# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:53:42 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-azanyl-5-[3-chloranyl-1-(pyridin-3-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n[nH]c(c2ccc3c(Cl)cn(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
 JFT  JFT  3-azanyl-5-[3-chloranyl-1-(pyridin-3-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile  ligand  38  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JFT
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
 JFT  C13  C   CR16  0  -0.338   0.1922  -0.0365   0.7912
 JFT  C15  C   CR5   0   0.521   2.6143  -0.0019   0.3573
 JFT  C20  C   CR5   0  -0.310   3.6878   0.0139  -0.5339
 JFT  C21  C   CSP   0  -0.035   3.7854  -0.6082  -1.7876
 JFT  C24  C   CR16  0  -0.315   0.0379  -2.6432  -0.3139
 JFT  C02  C   CR5   0  -0.252  -2.4771  -2.3846   0.2825
 JFT  C03  C   CR15  0   0.038  -3.1462  -1.3497   0.8659
 JFT  C06  C   CR6   0   0.029  -2.6054   2.0192   0.5937
 JFT  C07  C   CR16  0  -0.168  -3.4196   1.9283  -0.5299
 JFT  C08  C   CR16  0  -0.315  -3.3605   2.9268  -1.4857
 JFT  C09  C   CR16  0  -0.066  -2.4861   3.9868  -1.2834
 JFT  C11  C   CR16  0  -0.106  -1.7693   3.1233   0.6929
 JFT  C12  C   CR56  0   0.396  -1.0160  -0.7209   0.7302
 JFT  C14  C   CR6   0   0.043   1.3224  -0.6748   0.2981
 JFT  C18  C   CR5   0   0.458   4.6589   0.8611   0.0707
 JFT  C23  C   CR16  0  -0.319   1.2375  -1.9714  -0.2516
 JFT  C25  C   CR56  0   0.175  -1.1088  -2.0172   0.1790
 JFT  N04  N   NR5   0  -0.535  -2.2634  -0.3437   1.1443
 JFT  N10  N   N     0  -0.398  -1.7048   4.0887  -0.2169
 JFT  N16  N   NR15  0  -0.514   2.9904   0.7824   1.3638
 JFT  N17  N   N     0  -0.298   4.2154   1.3174   1.2213
 JFT  N19  N   NH2   0  -0.846   5.9082   1.1393  -0.4049
 JFT  N22  N   NS    0  -0.258   3.8963  -1.1022  -2.8262
 JFT  CL1  CL  CL    0  -0.154  -3.1496  -3.8743  -0.2299
 JFT  H1   H   HCR6  0   0.267   0.2515   0.9682   1.1897
 JFT  H2   H   HCR6  0   0.260  -0.0109  -3.6406  -0.7309
 JFT  H3   H   HCR5  0   0.317  -4.1917  -1.2559   1.1133
 JFT  H4   H   HCH2  0   0.291  -1.9429   1.2239   2.4762
 JFT  H5   H   HCH2  0   0.305  -3.6153   0.8725   2.1025
 JFT  H6   H   HCR6  0   0.272  -4.0956   1.0910  -0.6583
 JFT  H7   H   HCR6  0   0.276  -3.9791   2.8915  -2.3717
 JFT  H8   H   HCR6  0   0.269  -2.4165   4.7836  -2.0153
 JFT  H9   H   HCR6  0   0.264  -1.1179   3.2309   1.5557
 JFT  H10  H   HCR6  0   0.261   2.1351  -2.4599  -0.6063
 JFT  H11  H   HNR5  0   0.431   2.4788   0.9519   2.2165
 JFT  H12  H   HNH2  0   0.388   6.3501   1.9418   0.0162
 JFT  H13  H   HNH2  0   0.391   6.0038   1.1444  -1.4080
 JFT  C05  C   CH2   0  -0.424  -2.6212   0.9592   1.6631

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
