# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:39:08 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-[[6-(5-azanyl-1~{H}-pyrazol-3-yl)indol-1-yl]methyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c1)c2ccc3ccn(Cc4ccccc4C#N)c3c2
#
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
 JEW  JEW  2-[[6-(5-azanyl-1~{H}-pyrazol-3-yl)indol-1-yl]methyl]benzenecarbonitrile  ligand  39  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 OK
;

data_comp_JEW
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
 JEW  C13  C  CR6   0   0.044  -1.8065  -0.9174   0.1215
 JEW  C15  C  CR16  0  -0.326  -0.9642  -3.1394   0.6595
 JEW  C17  C  CR15  0  -0.427   1.5193  -3.4774  -0.0541
 JEW  C20  C  CR15  0  -0.585  -4.2110  -0.1339   0.6660
 JEW  C21  C  CR5   0   0.550  -4.8682   1.0502   0.3880
 JEW  N01  N  NS    0  -0.246   4.3826  -1.0060   1.4167
 JEW  C03  C  CR6   0  -0.008   3.0571   1.0322   0.5538
 JEW  C04  C  CR6   0   0.167   2.3673   0.9923  -0.6640
 JEW  C05  C  CR16  0  -0.311   1.7264   2.1476  -1.0864
 JEW  C06  C  CR16  0  -0.222   1.7562   3.3076  -0.3235
 JEW  C07  C  CR16  0  -0.256   2.4342   3.3310   0.8862
 JEW  C08  C  CR16  0  -0.235   3.0887   2.1928   1.3262
 JEW  N10  N  NR5   0  -0.532   1.7426  -1.3914  -0.8497
 JEW  C11  C  CR56  0   0.414   0.4533  -1.4875  -0.3907
 JEW  C12  C  CR16  0  -0.356  -0.5740  -0.5517  -0.4059
 JEW  C14  C  CR16  0  -0.350  -1.9841  -2.2106   0.6531
 JEW  C16  C  CR56  0   0.037   0.2800  -2.7904   0.1270
 JEW  C18  C  CR15  0  -0.012   2.3681  -2.5957  -0.6509
 JEW  C19  C  CR5   0   0.282  -2.9204   0.0372   0.1171
 JEW  N22  N  NR15  0  -0.481  -3.9829   1.8191  -0.2719
 JEW  N23  N  N     0  -0.329  -2.7935   1.2250  -0.4464
 JEW  H1   H  HCR6  0   0.247  -1.1323  -4.1286   1.0668
 JEW  H2   H  HCR5  0   0.249   1.7520  -4.4923   0.2258
 JEW  H3   H  HCR5  0   0.259  -4.6152  -0.9816   1.1935
 JEW  H4   H  HCR6  0   0.278   1.1875   2.1380  -2.0263
 JEW  H5   H  HCR6  0   0.276   1.2437   4.1928  -0.6755
 JEW  H6   H  HCR6  0   0.277   2.4593   4.2309   1.4851
 JEW  H7   H  HCR6  0   0.285   3.6301   2.1998   2.2624
 JEW  H8   H  HCH2  0   0.293   1.7537  -0.0294  -2.4291
 JEW  H9   H  HCH2  0   0.299   3.3235  -0.5302  -1.8381
 JEW  H10  H  HCR6  0   0.260  -0.4356   0.4418  -0.8111
 JEW  H11  H  HCR6  0   0.239  -2.9463  -2.4920   1.0610
 JEW  H12  H  HCR5  0   0.287   3.3947  -2.7276  -0.9542
 JEW  H13  H  HNR5  0   0.412  -4.1366   2.7448  -0.6378
 JEW  H14  H  HNH2  0   0.390  -6.6205   0.9136   1.3422
 JEW  H15  H  HNH2  0   0.387  -6.3017   2.4281   0.7500
 JEW  C09  C  CH2   0  -0.429   2.3180  -0.2495  -1.5200
 JEW  N24  N  NH2   0  -0.857  -6.1660   1.4379   0.6115
 JEW  C02  C  CSP   0   0.032   3.7761  -0.1084   1.0240

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
 JEW  C07  C08  aromatic  1.385  0.020  1.385
