# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:00:19 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-azanyl-3-[1-(pyridin-4-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c2ccc3ccn(Cc4ccncc4)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
 JFB  JFB  5-azanyl-3-[1-(pyridin-4-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_JFB
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
 JFB  C10  C  CR16  0  -0.331   1.4389   1.8842   0.8649
 JFB  C13  C  CR56  0   0.405  -0.9762   1.4674  -0.3767
 JFB  C17  C  CR6   0   0.181  -3.2261  -0.7170  -0.7089
 JFB  C21  C  CR16  0  -0.057  -3.5059  -3.0622  -0.3324
 JFB  C22  C  CR16  0  -0.373  -3.1494  -2.0216  -1.1771
 JFB  C24  C  CR15  0  -0.427  -1.8854   3.5144   0.0491
 JFB  C02  C  CR5   0   0.619   4.0511  -1.6374   0.2508
 JFB  N03  N  NR15  0  -0.491   2.9506  -2.3953   0.2664
 JFB  N04  N  N     0  -0.297   1.8047  -1.6853   0.2780
 JFB  C05  C  CR5   0   0.320   2.1645  -0.4271   0.2634
 JFB  C06  C  CR5   0  -0.286   3.5867  -0.3170   0.2469
 JFB  C07  C  CSP   0  -0.037   4.3988   0.8211   0.1647
 JFB  N08  N  NS    0  -0.267   5.0888   1.7463   0.0929
 JFB  C09  C  CR6   0   0.042   1.1706   0.6484   0.2408
 JFB  C11  C  CR16  0  -0.329   0.5132   2.9066   0.8699
 JFB  C12  C  CR56  0   0.052  -0.7209   2.7113   0.2420
 JFB  C14  C  CR16  0  -0.340  -0.0495   0.4323  -0.3851
 JFB  N15  N  NR5   0  -0.532  -2.2298   1.5222  -0.9225
 JFB  C16  C  CH2   0  -0.381  -2.8825   0.4398  -1.6119
 JFB  C18  C  CR16  0  -0.349  -3.6538  -0.5257   0.5990
 JFB  C19  C  CR16  0  -0.058  -3.9861  -1.6337   1.3624
 JFB  N20  N  N     0  -0.409  -3.9181  -2.8836   0.9164
 JFB  C23  C  CR15  0  -0.022  -2.7701   2.7525  -0.6558
 JFB  H1   H  HCR6  0   0.248   2.3815   2.0323   1.3755
 JFB  H2   H  HCR6  0   0.266  -3.4494  -4.0863  -0.6842
 JFB  H3   H  HCR6  0   0.271  -2.8107  -2.2347  -2.1832
 JFB  H4   H  HCR5  0   0.252  -2.0471   4.5256   0.3862
 JFB  H5   H  HNH2  0   0.409   5.4575  -3.0731   0.0009
 JFB  H6   H  HNH2  0   0.408   6.0441  -1.4968   0.0007
 JFB  H7   H  HNR5  0   0.429   2.9115  -3.4024   0.2909
 JFB  H8   H  HCR6  0   0.252   0.7410   3.8433   1.3628
 JFB  H9   H  HCR6  0   0.259  -0.2573  -0.5136  -0.8694
 JFB  H10  H  HCH2  0   0.284  -2.2567   0.0952  -2.4382
 JFB  H11  H  HCH2  0   0.302  -3.7970   0.8331  -2.0591
 JFB  H12  H  HCR6  0   0.269  -3.7321   0.4643   1.0299
 JFB  H13  H  HCR6  0   0.266  -4.3239  -1.5017   2.3844
 JFB  H14  H  HCR5  0   0.292  -3.7636   2.9908  -1.0027
 JFB  N01  N  NH2   0  -0.841   5.3097  -2.1205   0.2938

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
 JFB  N01  C02  single    1.349  0.020  1.349
 JFB  C02  N03  aromatic  1.336  0.020  1.336