 JFT  N19  C18  single    1.365  0.020  1.365
 JFT  C18  N17  aromatic  1.315  0.020  1.315
 JFT  C18  C20  aromatic  1.423  0.020  1.423
 JFT  N17  N16  aromatic  1.344  0.020  1.344
 JFT  N22  C21  triple    1.155  0.020  1.155
 JFT  C21  C20  single    1.403  0.020  1.403
 JFT  C20  C15  aromatic  1.395  0.020  1.395
 JFT  N16  C15  aromatic  1.330  0.020  1.330
 JFT  C15  C14  single    1.458  0.020  1.458
 JFT  C14  C23  aromatic  1.411  0.020  1.411
 JFT  C14  C13  aromatic  1.388  0.020  1.388
 JFT  C23  C24  aromatic  1.376  0.020  1.376
 JFT  C13  C12  aromatic  1.390  0.020  1.390
 JFT  C24  C25  aromatic  1.396  0.020  1.396
 JFT  C12  C25  aromatic  1.412  0.020  1.412
 JFT  C12  N04  aromatic  1.367  0.020  1.367
 JFT  C25  C02  aromatic  1.420  0.020  1.420
 JFT  C05  N04  single    1.447  0.020  1.447
 JFT  C05  C06  single    1.506  0.020  1.506
 JFT  N04  C03  aromatic  1.367  0.020  1.367
 JFT  C02  C03  aromatic  1.364  0.020  1.364
 JFT  C02  CL1  single    1.713  0.020  1.713
 JFT  C11  C06  aromatic  1.388  0.020  1.388
 JFT  C11  N10  aromatic  1.328  0.020  1.328
 JFT  C06  C07  aromatic  1.391  0.020  1.391
 JFT  N10  C09  aromatic  1.326  0.020  1.326
 JFT  C07  C08  aromatic  1.384  0.020  1.384
 JFT  C09  C08  aromatic  1.389  0.020  1.389
 JFT  C13  H1   single    0.930  0.020  1.080
 JFT  C24  H2   single    0.930  0.020  1.080
 JFT  C03  H3   single    0.930  0.020  1.080
 JFT  C05  H4   single    0.970  0.020  1.090
 JFT  C05  H5   single    0.970  0.020  1.090
 JFT  C07  H6   single    0.930  0.020  1.080
 JFT  C08  H7   single    0.930  0.020  1.080
 JFT  C09  H8   single    0.930  0.020  1.080
 JFT  C11  H9   single    0.930  0.020  1.080
 JFT  C23  H10  single    0.930  0.020  1.080
 JFT  N16  H11  single    0.860  0.020  1.020
 JFT  N19  H12  single    0.890  0.020  1.040
 JFT  N19  H13  single    0.890  0.020  1.040

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
 JFT  H1   C13  C14  120.85  3.000
 JFT  H1   C13  C12  121.39  3.000
 JFT  C14  C13  C12  117.75  3.000
 JFT  N16  C15  C14  123.60  3.000
 JFT  C14  C15  C20  131.38  3.000
 JFT  N16  C15  C20  105.02  3.000
 JFT  C18  C20  C21  126.59  3.000
 JFT  C21  C20  C15  128.26  3.000
 JFT  C18  C20  C15  105.08  3.000
 JFT  N22  C21  C20  180.00  3.000
 JFT  H2   C24  C25  120.81  3.000
 JFT  H2   C24  C23  120.44  3.000
 JFT  C25  C24  C23  118.75  3.000
 JFT  CL1  C02  C25  125.54  3.000
 JFT  CL1  C02  C03  126.54  3.000
 JFT  C25  C02  C03  107.91  3.000
 JFT  H3   C03  N04  121.02  3.000
 JFT  H3   C03  C02  129.79  3.000
 JFT  N04  C03  C02  109.19  3.000
 JFT  C11  C06  C07  117.54  3.000
 JFT  C07  C06  C05  121.44  3.000
 JFT  C11  C06  C05  121.02  3.000
 JFT  H6   C07  C08  120.16  3.000
 JFT  H6   C07  C06  120.76  3.000
