# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:00:57 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-azanyl-3-[1-(pyridin-3-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c2ccc3ccn(Cc4cccnc4)c3c2)c1C#N
#
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
 JEB  JEB  5-azanyl-3-[1-(pyridin-3-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  38  24  .  2021-08-12  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JEB
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
 JEB  C10  C  CR16  0  -0.333   1.6029   1.6861   0.9178
 JEB  C13  C  CR56  0   0.409  -0.8279   1.2771  -0.3107
 JEB  C17  C  CR6   0   0.054  -3.4629  -0.7019  -0.6496
 JEB  C20  C  CR16  0  -0.067  -4.8190  -2.3472   1.0454
 JEB  C21  C  CR16  0  -0.317  -3.4811  -2.6121   0.7919
 JEB  C22  C  CR16  0  -0.179  -2.7941  -1.7749  -0.0716
 JEB  C24  C  CR15  0  -0.419  -1.8562   3.1635   0.4550
 JEB  C02  C  CR5   0   0.622   4.4196  -1.5120  -0.2934
 JEB  N03  N  NR15  0  -0.491   3.3713  -2.3372  -0.3676
 JEB  N04  N  N     0  -0.298   2.1833  -1.7170  -0.2210
 JEB  C05  C  CR5   0   0.321   2.4612  -0.4492  -0.0513
 JEB  C06  C  CR5   0  -0.288   3.8722  -0.2411  -0.0839
 JEB  C07  C  CSP   0  -0.036   4.6054   0.9507  -0.0153
 JEB  N08  N  NS    0  -0.267   5.2287   1.9234   0.0354
 JEB  C09  C  CR6   0   0.045   1.3982   0.5436   0.1175
 JEB  C11  C  CR16  0  -0.328   0.6073   2.6222   1.1012
 JEB  C12  C  CR56  0   0.052  -0.6337   2.4284   0.4867
 JEB  C14  C  CR16  0  -0.359   0.1746   0.3341  -0.5037
 JEB  N15  N  NR5   0  -0.517  -2.1014   1.3269  -0.8106
 JEB  C16  C  CH2   0  -0.453  -2.7689   0.2793  -1.5555
 JEB  C18  C  CR16  0  -0.098  -4.8066  -0.5389  -0.3311
 JEB  N19  N  N     0  -0.400  -5.4756  -1.3338   0.4936
 JEB  C23  C  CR15  0  -0.021  -2.7141   2.4548  -0.3335
 JEB  H1   H  HCR6  0   0.248   2.5511   1.8249   1.4205
 JEB  H2   H  HCR6  0   0.267  -5.3836  -2.9827   1.7178
 JEB  H3   H  HCR6  0   0.275  -2.9934  -3.4569   1.2580
 JEB  H4   H  HCR6  0   0.269  -1.7511  -1.9615  -0.2955
 JEB  H5   H  HCR5  0   0.252  -2.0675   4.1028   0.9400
 JEB  H6   H  HNH2  0   0.409   5.9220  -2.8681  -0.3489
 JEB  H7   H  HNH2  0   0.408   6.4125  -1.2741  -0.1162
 JEB  H8   H  HNR5  0   0.429   3.3969  -3.3368  -0.4948
 JEB  H9   H  HCR6  0   0.252   0.7851   3.4906   1.7231
 JEB  H10  H  HCR6  0   0.261   0.0306  -0.5336  -1.1341
 JEB  H11  H  HCH2  0   0.293  -2.0352  -0.2253  -2.1848
 JEB  H12  H  HCH2  0   0.297  -3.4861   0.7504  -2.2283
 JEB  H13  H  HCR6  0   0.263  -5.3690   0.2779  -0.7745
 JEB  H14  H  HCR5  0   0.287  -3.7352   2.6721  -0.6061
 JEB  N01  N  NH2   0  -0.843   5.7014  -1.8927  -0.4707

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
