# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:27:54 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazol-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc([nH]n1)c2ccc3ccn(Cc4ccccn4)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
 JCE  JCE  5-[1-(pyridin-2-ylmethyl)indol-6-yl]-1~{H}-pyrazol-3-amine  ligand  37  22  .  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_JCE
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
 JCE  C10  C  CR56  0   0.411   0.5518  -1.3247  -0.2607
 JCE  C13  C  CR6   0   0.259   3.0552   0.8725  -0.5663
 JCE  C15  C  CR16  0  -0.074   2.8115   2.3151   1.1819
 JCE  C17  C  CR16  0  -0.145   4.9533   2.1264   0.1640
 JCE  C20  C  CR15  0  -0.425   1.7081  -3.1852   0.3723
 JCE  C21  C  CR16  0  -0.357  -0.5149  -0.4426  -0.3982
 JCE  C22  C  CR15  0  -0.581  -4.2429  -0.2026   0.1450
 JCE  C02  C  CR5   0   0.397  -4.8841   1.0372  -0.0582
 JCE  N03  N  N     0  -0.320  -4.0067   2.0059  -0.2481
 JCE  N04  N  NR15  0  -0.531  -2.8101   1.4036  -0.1719
 JCE  C05  C  CR5   0   0.441  -2.8926   0.0825   0.0620
 JCE  C06  C  CR6   0   0.051  -1.7300  -0.7937   0.1735
 JCE  C07  C  CR16  0  -0.334  -1.8592  -2.0132   0.8738
 JCE  C08  C  CR16  0  -0.328  -0.7995  -2.8814   1.0090
 JCE  C09  C  CR56  0   0.048   0.4346  -2.5463   0.4394
 JCE  N11  N  NR5   0  -0.522   1.8287  -1.2435  -0.7437
 JCE  C12  C  CH2   0  -0.402   2.4036  -0.1391  -1.4746
 JCE  N14  N  N     0  -0.401   2.2755   1.4276   0.3563
 JCE  C16  C  CR16  0  -0.328   4.1441   2.7022   1.1293
 JCE  C18  C  CR16  0  -0.346   4.4000   1.1913  -0.6994
 JCE  C19  C  CR15  0  -0.021   2.5185  -2.3584  -0.3487
 JCE  H1   H  HCR6  0   0.264   2.1483   2.7464   1.9238
 JCE  H2   H  HCR6  0   0.276   5.9983   2.3953   0.0845
 JCE  H3   H  HCR5  0   0.251   1.9849  -4.1388   0.7922
 JCE  H4   H  HCR6  0   0.253  -0.3984   0.4825  -0.9488
 JCE  H5   H  HCR5  0   0.262  -4.7030  -1.1643   0.3021
 JCE  H6   H  HNH2  0   0.376  -6.8046   0.5121  -0.3315
 JCE  H7   H  HNH2  0   0.369  -6.5089   2.1300  -0.5056
 JCE  H9   H  HCR6  0   0.247  -2.8109  -2.2626   1.3252
 JCE  H10  H  HCR6  0   0.249  -0.9213  -3.8091   1.5541
 JCE  H11  H  HCH2  0   0.288   1.6173   0.3388  -2.0616
 JCE  H12  H  HCH2  0   0.289   3.1271  -0.5366  -2.1864
 JCE  H13  H  HCR6  0   0.272   4.5294   3.4328   1.8272
 JCE  H14  H  HCR6  0   0.272   5.0036   0.7133  -1.4597
 JCE  H15  H  HCR5  0   0.286   3.5528  -2.4841  -0.6294
 JCE  H8   H  HNR5  0   0.411  -1.9767   1.9645  -0.2313
 JCE  N01  N  NH2   0  -0.857  -6.2431   1.2882  -0.0174

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
 JCE  N03  N04  aromatic  1.342  0.020  1.342