 JEW  C07  C06  aromatic  1.387  0.020  1.387
 JEW  C08  C03  aromatic  1.395  0.020  1.395
 JEW  N01  C02  triple    1.152  0.020  1.152
 JEW  C02  C03  single    1.428  0.020  1.428
 JEW  C06  C05  aromatic  1.389  0.020  1.389
 JEW  C03  C04  aromatic  1.400  0.020  1.400
 JEW  C05  C04  aromatic  1.387  0.020  1.387
 JEW  C04  C09  single    1.509  0.020  1.509
 JEW  C18  C17  aromatic  1.362  0.020  1.362
 JEW  C18  N10  aromatic  1.371  0.020  1.371
 JEW  C17  C16  aromatic  1.428  0.020  1.428
 JEW  C09  N10  single    1.444  0.020  1.444
 JEW  N10  C11  aromatic  1.372  0.020  1.372
 JEW  C16  C11  aromatic  1.413  0.020  1.413
 JEW  C16  C15  aromatic  1.398  0.020  1.398
 JEW  C11  C12  aromatic  1.390  0.020  1.390
 JEW  C15  C14  aromatic  1.379  0.020  1.379
 JEW  C12  C13  aromatic  1.390  0.020  1.390
 JEW  C14  C13  aromatic  1.409  0.020  1.409
 JEW  C13  C19  single    1.467  0.020  1.467
 JEW  C20  C19  aromatic  1.413  0.020  1.413
 JEW  C20  C21  aromatic  1.383  0.020  1.383
 JEW  C19  N23  aromatic  1.321  0.020  1.321
 JEW  C21  N24  single    1.373  0.020  1.373
 JEW  C21  N22  aromatic  1.345  0.020  1.345
 JEW  N23  N22  aromatic  1.341  0.020  1.341
 JEW  C15  H1   single    0.930  0.020  1.080
 JEW  C17  H2   single    0.930  0.020  1.080
 JEW  C20  H3   single    0.930  0.020  1.080
 JEW  C05  H4   single    0.930  0.020  1.080
 JEW  C06  H5   single    0.930  0.020  1.080
 JEW  C07  H6   single    0.930  0.020  1.080
 JEW  C08  H7   single    0.930  0.020  1.080
 JEW  C09  H8   single    0.970  0.020  1.090
 JEW  C09  H9   single    0.970  0.020  1.090
 JEW  C12  H10  single    0.930  0.020  1.080
 JEW  C14  H11  single    0.930  0.020  1.080
 JEW  C18  H12  single    0.930  0.020  1.080
 JEW  N22  H13  single    0.860  0.020  1.020
 JEW  N24  H14  single    0.890  0.020  1.040
 JEW  N24  H15  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
 JEW  C19  C13  C14  120.17  3.000
 JEW  C19  C13  C12  120.07  3.000
 JEW  C14  C13  C12  119.76  3.000
 JEW  H1   C15  C16  120.63  3.000
 JEW  H1   C15  C14  120.14  3.000
 JEW  C16  C15  C14  119.23  3.000
 JEW  H2   C17  C18  126.07  3.000
 JEW  H2   C17  C16  127.37  3.000
 JEW  C18  C17  C16  106.56  3.000
 JEW  H3   C20  C19  128.93  3.000
 JEW  H3   C20  C21  126.45  3.000
 JEW  C19  C20  C21  104.62  3.000
 JEW  N24  C21  N22  122.72  3.000
 JEW  N22  C21  C20  105.98  3.000
 JEW  N24  C21  C20  131.19  3.000
 JEW  C08  C03  C04  121.11  3.000
 JEW  C04  C03  C02  120.78  3.000
 JEW  C08  C03  C02  118.10  3.000
 JEW  C09  C04  C05  119.84  3.000
 JEW  C09  C04  C03  122.20  3.000
 JEW  C05  C04  C03  117.96  3.000
 JEW  H4   C05  C06  119.64  3.000
 JEW  H4   C05  C04  119.12  3.000
 JEW  C06  C05  C04  121.23  3.000
 JEW  H5   C06  C07  120.11  3.000
 JEW  H5   C06  C05  119.65  3.000