 JEB  N01  C02  single    1.349  0.020  1.349
 JEB  C02  N03  aromatic  1.336  0.020  1.336
 JEB  C02  C06  aromatic  1.400  0.020  1.400
 JEB  N08  C07  triple    1.156  0.020  1.156
 JEB  N03  N04  aromatic  1.348  0.020  1.348
 JEB  C07  C06  single    1.401  0.020  1.401
 JEB  C06  C05  aromatic  1.427  0.020  1.427
 JEB  N04  C05  aromatic  1.309  0.020  1.309
 JEB  C05  C09  single    1.464  0.020  1.464
 JEB  C09  C10  aromatic  1.410  0.020  1.410
 JEB  C09  C14  aromatic  1.388  0.020  1.388
 JEB  C10  C11  aromatic  1.379  0.020  1.379
 JEB  C14  C13  aromatic  1.390  0.020  1.390
 JEB  C11  C12  aromatic  1.398  0.020  1.398
 JEB  C13  C12  aromatic  1.414  0.020  1.414
 JEB  C13  N15  aromatic  1.369  0.020  1.369
 JEB  C12  C24  aromatic  1.427  0.020  1.427
 JEB  N15  C16  single    1.448  0.020  1.448
 JEB  N15  C23  aromatic  1.369  0.020  1.369
 JEB  C16  C17  single    1.505  0.020  1.505
 JEB  C24  C23  aromatic  1.364  0.020  1.364
 JEB  C22  C17  aromatic  1.390  0.020  1.390
 JEB  C22  C21  aromatic  1.385  0.020  1.385
 JEB  C17  C18  aromatic  1.390  0.020  1.390
 JEB  C21  C20  aromatic  1.387  0.020  1.387
 JEB  C18  N19  aromatic  1.327  0.020  1.327
 JEB  C20  N19  aromatic  1.328  0.020  1.328
 JEB  C10  H1   single    0.930  0.020  1.080
 JEB  C20  H2   single    0.930  0.020  1.080
 JEB  C21  H3   single    0.930  0.020  1.080
 JEB  C22  H4   single    0.930  0.020  1.080
 JEB  C24  H5   single    0.930  0.020  1.080
 JEB  N01  H6   single    0.890  0.020  1.040
 JEB  N01  H7   single    0.890  0.020  1.040
 JEB  N03  H8   single    0.860  0.020  1.020
 JEB  C11  H9   single    0.930  0.020  1.080
 JEB  C14  H10  single    0.930  0.020  1.080
 JEB  C16  H11  single    0.970  0.020  1.090
 JEB  C16  H12  single    0.970  0.020  1.090
 JEB  C18  H13  single    0.930  0.020  1.080
 JEB  C23  H14  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
 JEB  H1   C10  C11  118.93  3.000
 JEB  H1   C10  C09  119.66  3.000
 JEB  C11  C10  C09  121.39  3.000
 JEB  N15  C13  C14  130.16  3.000
 JEB  N15  C13  C12  107.71  3.000
 JEB  C14  C13  C12  122.12  3.000
 JEB  C18  C17  C16  120.46  3.000
 JEB  C18  C17  C22  117.40  3.000
 JEB  C16  C17  C22  122.11  3.000
 JEB  H2   C20  N19  116.60  3.000
 JEB  H2   C20  C21  120.25  3.000
 JEB  N19  C20  C21  123.15  3.000
 JEB  H3   C21  C22  121.15  3.000
 JEB  H3   C21  C20  120.37  3.000
 JEB  C22  C21  C20  118.48  3.000
 JEB  H4   C22  C21  120.16  3.000
 JEB  H4   C22  C17  120.69  3.000
 JEB  C21  C22  C17  119.15  3.000
 JEB  H5   C24  C23  126.12  3.000
 JEB  H5   C24  C12  127.36  3.000
 JEB  C23  C24  C12  106.51  3.000
 JEB  C06  C02  N03  105.20  3.000
 JEB  C06  C02  N01  130.36  3.000
