C14    -2.85  30.0  1
 JRF  Var_11    H151  C15  C12  O04     1.97  30.0  1

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
 JRF  plan-1  C08   0.020
 JRF  plan-1  C09   0.020
 JRF  plan-1  C10   0.020
 JRF  plan-1  C12   0.020
 JRF  plan-1  C13   0.020
 JRF  plan-1  C16   0.020
 JRF  plan-1  C18   0.020
 JRF  plan-1  C19   0.020
 JRF  plan-1  C20   0.020
 JRF  plan-1  N05   0.020
 JRF  plan-1  N06   0.020
 JRF  plan-1  H161  0.020
 JRF  plan-1  H181  0.020
 JRF  plan-1  H191  0.020
 JRF  plan-1  H201  0.020

