# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:21:53 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-[1-[(4-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cn2ccc3ccc(cc23)c4cc(N)[nH]n4)cc1
#
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
 JCH  JCH  3-[1-[(4-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine  ligand  42  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JCH
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
 JCH  C10  C  CR56  0   0.415  -0.1437  -2.0456  -0.3809
 JCH  C13  C  CR6   0   0.096   2.3904  -0.3743  -1.2411
 JCH  C15  C  CR16  0  -0.331   2.6853   2.0243  -1.1307
 JCH  C20  C  CR16  0  -0.268   3.2184  -0.4984  -0.1332
 JCH  C21  C  CR15  0  -0.026   1.3747  -3.6608  -0.5553
 JCH  C22  C  CR15  0  -0.432   0.4467  -4.1323   0.3265
 JCH  C24  C  CR15  0  -0.586  -4.0255   0.7837   0.8863
 JCH  C02  C  CR5   0   0.549  -4.3898   2.0385   0.4346
 JCH  N03  N  NR15  0  -0.481  -3.4795   2.3752  -0.4973
 JCH  N04  N  N     0  -0.329  -2.5426   1.4344  -0.6857
 JCH  C05  C  CR5   0   0.280  -2.8650   0.4615   0.1473
 JCH  C06  C  CR6   0   0.042  -2.0557  -0.7587   0.2340
 JCH  C07  C  CR16  0  -0.350  -2.4658  -1.8196   1.0686
 JCH  C08  C  CR16  0  -0.326  -1.7301  -2.9800   1.1849
 JCH  C09  C  CR56  0   0.039  -0.5436  -3.1118   0.4560
 JCH  N11  N  NR5   0  -0.524   1.0263  -2.4101  -0.9905
 JCH  C12  C  CH2   0  -0.404   1.7920  -1.5895  -1.9024
 JCH  C14  C  CR16  0  -0.295   2.1338   0.9042  -1.7274
 JCH  C16  C  CR6   0   0.372   3.5154   1.8876  -0.0179
 JCH  O17  O  O2    0  -0.471   4.0097   3.0259   0.5048
 JCH  C18  C  CH3   0  -0.437   4.8817   2.9371   1.6140
 JCH  C19  C  CR16  0  -0.369   3.7806   0.6125   0.4809
 JCH  C23  C  CR16  0  -0.358  -0.8818  -0.8736  -0.4996
 JCH  H1   H  HCR6  0   0.262   2.4740   3.0118  -1.5217
 JCH  H2   H  HCR6  0   0.255   3.4369  -1.4793   0.2729
 JCH  H3   H  HCR5  0   0.286   2.2756  -4.1287  -0.9217
 JCH  H4   H  HCR5  0   0.247   0.4674  -5.0912   0.8192
 JCH  H5   H  HCR5  0   0.261  -4.5265   0.2025   1.6423
 JCH  H6   H  HNH2  0   0.390  -5.8913   2.6107   1.6250
 JCH  H7   H  HNH2  0   0.386  -5.3032   3.8250   0.6647
 JCH  H8   H  HNR5  0   0.412  -3.4448   3.2276  -1.0329
 JCH  H9   H  HCR6  0   0.241  -3.3831  -1.7256   1.6356
 JCH  H10  H  HCR6  0   0.246  -2.0710  -3.7774   1.8335
 JCH  H11  H  HCH2  0   0.274   1.1586  -1.2874  -2.7401
 JCH  H12  H  HCH2  0   0.283   2.5748  -2.2229  -2.3216
 JCH  H13  H  HCR6  0   0.256   1.4874   1.0323  -2.5882
 JCH  H14  H  HCH3  0   0.228   4.3973   2.4818   2.4817
 JCH  H15  H  HCH3  0   0.228   5.7854   2.3697   1.3770
 JCH  H16  H  HCH3  0   0.260   5.1648   3.9556   1.8675
 JCH  H17  H  HCR6  0   0.279   4.4214   0.4648   1.3393
 JCH  H18  H  HCR6  0   0.254  -0.5575  -0.0609  -1.1362
 JCH  N01  N  NH2   0  -0.856  -5.4687   2.8322   0.7374

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
 JCH  N03  N04  aromatic  1.341  0.020  1.341