 JFB  C02  C06  aromatic  1.400  0.020  1.400
 JFB  N03  N04  aromatic  1.348  0.020  1.348
 JFB  N08  C07  triple    1.156  0.020  1.156
 JFB  C07  C06  single    1.401  0.020  1.401
 JFB  C06  C05  aromatic  1.427  0.020  1.427
 JFB  N04  C05  aromatic  1.309  0.020  1.309
 JFB  C05  C09  single    1.465  0.020  1.465
 JFB  C09  C10  aromatic  1.410  0.020  1.410
 JFB  C09  C14  aromatic  1.388  0.020  1.388
 JFB  C10  C11  aromatic  1.379  0.020  1.379
 JFB  C14  C13  aromatic  1.389  0.020  1.389
 JFB  C11  C12  aromatic  1.398  0.020  1.398
 JFB  C13  C12  aromatic  1.413  0.020  1.413
 JFB  C13  N15  aromatic  1.368  0.020  1.368
 JFB  C12  C24  aromatic  1.428  0.020  1.428
 JFB  C16  N15  single    1.440  0.020  1.440
 JFB  C16  C17  single    1.507  0.020  1.507
 JFB  N15  C23  aromatic  1.370  0.020  1.370
 JFB  C24  C23  aromatic  1.364  0.020  1.364
 JFB  C22  C17  aromatic  1.388  0.020  1.388
 JFB  C22  C21  aromatic  1.387  0.020  1.387
 JFB  C17  C18  aromatic  1.389  0.020  1.389
 JFB  C21  N20  aromatic  1.327  0.020  1.327
 JFB  C18  C19  aromatic  1.386  0.020  1.386
 JFB  N20  C19  aromatic  1.329  0.020  1.329
 JFB  C10  H1   single    0.930  0.020  1.080
 JFB  C21  H2   single    0.930  0.020  1.080
 JFB  C22  H3   single    0.930  0.020  1.080
 JFB  C24  H4   single    0.930  0.020  1.080
 JFB  N01  H5   single    0.890  0.020  1.040
 JFB  N01  H6   single    0.890  0.020  1.040
 JFB  N03  H7   single    0.860  0.020  1.020
 JFB  C11  H8   single    0.930  0.020  1.080
 JFB  C14  H9   single    0.930  0.020  1.080
 JFB  C16  H10  single    0.970  0.020  1.090
 JFB  C16  H11  single    0.970  0.020  1.090
 JFB  C18  H12  single    0.930  0.020  1.080
 JFB  C19  H13  single    0.930  0.020  1.080
 JFB  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
 JFB  H1   C10  C11  118.78  3.000
 JFB  H1   C10  C09  119.63  3.000
 JFB  C11  C10  C09  121.57  3.000
 JFB  N15  C13  C14  129.67  3.000
 JFB  N15  C13  C12  107.76  3.000
 JFB  C14  C13  C12  122.56  3.000
 JFB  C18  C17  C16  121.90  3.000
 JFB  C18  C17  C22  117.65  3.000
 JFB  C16  C17  C22  120.44  3.000
 JFB  H2   C21  N20  116.65  3.000
 JFB  H2   C21  C22  119.84  3.000
 JFB  N20  C21  C22  123.51  3.000
 JFB  H3   C22  C21  119.91  3.000
 JFB  H3   C22  C17  121.05  3.000
 JFB  C21  C22  C17  119.04  3.000
 JFB  H4   C24  C23  126.03  3.000
 JFB  H4   C24  C12  127.42  3.000
 JFB  C23  C24  C12  106.54  3.000
 JFB  C06  C02  N03  105.18  3.000
 JFB  C06  C02  N01  130.36  3.000
 JFB  N03  C02  N01  124.40  3.000
 JFB  H7   N03  N04  119.53  3.000
 JFB  H7   N03  C02  126.78  3.000
 JFB  N04  N03  C02  113.67  3.000
 JFB  C05  N04  N03  105.82  3.000