 JEB  N03  C02  N01  124.33  3.000
 JEB  H8   N03  N04  119.50  3.000
 JEB  H8   N03  C02  126.83  3.000
 JEB  N04  N03  C02  113.65  3.000
 JEB  C05  N04  N03  105.82  3.000
 JEB  C09  C05  C06  128.44  3.000
 JEB  C09  C05  N04  121.17  3.000
 JEB  C06  C05  N04  110.38  3.000
 JEB  C07  C06  C05  129.84  3.000
 JEB  C05  C06  C02  104.94  3.000
 JEB  C07  C06  C02  125.11  3.000
 JEB  N08  C07  C06  180.00  3.000
 JEB  C14  C09  C05  119.08  3.000
 JEB  C14  C09  C10  120.28  3.000
 JEB  C05  C09  C10  120.63  3.000
 JEB  H9   C11  C12  120.61  3.000
 JEB  H9   C11  C10  120.16  3.000
 JEB  C12  C11  C10  119.23  3.000
 JEB  C11  C12  C24  134.33  3.000
 JEB  C24  C12  C13  106.81  3.000
 JEB  C11  C12  C13  118.86  3.000
 JEB  H10  C14  C09  119.93  3.000
 JEB  H10  C14  C13  121.94  3.000
 JEB  C09  C14  C13  118.12  3.000
 JEB  C23  N15  C16  124.66  3.000
 JEB  C23  N15  C13  108.59  3.000
 JEB  C16  N15  C13  126.17  3.000
 JEB  H12  C16  H11  106.65  3.000
 JEB  H12  C16  N15  107.94  3.000
 JEB  H11  C16  N15  108.75  3.000
 JEB  H12  C16  C17  110.47  3.000
 JEB  H11  C16  C17  110.85  3.000
 JEB  N15  C16  C17  111.99  3.000
 JEB  H13  C18  N19  116.31  3.000
 JEB  H13  C18  C17  119.67  3.000
 JEB  N19  C18  C17  124.02  3.000
 JEB  C18  N19  C20  117.80  3.000
 JEB  H14  C23  N15  120.09  3.000
 JEB  H14  C23  C24  129.55  3.000
 JEB  N15  C23  C24  110.37  3.000
 JEB  H7   N01  H6   113.43  3.000
 JEB  H7   N01  C02  116.84  3.000
 JEB  H6   N01  C02  117.73  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
 JEB  CONST_03  C13  C14  C09  C10    0.00   0.0  0
 JEB  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 JEB  CONST_05  C24  C12  C11  C10  180.00   0.0  0
 JEB  CONST_06  C05  C09  C14  C13  180.00   0.0  0
 JEB  CONST_07  C23  C24  C12  C13    0.00   0.0  0
 JEB  CONST_08  C24  C23  N15  C13    0.00   0.0  0
 JEB  CONST_09  C20  C21  C22  C17    0.00   0.0  0
 JEB  CONST_10  C20  N19  C18  C17    0.00   0.0  0
 JEB  CONST_11  C18  C17  C22  C21    0.00   0.0  0
 JEB  CONST_12  C18  N19  C20  C21    0.00   0.0  0
 JEB  CONST_13  N19  C18  C17  C22    0.00   0.0  0
 JEB  CONST_14  N19  C20  C21  C22    0.00   0.0  0
 JEB  CONST_15  C14  C13  C12  C24  180.00   0.0  0
 JEB  CONST_16  N15  C13  C12  C24    0.00   0.0  0
 JEB  CONST_17  C05  N04  N03  C02    0.00   0.0  0
 JEB  CONST_18  N04  C05  C06  C02    0.00   0.0  0
 JEB  CONST_19  C09  C05  C06  C02  180.00   0.0  0
 JEB  CONST_20  C05  C06  C02  N03    0.00   0.0  0
 JEB  CONST_21  C06  C05  N04  N03    0.00   0.0  0
 JEB  CONST_22  C09  C05  N04  N03  180.00   0.0  0
 JEB  CONST_23  C06  C02  N03  N04    0.00   0.0  0
 JEB  CONST_25  C11  C10  C09  C05  180.00   0.0  0