 JCE  N03  C02  aromatic  1.321  0.020  1.321
 JCE  N04  C05  aromatic  1.344  0.020  1.344
 JCE  C02  N01  single    1.383  0.020  1.383
 JCE  C02  C22  aromatic  1.410  0.020  1.410
 JCE  C05  C22  aromatic  1.383  0.020  1.383
 JCE  C05  C06  single    1.460  0.020  1.460
 JCE  C06  C07  aromatic  1.412  0.020  1.412
 JCE  C06  C21  aromatic  1.388  0.020  1.388
 JCE  C07  C08  aromatic  1.377  0.020  1.377
 JCE  C21  C10  aromatic  1.391  0.020  1.391
 JCE  C08  C09  aromatic  1.400  0.020  1.400
 JCE  C10  C09  aromatic  1.413  0.020  1.413
 JCE  C10  N11  aromatic  1.368  0.020  1.368
 JCE  C09  C20  aromatic  1.426  0.020  1.426
 JCE  N11  C12  single    1.444  0.020  1.444
 JCE  N11  C19  aromatic  1.369  0.020  1.369
 JCE  C12  C13  single    1.508  0.020  1.508
 JCE  C20  C19  aromatic  1.364  0.020  1.364
 JCE  C13  C18  aromatic  1.389  0.020  1.389
 JCE  C13  N14  aromatic  1.329  0.020  1.329
 JCE  C18  C17  aromatic  1.388  0.020  1.388
 JCE  N14  C15  aromatic  1.325  0.020  1.325
 JCE  C17  C16  aromatic  1.385  0.020  1.385
 JCE  C15  C16  aromatic  1.389  0.020  1.389
 JCE  C15  H1   single    0.930  0.020  1.080
 JCE  C17  H2   single    0.930  0.020  1.080
 JCE  C20  H3   single    0.930  0.020  1.080
 JCE  C21  H4   single    0.930  0.020  1.080
 JCE  C22  H5   single    0.930  0.020  1.080
 JCE  N01  H6   single    0.890  0.020  1.040
 JCE  N01  H7   single    0.890  0.020  1.040
 JCE  C07  H9   single    0.930  0.020  1.080
 JCE  C08  H10  single    0.930  0.020  1.080
 JCE  C12  H11  single    0.970  0.020  1.090
 JCE  C12  H12  single    0.970  0.020  1.090
 JCE  C16  H13  single    0.930  0.020  1.080
 JCE  C18  H14  single    0.930  0.020  1.080
 JCE  C19  H15  single    0.930  0.020  1.080
 JCE  N04  H8   single    0.860  0.020  1.020

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
 JCE  N11  C10  C09  107.69  3.000
 JCE  N11  C10  C21  130.05  3.000
 JCE  C09  C10  C21  122.25  3.000
 JCE  C18  C13  N14  122.59  3.000
 JCE  N14  C13  C12  116.41  3.000
 JCE  C18  C13  C12  120.99  3.000
 JCE  H1   C15  C16  120.12  3.000
 JCE  H1   C15  N14  116.44  3.000
 JCE  C16  C15  N14  123.44  3.000
 JCE  H2   C17  C18  120.45  3.000
 JCE  H2   C17  C16  120.81  3.000
 JCE  C18  C17  C16  118.74  3.000
 JCE  H3   C20  C19  126.13  3.000
 JCE  H3   C20  C09  127.37  3.000
 JCE  C19  C20  C09  106.49  3.000
 JCE  H4   C21  C06  121.31  3.000
 JCE  H4   C21  C10  120.63  3.000
 JCE  C06  C21  C10  118.05  3.000
 JCE  H5   C22  C05  127.57  3.000
 JCE  H5   C22  C02  127.69  3.000
 JCE  C05  C22  C02  104.72  3.000
 JCE  N03  C02  N01  121.61  3.000