 JFB  C09  C05  C06  128.30  3.000
 JFB  C09  C05  N04  121.31  3.000
 JFB  C06  C05  N04  110.38  3.000
 JFB  C07  C06  C05  129.90  3.000
 JFB  C05  C06  C02  104.95  3.000
 JFB  C07  C06  C02  125.06  3.000
 JFB  N08  C07  C06  180.00  3.000
 JFB  C14  C09  C05  119.28  3.000
 JFB  C14  C09  C10  120.21  3.000
 JFB  C05  C09  C10  120.50  3.000
 JFB  H8   C11  C12  120.73  3.000
 JFB  H8   C11  C10  120.12  3.000
 JFB  C12  C11  C10  119.16  3.000
 JFB  C11  C12  C24  134.59  3.000
 JFB  C24  C12  C13  106.78  3.000
 JFB  C11  C12  C13  118.63  3.000
 JFB  H9   C14  C09  120.42  3.000
 JFB  H9   C14  C13  121.71  3.000
 JFB  C09  C14  C13  117.87  3.000
 JFB  C23  N15  C16  126.12  3.000
 JFB  C23  N15  C13  108.64  3.000
 JFB  C16  N15  C13  125.19  3.000
 JFB  H11  C16  H10  106.49  3.000
 JFB  H11  C16  N15  107.77  3.000
 JFB  H10  C16  N15  109.85  3.000
 JFB  H11  C16  C17  109.34  3.000
 JFB  H10  C16  C17  109.98  3.000
 JFB  N15  C16  C17  113.17  3.000
 JFB  H12  C18  C19  119.64  3.000
 JFB  H12  C18  C17  121.53  3.000
 JFB  C19  C18  C17  118.83  3.000
 JFB  H13  C19  N20  116.53  3.000
 JFB  H13  C19  C18  119.77  3.000
 JFB  N20  C19  C18  123.70  3.000
 JFB  C19  N20  C21  117.27  3.000
 JFB  H14  C23  N15  119.93  3.000
 JFB  H14  C23  C24  129.80  3.000
 JFB  N15  C23  C24  110.27  3.000
 JFB  H6   N01  H5   113.21  3.000
 JFB  H6   N01  C02  116.70  3.000
 JFB  H5   N01  C02  117.79  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
 JFB  CONST_03  C13  C14  C09  C10     0.00   0.0  0
 JFB  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 JFB  CONST_05  C24  C12  C11  C10   180.00   0.0  0
 JFB  CONST_06  C05  C09  C14  C13   180.00   0.0  0
 JFB  CONST_07  C23  C24  C12  C13     0.00   0.0  0
 JFB  CONST_08  C24  C23  N15  C13     0.00   0.0  0
 JFB  CONST_09  N20  C21  C22  C17     0.00   0.0  0
 JFB  CONST_10  N20  C19  C18  C17     0.00   0.0  0
 JFB  CONST_11  C18  C17  C22  C21     0.00   0.0  0
 JFB  CONST_12  C18  C19  N20  C21     0.00   0.0  0
 JFB  CONST_13  C19  C18  C17  C22     0.00   0.0  0
 JFB  CONST_14  C19  N20  C21  C22     0.00   0.0  0
 JFB  CONST_15  C14  C13  C12  C24   180.00   0.0  0
 JFB  CONST_16  N15  C13  C12  C24     0.00   0.0  0
 JFB  CONST_17  C05  N04  N03  C02     0.00   0.0  0
 JFB  CONST_18  N04  C05  C06  C02     0.00   0.0  0
 JFB  CONST_19  C09  C05  C06  C02   180.00   0.0  0
 JFB  CONST_20  C05  C06  C02  N03     0.00   0.0  0
 JFB  CONST_21  C06  C05  N04  N03     0.00   0.0  0
 JFB  CONST_22  C09  C05  N04  N03   180.00   0.0  0
 JFB  CONST_23  C06  C02  N03  N04     0.00   0.0  0
 JFB  CONST_25  C11  C10  C09  C05   180.00   0.0  0
 JFB  CONST_27  C12  C11  C10  C09     0.00   0.0  0