 JEB  CONST_27  C12  C11  C10  C09    0.00   0.0  0
 JEB  CONST_28  C12  C13  C14  C09    0.00   0.0  0
 JEB  CONST_29  N15  C13  C14  C09  180.00   0.0  0
 JEB  CONST_30  C14  C09  C10  C11    0.00   0.0  0
 JEB  CONST_31  C14  C13  C12  C11    0.00   0.0  0
 JEB  CONST_32  N15  C13  C12  C11  180.00   0.0  0
 JEB  CONST_33  C23  C24  C12  C11  180.00   0.0  0
 JEB  CONST_34  C23  N15  C13  C12    0.00   0.0  0
 JEB  CONST_35  N15  C23  C24  C12    0.00   0.0  0
 JEB  CONST_36  C23  N15  C13  C14  180.00   0.0  0
 JEB  CONST_37  C16  C17  C22  C21  180.00   0.0  0
 JEB  CONST_38  C16  N15  C23  C24  180.00   0.0  0
 JEB  CONST_39  N04  N03  C02  N01  180.00   0.0  0
 JEB  CONST_40  C05  C06  C02  N01  180.00   0.0  0
 JEB  CONST_41  C07  C06  C02  N03  180.00   0.0  0
 JEB  CONST_42  C07  C06  C05  N04  180.00   0.0  0
 JEB  CONST_43  C09  C05  C06  C07    0.00   0.0  0
 JEB  CONST_44  C16  N15  C13  C12  180.00   0.0  0
 JEB  CONST_45  C16  N15  C13  C14    0.00   0.0  0
 JEB  CONST_46  N19  C18  C17  C16  180.00   0.0  0
 JEB  CONST_47  H10  C14  C09  C10  180.00   0.0  0
 JEB  CONST_48  H9   C11  C12  C13  180.00   0.0  0
 JEB  CONST_49  H5   C24  C12  C13  180.00   0.0  0
 JEB  CONST_50  H14  C23  N15  C13  180.00   0.0  0
 JEB  CONST_51  H3   C21  C22  C17  180.00   0.0  0
 JEB  CONST_52  H4   C22  C21  C20  180.00   0.0  0
 JEB  CONST_53  H13  C18  N19  C20  180.00   0.0  0
 JEB  CONST_54  H2   C20  C21  C22  180.00   0.0  0
 JEB  CONST_55  H8   N03  N04  C05  180.00   0.0  0
 JEB  CONST_56  H1   C10  C09  C05    0.00   0.0  0
 JEB  Var_01    C17  C16  N15  C13   87.27  30.0  2
 JEB  Var_02    N15  C16  C17  C22  -84.42  30.0  2

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
 JEB  plan-1  C02  0.020
 JEB  plan-1  N03  0.020
 JEB  plan-1  N04  0.020
 JEB  plan-1  C05  0.020
 JEB  plan-1  C06  0.020
 JEB  plan-1  C07  0.020
 JEB  plan-1  N08  0.020
 JEB  plan-1  C09  0.020
 JEB  plan-1  H8   0.020
 JEB  plan-1  N01  0.020
 JEB  plan-2  C17  0.020
 JEB  plan-2  C20  0.020
 JEB  plan-2  C21  0.020
 JEB  plan-2  C22  0.020
 JEB  plan-2  C16  0.020
 JEB  plan-2  C18  0.020
 JEB  plan-2  N19  0.020
 JEB  plan-2  H2   0.020
 JEB  plan-2  H3   0.020
 JEB  plan-2  H4   0.020
 JEB  plan-2  H13  0.020
 JEB  plan-3  C10  0.020
 JEB  plan-3  C13  0.020
 JEB  plan-3  C24  0.020
 JEB  plan-3  C05  0.020
 JEB  plan-3  C09  0.020
 JEB  plan-3  C11  0.020
 JEB  plan-3  C12  0.020
 JEB  plan-3  C14  0.020
 JEB  plan-3  N15  0.020
 JEB  plan-3  C16  0.020
 JEB  plan-3  C23  0.020
 JEB  plan-3  H1   0.020
 JEB  plan-3  H5   0.020
 JEB  plan-3  H9   0.020
 JEB  plan-3  H10  0.020
 JEB  plan-3  H14  0.020
 JEB  plan-4  C02  0.020
 JEB  plan-4  H6   0.020
 JEB  plan-4  H7   0.020
 JEB  plan-4  N01  0.020