 JCE  N01  C02  C22  127.02  3.000
 JCE  N03  C02  C22  111.31  3.000
 JCE  N04  N03  C02  104.78  3.000
 JCE  H8   N04  C05  127.51  3.000
 JCE  H8   N04  N03  119.02  3.000
 JCE  C05  N04  N03  113.34  3.000
 JCE  C06  C05  N04  123.66  3.000
 JCE  C06  C05  C22  130.49  3.000
 JCE  N04  C05  C22  105.85  3.000
 JCE  C07  C06  C05  118.90  3.000
 JCE  C07  C06  C21  120.18  3.000
 JCE  C05  C06  C21  120.92  3.000
 JCE  H9   C07  C08  119.37  3.000
 JCE  H9   C07  C06  119.09  3.000
 JCE  C08  C07  C06  121.53  3.000
 JCE  H10  C08  C09  120.60  3.000
 JCE  H10  C08  C07  120.21  3.000
 JCE  C09  C08  C07  119.19  3.000
 JCE  C08  C09  C20  134.35  3.000
 JCE  C20  C09  C10  106.85  3.000
 JCE  C08  C09  C10  118.80  3.000
 JCE  C19  N11  C12  124.64  3.000
 JCE  C19  N11  C10  108.67  3.000
 JCE  C12  N11  C10  126.58  3.000
 JCE  H12  C12  H11  106.66  3.000
 JCE  H12  C12  N11  108.41  3.000
 JCE  H11  C12  N11  108.68  3.000
 JCE  H12  C12  C13  110.57  3.000
 JCE  H11  C12  C13  109.98  3.000
 JCE  N11  C12  C13  112.35  3.000
 JCE  C15  N14  C13  118.35  3.000
 JCE  H13  C16  C17  121.50  3.000
 JCE  H13  C16  C15  120.39  3.000
 JCE  C17  C16  C15  118.11  3.000
 JCE  H14  C18  C17  120.83  3.000
 JCE  H14  C18  C13  120.41  3.000
 JCE  C17  C18  C13  118.76  3.000
 JCE  H15  C19  N11  120.17  3.000
 JCE  H15  C19  C20  129.53  3.000
 JCE  N11  C19  C20  110.29  3.000
 JCE  H7   N01  H6   110.18  3.000
 JCE  H7   N01  C02  113.34  3.000
 JCE  H6   N01  C02  113.48  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
 JCE  CONST_01  C05  C06  C21  C10  180.00   0.0  0
 JCE  CONST_02  C07  C06  C21  C10    0.00   0.0  0
 JCE  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 JCE  CONST_04  C19  C20  C09  C10    0.00   0.0  0
 JCE  CONST_05  C20  C19  N11  C10    0.00   0.0  0
 JCE  CONST_06  C16  C17  C18  C13    0.00   0.0  0
 JCE  CONST_07  C16  C15  N14  C13    0.00   0.0  0
 JCE  CONST_08  C18  C13  N14  C15    0.00   0.0  0
 JCE  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 JCE  CONST_10  N14  C13  C18  C17    0.00   0.0  0
 JCE  CONST_11  N14  C15  C16  C17    0.00   0.0  0
 JCE  CONST_12  C07  C08  C09  C20  180.00   0.0  0
 JCE  CONST_13  C21  C10  C09  C20  180.00   0.0  0
 JCE  CONST_14  N11  C10  C09  C20    0.00   0.0  0
 JCE  CONST_17  C08  C07  C06  C21    0.00   0.0  0
 JCE  CONST_18  C08  C09  C10  C21    0.00   0.0  0
 JCE  CONST_19  C19  N11  C10  C21  180.00   0.0  0
 JCE  CONST_20  N04  N03  C02  C22    0.00   0.0  0
 JCE  CONST_21  N03  N04  C05  C22    0.00   0.0  0
 JCE  CONST_23  C05  N04  N03  C02    0.00   0.0  0
 JCE  CONST_24  N04  C05  C22  C02    0.00   0.0  0