 JFT  C08  C07  C06  119.08  3.000
 JFT  H7   C08  C09  120.30  3.000
 JFT  H7   C08  C07  121.20  3.000
 JFT  C09  C08  C07  118.50  3.000
 JFT  H8   C09  N10  116.66  3.000
 JFT  H8   C09  C08  120.20  3.000
 JFT  N10  C09  C08  123.14  3.000
 JFT  H9   C11  N10  116.29  3.000
 JFT  H9   C11  C06  119.77  3.000
 JFT  N10  C11  C06  123.94  3.000
 JFT  N04  C12  C25  108.16  3.000
 JFT  N04  C12  C13  130.08  3.000
 JFT  C25  C12  C13  121.76  3.000
 JFT  C23  C14  C15  119.56  3.000
 JFT  C23  C14  C13  120.78  3.000
 JFT  C15  C14  C13  119.65  3.000
 JFT  N19  C18  N17  122.87  3.000
 JFT  N17  C18  C20  110.37  3.000
 JFT  N19  C18  C20  126.69  3.000
 JFT  H10  C23  C14  119.52  3.000
 JFT  H10  C23  C24  119.21  3.000
 JFT  C14  C23  C24  121.25  3.000
 JFT  C12  C25  C02  105.81  3.000
 JFT  C02  C25  C24  134.49  3.000
 JFT  C12  C25  C24  119.70  3.000
 JFT  C12  N04  C05  125.62  3.000
 JFT  C05  N04  C03  125.16  3.000
 JFT  C12  N04  C03  108.93  3.000
 JFT  C11  N10  C09  117.81  3.000
 JFT  H11  N16  N17  119.00  3.000
 JFT  H11  N16  C15  126.54  3.000
 JFT  N17  N16  C15  114.33  3.000
 JFT  N16  N17  C18  105.19  3.000
 JFT  H13  N19  H12  111.73  3.000
 JFT  H13  N19  C18  115.75  3.000
 JFT  H12  N19  C18  114.69  3.000
 JFT  H5   C05  H4   106.60  3.000
 JFT  H5   C05  N04  107.36  3.000
 JFT  H4   C05  N04  109.37  3.000
 JFT  H5   C05  C06  110.59  3.000
 JFT  H4   C05  C06  110.60  3.000
 JFT  N04  C05  C06  112.12  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
 JFT  CONST_03  C24  C23  C14  C13     0.00   0.0  0
 JFT  CONST_04  C24  C25  C12  C13     0.00   0.0  0
 JFT  CONST_05  C02  C25  C12  C13   180.00   0.0  0
 JFT  CONST_06  C03  N04  C12  C13   180.00   0.0  0
 JFT  CONST_07  N17  C18  C20  C15     0.00   0.0  0
 JFT  CONST_08  C18  N17  N16  C15     0.00   0.0  0
 JFT  CONST_09  C24  C23  C14  C15   180.00   0.0  0
 JFT  CONST_10  C12  C13  C14  C15   180.00   0.0  0
 JFT  CONST_11  N16  N17  C18  C20     0.00   0.0  0
 JFT  CONST_12  N17  N16  C15  C20     0.00   0.0  0
 JFT  CONST_14  N04  C12  C25  C24   180.00   0.0  0
 JFT  CONST_15  C03  C02  C25  C24   180.00   0.0  0
 JFT  CONST_16  C23  C24  C25  C02   180.00   0.0  0
 JFT  CONST_17  N04  C12  C25  C02     0.00   0.0  0
 JFT  CONST_18  C12  N04  C03  C02     0.00   0.0  0
 JFT  CONST_19  C25  C12  N04  C03     0.00   0.0  0
 JFT  CONST_20  C12  C25  C02  C03     0.00   0.0  0
 JFT  CONST_21  C09  N10  C11  C06     0.00   0.0  0
 JFT  CONST_22  C09  C08  C07  C06     0.00   0.0  0
 JFT  CONST_23  N10  C11  C06  C07     0.00   0.0  0
 JFT  CONST_24  N10  C09  C08  C07     0.00   0.0  0
 JFT  CONST_25  C11  C06  C07  C08     0.00   0.0  0
 JFT  CONST_26  C11  N10  C09  C08     0.00   0.0  0
 JFT  CONST_27  C23  C14  C13  C12     0.00   0.0  0