 JEW  C07  C06  C05  120.25  3.000
 JEW  H6   C07  C08  119.81  3.000
 JEW  H6   C07  C06  120.56  3.000
 JEW  C08  C07  C06  119.63  3.000
 JEW  H7   C08  C07  120.42  3.000
 JEW  H7   C08  C03  119.75  3.000
 JEW  C07  C08  C03  119.83  3.000
 JEW  C18  N10  C11  108.58  3.000
 JEW  C11  N10  C09  125.82  3.000
 JEW  C18  N10  C09  125.45  3.000
 JEW  C16  C11  C12  122.30  3.000
 JEW  C12  C11  N10  130.08  3.000
 JEW  C16  C11  N10  107.61  3.000
 JEW  H10  C12  C11  121.87  3.000
 JEW  H10  C12  C13  119.82  3.000
 JEW  C11  C12  C13  118.31  3.000
 JEW  H11  C14  C15  118.72  3.000
 JEW  H11  C14  C13  119.52  3.000
 JEW  C15  C14  C13  121.76  3.000
 JEW  C11  C16  C17  106.90  3.000
 JEW  C11  C16  C15  118.63  3.000
 JEW  C17  C16  C15  134.47  3.000
 JEW  H12  C18  N10  120.05  3.000
 JEW  H12  C18  C17  129.60  3.000
 JEW  N10  C18  C17  110.35  3.000
 JEW  N23  C19  C20  111.25  3.000
 JEW  N23  C19  C13  120.90  3.000
 JEW  C20  C19  C13  127.85  3.000
 JEW  H13  N22  N23  119.69  3.000
 JEW  H13  N22  C21  127.08  3.000
 JEW  N23  N22  C21  113.22  3.000
 JEW  N22  N23  C19  104.93  3.000
 JEW  H9   C09  H8   106.57  3.000
 JEW  H9   C09  N10  107.40  3.000
 JEW  H8   C09  N10  109.87  3.000
 JEW  H9   C09  C04  110.30  3.000
 JEW  H8   C09  C04  108.85  3.000
 JEW  N10  C09  C04  113.61  3.000
 JEW  H15  N24  H14  110.52  3.000
 JEW  H15  N24  C21  115.26  3.000
 JEW  H14  N24  C21  113.42  3.000
 JEW  C03  C02  N01  180.00  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
 JEW  CONST_01  N10  C11  C12  C13   180.00   0.0  0
 JEW  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 JEW  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 JEW  CONST_04  C21  C20  C19  C13   180.00   0.0  0
 JEW  CONST_05  N22  N23  C19  C13   180.00   0.0  0
 JEW  CONST_06  C18  C17  C16  C15   180.00   0.0  0
 JEW  CONST_07  N10  C11  C16  C15   180.00   0.0  0
 JEW  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 JEW  CONST_09  C12  C13  C14  C15     0.00   0.0  0
 JEW  CONST_10  C19  C13  C14  C15   180.00   0.0  0
 JEW  CONST_11  C11  N10  C18  C17     0.00   0.0  0
 JEW  CONST_12  N10  C11  C16  C17     0.00   0.0  0
 JEW  CONST_13  C12  C11  C16  C17   180.00   0.0  0
 JEW  CONST_14  C14  C15  C16  C17   180.00   0.0  0
 JEW  CONST_15  C12  C13  C19  C20   180.00   0.0  0
 JEW  CONST_16  C14  C13  C19  C20     0.00   0.0  0
 JEW  CONST_17  N22  N23  C19  C20     0.00   0.0  0
 JEW  CONST_18  N23  N22  C21  C20     0.00   0.0  0
 JEW  CONST_19  N23  C19  C20  C21     0.00   0.0  0
 JEW  CONST_20  C19  N23  N22  C21     0.00   0.0  0
 JEW  CONST_21  C06  C07  C08  C03     0.00   0.0  0
 JEW  CONST_22  C06  C05  C04  C03     0.00   0.0  0
 JEW  CONST_23  C07  C08  C03  C04     0.00   0.0  0
 JEW  CONST_24  C07  C06  C05  C04     0.00   0.0  0
 JEW  CONST_25  C08  C07  C06  C05     0.00   0.0  0