 JCE  CONST_25  C06  C05  C22  C02  180.00   0.0  0
 JCE  CONST_26  C06  C05  N04  N03  180.00   0.0  0
 JCE  CONST_27  C05  C22  C02  N03    0.00   0.0  0
 JCE  CONST_29  C08  C07  C06  C05  180.00   0.0  0
 JCE  CONST_30  C09  C08  C07  C06    0.00   0.0  0
 JCE  CONST_31  C09  C10  C21  C06    0.00   0.0  0
 JCE  CONST_32  N11  C10  C21  C06  180.00   0.0  0
 JCE  CONST_33  N11  C10  C09  C08  180.00   0.0  0
 JCE  CONST_34  C19  C20  C09  C08  180.00   0.0  0
 JCE  CONST_35  C19  N11  C10  C09    0.00   0.0  0
 JCE  CONST_36  N11  C19  C20  C09    0.00   0.0  0
 JCE  CONST_37  C12  C13  N14  C15  180.00   0.0  0
 JCE  CONST_38  C12  C13  C18  C17  180.00   0.0  0
 JCE  CONST_39  C12  N11  C19  C20  180.00   0.0  0
 JCE  CONST_40  C12  N11  C10  C21    0.00   0.0  0
 JCE  CONST_41  N04  N03  C02  N01  180.00   0.0  0
 JCE  CONST_42  C05  C22  C02  N01  180.00   0.0  0
 JCE  CONST_43  C12  N11  C10  C09  180.00   0.0  0
 JCE  CONST_44  H10  C08  C09  C10  180.00   0.0  0
 JCE  CONST_45  H3   C20  C09  C10  180.00   0.0  0
 JCE  CONST_46  H15  C19  N11  C10  180.00   0.0  0
 JCE  CONST_47  H2   C17  C18  C13  180.00   0.0  0
 JCE  CONST_48  H1   C15  N14  C13  180.00   0.0  0
 JCE  CONST_49  H9   C07  C06  C21  180.00   0.0  0
 JCE  CONST_50  H8   N04  C05  C22  180.00   0.0  0
 JCE  CONST_51  H5   C22  C02  N03  180.00   0.0  0
 JCE  CONST_52  H4   C21  C06  C05    0.00   0.0  0
 JCE  CONST_53  H14  C18  C13  N14  180.00   0.0  0
 JCE  CONST_54  H13  C16  C15  N14  180.00   0.0  0
 JCE  Var_01    C13  C12  N11  C10   90.30  30.0  2
 JCE  Var_02    C18  C13  C12  N11  121.48  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
 JCE  plan-1  C22  0.020
 JCE  plan-1  C02  0.020
 JCE  plan-1  N03  0.020
 JCE  plan-1  N04  0.020
 JCE  plan-1  C05  0.020
 JCE  plan-1  C06  0.020
 JCE  plan-1  H5   0.020
 JCE  plan-1  H8   0.020
 JCE  plan-1  N01  0.020
 JCE  plan-2  C13  0.020
 JCE  plan-2  C15  0.020
 JCE  plan-2  C17  0.020
 JCE  plan-2  C12  0.020
 JCE  plan-2  N14  0.020
 JCE  plan-2  C16  0.020
 JCE  plan-2  C18  0.020
 JCE  plan-2  H1   0.020
 JCE  plan-2  H2   0.020
 JCE  plan-2  H13  0.020
 JCE  plan-2  H14  0.020
 JCE  plan-3  C10  0.020
 JCE  plan-3  C20  0.020
 JCE  plan-3  C21  0.020
 JCE  plan-3  C05  0.020
 JCE  plan-3  C06  0.020
 JCE  plan-3  C07  0.020
 JCE  plan-3  C08  0.020
 JCE  plan-3  C09  0.020
 JCE  plan-3  N11  0.020
 JCE  plan-3  C12  0.020
 JCE  plan-3  C19  0.020
 JCE  plan-3  H3   0.020
 JCE  plan-3  H4   0.020
 JCE  plan-3  H9   0.020
 JCE  plan-3  H10  0.020
 JCE  plan-3  H15  0.020
 JCE  plan-4  C02  0.020
 JCE  plan-4  H6   0.020
 JCE  plan-4  H7   0.020
 JCE  plan-4  N01  0.020