 JCH  N03  C02  aromatic  1.346  0.020  1.346
 JCH  N01  C02  single    1.373  0.020  1.373
 JCH  N04  C05  aromatic  1.321  0.020  1.321
 JCH  C02  C24  aromatic  1.382  0.020  1.382
 JCH  C05  C24  aromatic  1.413  0.020  1.413
 JCH  C05  C06  single    1.467  0.020  1.467
 JCH  C06  C07  aromatic  1.411  0.020  1.411
 JCH  C06  C23  aromatic  1.389  0.020  1.389
 JCH  C07  C08  aromatic  1.379  0.020  1.379
 JCH  C23  C10  aromatic  1.390  0.020  1.390
 JCH  C08  C09  aromatic  1.399  0.020  1.399
 JCH  C10  C09  aromatic  1.413  0.020  1.413
 JCH  C10  N11  aromatic  1.369  0.020  1.369
 JCH  C09  C22  aromatic  1.428  0.020  1.428
 JCH  N11  C12  single    1.446  0.020  1.446
 JCH  N11  C21  aromatic  1.369  0.020  1.369
 JCH  C12  C13  single    1.507  0.020  1.507
 JCH  C22  C21  aromatic  1.364  0.020  1.364
 JCH  C13  C20  aromatic  1.389  0.020  1.389
 JCH  C13  C14  aromatic  1.392  0.020  1.392
 JCH  C20  C19  aromatic  1.388  0.020  1.388
 JCH  C14  C15  aromatic  1.384  0.020  1.384
 JCH  C19  C16  aromatic  1.395  0.020  1.395
 JCH  C15  C16  aromatic  1.395  0.020  1.395
 JCH  C16  O17  single    1.347  0.020  1.347
 JCH  O17  C18  single    1.414  0.020  1.414
 JCH  C15  H1   single    0.930  0.020  1.080
 JCH  C20  H2   single    0.930  0.020  1.080
 JCH  C21  H3   single    0.930  0.020  1.080
 JCH  C22  H4   single    0.930  0.020  1.080
 JCH  C24  H5   single    0.930  0.020  1.080
 JCH  N01  H6   single    0.890  0.020  1.040
 JCH  N01  H7   single    0.890  0.020  1.040
 JCH  N03  H8   single    0.860  0.020  1.020
 JCH  C07  H9   single    0.930  0.020  1.080
 JCH  C08  H10  single    0.930  0.020  1.080
 JCH  C12  H11  single    0.970  0.020  1.090
 JCH  C12  H12  single    0.970  0.020  1.090
 JCH  C14  H13  single    0.930  0.020  1.080
 JCH  C18  H14  single    0.970  0.020  1.090
 JCH  C18  H15  single    0.970  0.020  1.090
 JCH  C18  H16  single    0.970  0.020  1.090
 JCH  C19  H17  single    0.930  0.020  1.080
 JCH  C23  H18  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
 JCH  C23  C10  N11  129.82  3.000
 JCH  N11  C10  C09  107.74  3.000
 JCH  C23  C10  C09  122.44  3.000
 JCH  C14  C13  C12  120.94  3.000
 JCH  C14  C13  C20  118.09  3.000
 JCH  C12  C13  C20  120.98  3.000
 JCH  H1   C15  C16  119.57  3.000
 JCH  H1   C15  C14  120.31  3.000
 JCH  C16  C15  C14  120.12  3.000
 JCH  H2   C20  C19  118.48  3.000
 JCH  H2   C20  C13  120.00  3.000
 JCH  C19  C20  C13  121.53  3.000
 JCH  H3   C21  N11  120.03  3.000
 JCH  H3   C21  C22  129.60  3.000
 JCH  N11  C21  C22  110.36  3.000
 JCH  H4   C22  C09  127.41  3.000
 JCH  H4   C22  C21  126.12  3.000
 JCH  C09  C22  C21  106.46  3.000
 JCH  H5   C24  C05  128.75  3.000
 JCH  H5   C24  C02  126.62  3.000
 JCH  C05  C24  C02  104.63  3.000
 JCH  N03  C02  N01  122.66  3.000
 JCH  N01  C02  C24  131.27  3.000
 JCH  N03  C02  C24  105.97  3.000
 JCH  H8   N03  N04  119.66  3.000
 JCH  H8   N03  C02  127.11  3.000