 JFB  CONST_28  C12  C13  C14  C09     0.00   0.0  0
 JFB  CONST_29  N15  C13  C14  C09   180.00   0.0  0
 JFB  CONST_30  C14  C09  C10  C11     0.00   0.0  0
 JFB  CONST_31  C14  C13  C12  C11     0.00   0.0  0
 JFB  CONST_32  N15  C13  C12  C11   180.00   0.0  0
 JFB  CONST_33  C23  C24  C12  C11   180.00   0.0  0
 JFB  CONST_34  C23  N15  C13  C12     0.00   0.0  0
 JFB  CONST_35  N15  C23  C24  C12     0.00   0.0  0
 JFB  CONST_36  C23  N15  C13  C14   180.00   0.0  0
 JFB  CONST_37  C16  C17  C22  C21   180.00   0.0  0
 JFB  CONST_38  C16  N15  C23  C24   180.00   0.0  0
 JFB  CONST_39  N04  N03  C02  N01   180.00   0.0  0
 JFB  CONST_40  C05  C06  C02  N01   180.00   0.0  0
 JFB  CONST_41  C07  C06  C02  N03   180.00   0.0  0
 JFB  CONST_42  C07  C06  C05  N04   180.00   0.0  0
 JFB  CONST_43  C09  C05  C06  C07     0.00   0.0  0
 JFB  CONST_44  C16  N15  C13  C12   180.00   0.0  0
 JFB  CONST_45  C16  N15  C13  C14     0.00   0.0  0
 JFB  CONST_46  C19  C18  C17  C16   180.00   0.0  0
 JFB  CONST_47  H9   C14  C09  C10   180.00   0.0  0
 JFB  CONST_48  H8   C11  C12  C13   180.00   0.0  0
 JFB  CONST_49  H4   C24  C12  C13   180.00   0.0  0
 JFB  CONST_50  H14  C23  N15  C13   180.00   0.0  0
 JFB  CONST_51  H2   C21  C22  C17   180.00   0.0  0
 JFB  CONST_52  H13  C19  C18  C17   180.00   0.0  0
 JFB  CONST_53  H12  C18  C17  C22   180.00   0.0  0
 JFB  CONST_54  H7   N03  N04  C05   180.00   0.0  0
 JFB  CONST_55  H1   C10  C09  C05     0.00   0.0  0
 JFB  CONST_56  H3   C22  C17  C18   180.00   0.0  0
 JFB  Var_01    C17  C16  N15  C13    67.49  30.0  3
 JFB  Var_02    N15  C16  C17  C22  -144.29  30.0  3

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
 JFB  plan-1  C02  0.020
 JFB  plan-1  N03  0.020
 JFB  plan-1  N04  0.020
 JFB  plan-1  C05  0.020
 JFB  plan-1  C06  0.020
 JFB  plan-1  C07  0.020
 JFB  plan-1  N08  0.020
 JFB  plan-1  C09  0.020
 JFB  plan-1  H7   0.020
 JFB  plan-1  N01  0.020
 JFB  plan-2  C17  0.020
 JFB  plan-2  C21  0.020
 JFB  plan-2  C22  0.020
 JFB  plan-2  C16  0.020
 JFB  plan-2  C18  0.020
 JFB  plan-2  C19  0.020
 JFB  plan-2  N20  0.020
 JFB  plan-2  H2   0.020
 JFB  plan-2  H3   0.020
 JFB  plan-2  H12  0.020
 JFB  plan-2  H13  0.020
 JFB  plan-3  C10  0.020
 JFB  plan-3  C13  0.020
 JFB  plan-3  C24  0.020
 JFB  plan-3  C05  0.020
 JFB  plan-3  C09  0.020
 JFB  plan-3  C11  0.020
 JFB  plan-3  C12  0.020
 JFB  plan-3  C14  0.020
 JFB  plan-3  N15  0.020
 JFB  plan-3  C16  0.020
 JFB  plan-3  C23  0.020
 JFB  plan-3  H1   0.020
 JFB  plan-3  H4   0.020
 JFB  plan-3  H8   0.020
 JFB  plan-3  H9   0.020
 JFB  plan-3  H14  0.020
 JFB  plan-4  C02  0.020
 JFB  plan-4  H5   0.020
 JFB  plan-4  H6   0.020
 JFB  plan-4  N01  0.020