 JEW  CONST_26  C08  C03  C04  C05     0.00   0.0  0
 JEW  CONST_27  C16  C17  C18  N10     0.00   0.0  0
 JEW  CONST_28  C18  C17  C16  C11     0.00   0.0  0
 JEW  CONST_29  C14  C15  C16  C11     0.00   0.0  0
 JEW  CONST_30  C14  C13  C12  C11     0.00   0.0  0
 JEW  CONST_31  C19  C13  C12  C11   180.00   0.0  0
 JEW  CONST_32  C18  N10  C11  C12   180.00   0.0  0
 JEW  CONST_33  N23  C19  C13  C12     0.00   0.0  0
 JEW  CONST_34  N23  C19  C13  C14   180.00   0.0  0
 JEW  CONST_35  C18  N10  C11  C16     0.00   0.0  0
 JEW  CONST_36  N22  C21  C20  C19     0.00   0.0  0
 JEW  CONST_37  C09  N10  C18  C17   180.00   0.0  0
 JEW  CONST_38  C07  C08  C03  C02   180.00   0.0  0
 JEW  CONST_39  C05  C04  C03  C02   180.00   0.0  0
 JEW  CONST_40  C09  C04  C05  C06   180.00   0.0  0
 JEW  CONST_41  C09  C04  C03  C08   180.00   0.0  0
 JEW  CONST_42  C16  C11  N10  C09   180.00   0.0  0
 JEW  CONST_43  C12  C11  N10  C09     0.00   0.0  0
 JEW  CONST_44  N24  C21  C20  C19   180.00   0.0  0
 JEW  CONST_45  N24  C21  N22  N23   180.00   0.0  0
 JEW  CONST_46  H1   C15  C14  C13   180.00   0.0  0
 JEW  CONST_47  H3   C20  C19  C13     0.00   0.0  0
 JEW  CONST_48  H2   C17  C16  C15     0.00   0.0  0
 JEW  CONST_49  H13  N22  C21  C20   180.00   0.0  0
 JEW  CONST_50  H6   C07  C08  C03   180.00   0.0  0
 JEW  CONST_51  H4   C05  C04  C03   180.00   0.0  0
 JEW  CONST_52  H7   C08  C03  C04   180.00   0.0  0
 JEW  CONST_53  H5   C06  C05  C04   180.00   0.0  0
 JEW  CONST_54  H10  C12  C11  N10     0.00   0.0  0
 JEW  CONST_55  H12  C18  N10  C11   180.00   0.0  0
 JEW  CONST_56  H11  C14  C13  C12   180.00   0.0  0
 JEW  Var_01    N10  C09  C04  C03    59.08  30.0  2
 JEW  Var_02    C18  N10  C09  C04  -121.79  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
 JEW  plan-1  C13  0.020
 JEW  plan-1  C20  0.020
 JEW  plan-1  C21  0.020
 JEW  plan-1  C19  0.020
 JEW  plan-1  N22  0.020
 JEW  plan-1  N23  0.020
 JEW  plan-1  H3   0.020
 JEW  plan-1  H13  0.020
 JEW  plan-1  N24  0.020
 JEW  plan-2  N01  0.020
 JEW  plan-2  C03  0.020
 JEW  plan-2  C04  0.020
 JEW  plan-2  C05  0.020
 JEW  plan-2  C06  0.020
 JEW  plan-2  C07  0.020
 JEW  plan-2  C08  0.020
 JEW  plan-2  H4   0.020
 JEW  plan-2  H5   0.020
 JEW  plan-2  H6   0.020
 JEW  plan-2  H7   0.020
 JEW  plan-2  C09  0.020
 JEW  plan-2  C02  0.020
 JEW  plan-3  C13  0.020
 JEW  plan-3  C15  0.020
 JEW  plan-3  C17  0.020
 JEW  plan-3  N10  0.020
 JEW  plan-3  C11  0.020
 JEW  plan-3  C12  0.020
 JEW  plan-3  C14  0.020
 JEW  plan-3  C16  0.020
 JEW  plan-3  C18  0.020
 JEW  plan-3  C19  0.020
 JEW  plan-3  H1   0.020
 JEW  plan-3  H2   0.020
 JEW  plan-3  H10  0.020
 JEW  plan-3  H11  0.020
 JEW  plan-3  H12  0.020
 JEW  plan-3  C09  0.020
 JEW  plan-4  C21  0.020
 JEW  plan-4  H14  0.020
 JEW  plan-4  H15  0.020
 JEW  plan-4  N24  0.020