 JFT  CONST_28  C23  C24  C25  C12     0.00   0.0  0
 JFT  CONST_29  C18  C20  C15  C14   180.00   0.0  0
 JFT  CONST_30  N17  N16  C15  C14   180.00   0.0  0
 JFT  CONST_31  C25  C24  C23  C14     0.00   0.0  0
 JFT  CONST_32  C25  C12  C13  C14     0.00   0.0  0
 JFT  CONST_33  N04  C12  C13  C14   180.00   0.0  0
 JFT  CONST_34  N16  C15  C20  C18     0.00   0.0  0
 JFT  CONST_36  N04  C03  C02  C25     0.00   0.0  0
 JFT  CONST_37  C05  N04  C12  C13     0.00   0.0  0
 JFT  CONST_38  N19  C18  C20  C15   180.00   0.0  0
 JFT  CONST_39  N17  C18  C20  C21   180.00   0.0  0
 JFT  CONST_40  N16  C15  C20  C21   180.00   0.0  0
 JFT  CONST_41  C14  C15  C20  C21     0.00   0.0  0
 JFT  CONST_42  CL1  C02  C25  C24     0.00   0.0  0
 JFT  CONST_43  C05  N04  C03  C02   180.00   0.0  0
 JFT  CONST_44  C25  C12  N04  C05   180.00   0.0  0
 JFT  CONST_45  N10  C11  C06  C05   180.00   0.0  0
 JFT  CONST_46  C08  C07  C06  C05   180.00   0.0  0
 JFT  CONST_47  CL1  C02  C25  C12   180.00   0.0  0
 JFT  CONST_48  CL1  C02  C03  N04   180.00   0.0  0
 JFT  CONST_49  N19  C18  N17  N16   180.00   0.0  0
 JFT  CONST_50  H10  C23  C14  C13   180.00   0.0  0
 JFT  CONST_51  H1   C13  C14  C15     0.00   0.0  0
 JFT  CONST_52  H11  N16  C15  C20   180.00   0.0  0
 JFT  CONST_53  H2   C24  C25  C02     0.00   0.0  0
 JFT  CONST_54  H7   C08  C07  C06   180.00   0.0  0
 JFT  CONST_55  H9   C11  C06  C07   180.00   0.0  0
 JFT  CONST_56  H8   C09  C08  C07   180.00   0.0  0
 JFT  CONST_57  H6   C07  C08  C09   180.00   0.0  0
 JFT  CONST_58  H3   C03  N04  C12   180.00   0.0  0
 JFT  Var_01    C06  C05  N04  C03  -102.46  30.0  2
 JFT  Var_02    N04  C05  C06  C07    59.58  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
 JFT  plan-1  C15  0.020
 JFT  plan-1  C20  0.020
 JFT  plan-1  C21  0.020
 JFT  plan-1  C14  0.020
 JFT  plan-1  C18  0.020
 JFT  plan-1  N16  0.020
 JFT  plan-1  N17  0.020
 JFT  plan-1  N19  0.020
 JFT  plan-1  N22  0.020
 JFT  plan-1  H11  0.020
 JFT  plan-2  C06  0.020
 JFT  plan-2  C07  0.020
 JFT  plan-2  C08  0.020
 JFT  plan-2  C09  0.020
 JFT  plan-2  C11  0.020
 JFT  plan-2  N10  0.020
 JFT  plan-2  H6   0.020
 JFT  plan-2  H7   0.020
 JFT  plan-2  H8   0.020
 JFT  plan-2  H9   0.020
 JFT  plan-2  C05  0.020
 JFT  plan-3  C13  0.020
 JFT  plan-3  C15  0.020
 JFT  plan-3  C24  0.020
 JFT  plan-3  C02  0.020
 JFT  plan-3  C03  0.020
 JFT  plan-3  C12  0.020
 JFT  plan-3  C14  0.020
 JFT  plan-3  C23  0.020
 JFT  plan-3  C25  0.020
 JFT  plan-3  N04  0.020
 JFT  plan-3  CL1  0.020
 JFT  plan-3  H1   0.020
 JFT  plan-3  H2   0.020
 JFT  plan-3  H3   0.020
 JFT  plan-3  H10  0.020
 JFT  plan-3  C05  0.020
 JFT  plan-4  C18  0.020
 JFT  plan-4  N19  0.020
 JFT  plan-4  H12  0.020
 JFT  plan-4  H13  0.020