 JCH  N04  N03  C02  113.23  3.000
 JCH  C05  N04  N03  104.93  3.000
 JCH  C06  C05  N04  121.02  3.000
 JCH  C06  C05  C24  127.73  3.000
 JCH  N04  C05  C24  111.24  3.000
 JCH  C23  C06  C07  119.73  3.000
 JCH  C23  C06  C05  120.26  3.000
 JCH  C07  C06  C05  120.01  3.000
 JCH  H9   C07  C08  118.75  3.000
 JCH  H9   C07  C06  119.40  3.000
 JCH  C08  C07  C06  121.85  3.000
 JCH  H10  C08  C09  120.65  3.000
 JCH  H10  C08  C07  120.15  3.000
 JCH  C09  C08  C07  119.20  3.000
 JCH  C08  C09  C22  134.66  3.000
 JCH  C22  C09  C10  106.81  3.000
 JCH  C08  C09  C10  118.53  3.000
 JCH  C12  N11  C21  125.73  3.000
 JCH  C21  N11  C10  108.61  3.000
 JCH  C12  N11  C10  125.62  3.000
 JCH  H12  C12  H11  106.38  3.000
 JCH  H12  C12  N11  107.03  3.000
 JCH  H11  C12  N11  109.48  3.000
 JCH  H12  C12  C13  110.60  3.000
 JCH  H11  C12  C13  110.09  3.000
 JCH  N11  C12  C13  113.01  3.000
 JCH  H13  C14  C15  118.97  3.000
 JCH  H13  C14  C13  119.73  3.000
 JCH  C15  C14  C13  121.29  3.000
 JCH  C19  C16  O17  124.35  3.000
 JCH  O17  C16  C15  116.44  3.000
 JCH  C19  C16  C15  119.21  3.000
 JCH  C18  O17  C16  118.55  3.000
 JCH  H16  C18  H15  108.76  3.000
 JCH  H16  C18  H14  108.70  3.000
 JCH  H15  C18  H14  108.80  3.000
 JCH  H16  C18  O17  106.54  3.000
 JCH  H15  C18  O17  111.86  3.000
 JCH  H14  C18  O17  112.06  3.000
 JCH  H17  C19  C16  121.43  3.000
 JCH  H17  C19  C20  118.81  3.000
 JCH  C16  C19  C20  119.76  3.000
 JCH  H18  C23  C06  120.12  3.000
 JCH  H18  C23  C10  121.62  3.000
 JCH  C06  C23  C10  118.26  3.000
 JCH  H7   N01  H6   110.39  3.000
 JCH  H7   N01  C02  115.09  3.000
 JCH  H6   N01  C02  113.37  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
 JCH  CONST_01  C05  C06  C23  C10  180.00   0.0  0
 JCH  CONST_02  C07  C06  C23  C10    0.00   0.0  0
 JCH  CONST_03  C07  C08  C09  C10    0.00   0.0  0
 JCH  CONST_04  C21  C22  C09  C10    0.00   0.0  0
 JCH  CONST_05  C22  C21  N11  C10    0.00   0.0  0
 JCH  CONST_06  C16  C19  C20  C13    0.00   0.0  0
 JCH  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 JCH  CONST_08  C20  C13  C14  C15    0.00   0.0  0
 JCH  CONST_09  C20  C19  C16  C15    0.00   0.0  0
 JCH  CONST_10  C23  C10  N11  C21  180.00   0.0  0
 JCH  CONST_11  C09  C10  N11  C21    0.00   0.0  0
 JCH  CONST_12  C08  C09  C22  C21  180.00   0.0  0
 JCH  CONST_13  C07  C08  C09  C22  180.00   0.0  0
 JCH  CONST_14  C23  C10  C09  C22  180.00   0.0  0
 JCH  CONST_15  N11  C10  C09  C22    0.00   0.0  0
 JCH  CONST_16  N04  N03  C02  C24    0.00   0.0  0
 JCH  CONST_17  N03  N04  C05  C24    0.00   0.0  0
 JCH  CONST_18  C07  C06  C05  C24    0.00   0.0  0
 JCH  CONST_19  C23  C06  C05  C24  180.00   0.0  0
 JCH  CONST_20  C05  N04  N03  C02    0.00   0.0  0
 JCH  CONST_21  N04  C05  C24  C02    0.00   0.0  0
 JCH  CONST_22  C06  C05  C24  C02  180.00   0.0  0
 JCH  CONST_23  C06  C05  N04  N03  180.00   0.0  0
 JCH  CONST_24  C05  C24  C02  N03    0.00   0.0  0
 JCH  CONST_25  C07  C06  C05  N04  180.00   0.0  0
 JCH  CONST_26  C23  C06  C05  N04    0.00   0.0  0
 JCH  CONST_27  C08  C07  C06  C05  180.00   0.0  0
 JCH  CONST_28  C09  C08  C07  C06    0.00   0.0  0
 JCH  CONST_29  C09  C10  C23  C06    0.00   0.0  0
 JCH  CONST_30  N11  C10  C23  C06  180.00   0.0  0
 JCH  CONST_31  C23  C06  C07  C08    0.00   0.0  0
 JCH  CONST_32  C23  C10  C09  C08    0.00   0.0  0
 JCH  CONST_33  N11  C10  C09  C08  180.00   0.0  0
 JCH  CONST_34  N11  C21  C22  C09    0.00   0.0  0
 JCH  CONST_35  C19  C20  C13  C14    0.00   0.0  0
 JCH  CONST_36  C19  C16  C15  C14    0.00   0.0  0
 JCH  CONST_37  C12  C13  C14  C15  180.00   0.0  0
 JCH  CONST_38  O17  C16  C19  C20  180.00   0.0  0
 JCH  CONST_39  C12  N11  C21  C22  180.00   0.0  0
 JCH  CONST_40  N04  N03  C02  N01  180.00   0.0  0
 JCH  CONST_41  C05  C24  C02  N01  180.00   0.0  0
 JCH  CONST_42  C12  N11  C10  C09  180.00   0.0  0
 JCH  CONST_43  C23  C10  N11  C12    0.00   0.0  0
 JCH  CONST_44  C19  C20  C13  C12  180.00   0.0  0
 JCH  CONST_45  O17  C16  C15  C14  180.00   0.0  0
 JCH  CONST_46  H10  C08  C09  C10  180.00   0.0  0
 JCH  CONST_47  H4   C22  C09  C10  180.00   0.0  0
 JCH  CONST_48  H3   C21  N11  C10  180.00   0.0  0
 JCH  CONST_49  H17  C19  C20  C13  180.00   0.0  0
 JCH  CONST_50  H1   C15  C14  C13  180.00   0.0  0
 JCH  CONST_51  H13  C14  C13  C20  180.00   0.0  0
 JCH  CONST_52  H8   N03  C02  C24  180.00   0.0  0
 JCH  CONST_53  H5   C24  C02  N03  180.00   0.0  0
 JCH  CONST_54  H9   C07  C06  C05    0.00   0.0  0
 JCH  CONST_55  H18  C23  C06  C05    0.00   0.0  0
 JCH  CONST_56  H2   C20  C13  C14  180.00   0.0  0
 JCH  Var_01    C13  C12  N11  C10   66.50  30.0  2
 JCH  Var_02    N11  C12  C13  C20   56.17  30.0  3
 JCH  Var_03    C19  C16  O17  C18    1.55  30.0  2
 JCH  Var_04    H14  C18  O17  C16  -61.68  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
 JCH  plan-1  C24  0.020
 JCH  plan-1  C02  0.020
 JCH  plan-1  N03  0.020
 JCH  plan-1  N04  0.020
 JCH  plan-1  C05  0.020
 JCH  plan-1  C06  0.020
 JCH  plan-1  H5   0.020
 JCH  plan-1  H8   0.020
 JCH  plan-1  N01  0.020
 JCH  plan-2  C13  0.020
 JCH  plan-2  C15  0.020
 JCH  plan-2  C20  0.020
 JCH  plan-2  C12  0.020
 JCH  plan-2  C14  0.020
 JCH  plan-2  C16  0.020
 JCH  plan-2  O17  0.020
 JCH  plan-2  C19  0.020
 JCH  plan-2  H1   0.020
 JCH  plan-2  H2   0.020
 JCH  plan-2  H13  0.020
 JCH  plan-2  H17  0.020
 JCH  plan-3  C10  0.020
 JCH  plan-3  C21  0.020
 JCH  plan-3  C22  0.020
 JCH  plan-3  C05  0.020
 JCH  plan-3  C06  0.020
 JCH  plan-3  C07  0.020
 JCH  plan-3  C08  0.020
 JCH  plan-3  C09  0.020
 JCH  plan-3  N11  0.020
 JCH  plan-3  C12  0.020
 JCH  plan-3  C23  0.020
 JCH  plan-3  H3   0.020
 JCH  plan-3  H4   0.020
 JCH  plan-3  H9   0.020
 JCH  plan-3  H10  0.020
 JCH  plan-3  H18  0.020
 JCH  plan-4  C02  0.020
 JCH  plan-4  H6   0.020
 JCH  plan-4  H7   0.020
 JCH  plan-4  N01  0.020

