# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:35:40 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-[1-[(3-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cn2ccc3ccc(cc23)c4cc(N)[nH]n4)c1
#
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
 JFE  JFE  3-[1-[(3-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_JFE
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
 JFE  C10  C  CR56  0   0.043   0.2338   2.9882   0.2962
 JFE  C15  C  CR6   0   0.113  -2.2801  -0.1568  -1.3659
 JFE  C17  C  CR16  0  -0.228  -2.5930  -2.5368  -1.3317
 JFE  C20  C  CR16  0  -0.373  -2.9281  -0.0636  -0.1446
 JFE  C22  C  CH3   0  -0.436  -4.5766  -2.1268   2.3439
 JFE  C24  C  CR15  0  -0.430  -0.8461   3.8898   0.0499
 JFE  C02  C  CR5   0   0.550   4.6012  -1.7101   0.7539
 JFE  N03  N  NR15  0  -0.481   3.7429  -2.2198  -0.1482
 JFE  N04  N  N     0  -0.330   2.7141  -1.4034  -0.4186
 JFE  C05  C  CR5   0   0.284   2.9207  -0.3348   0.3294
 JFE  C06  C  CR15  0  -0.587   4.0997  -0.4681   1.0968
 JFE  C07  C  CR6   0   0.041   1.9856   0.7952   0.3027
 JFE  C08  C  CR16  0  -0.348   2.2373   1.9405   1.0875
 JFE  C09  C  CR16  0  -0.327   1.3835   3.0236   1.0918
 JFE  C11  C  CR56  0   0.415  -0.0079   1.8377  -0.4863
 JFE  C12  C  CR16  0  -0.357   0.8486   0.7427  -0.4927
 JFE  N13  N  NR5   0  -0.530  -1.1736   2.0386  -1.1748
 JFE  C14  C  CH2   0  -0.381  -1.7876   1.0867  -2.0666
 JFE  C16  C  CR16  0  -0.331  -2.1079  -1.4029  -1.9625
 JFE  C18  C  CR16  0  -0.394  -3.2450  -2.4544  -0.1077
 JFE  C19  C  CR6   0   0.399  -3.4128  -1.2069   0.4912
 JFE  O21  O  O2    0  -0.473  -4.0276  -1.0098   1.6734
 JFE  C23  C  CR15  0  -0.028  -1.6714   3.2711  -0.8431
 JFE  H1   H  HCR6  0   0.259  -2.4576  -3.5077  -1.7904
 JFE  H2   H  HCR6  0   0.256  -3.0649   0.8998   0.3340
 JFE  H3   H  HCH3  0   0.228  -5.3389  -2.6286   1.7424
 JFE  H4   H  HCH3  0   0.228  -3.8100  -2.8554   2.6203
 JFE  H5   H  HCH3  0   0.259  -5.0404  -1.7466   3.2507
 JFE  H6   H  HCR5  0   0.248  -0.9915   4.8701   0.4745
 JFE  H7   H  HNH2  0   0.386   5.7008  -3.3609   1.1372
 JFE  H8   H  HNH2  0   0.390   6.1457  -2.0104   1.9882
 JFE  H9   H  HNR5  0   0.412   3.8067  -3.1115  -0.6125
 JFE  H10  H  HCR5  0   0.258   4.5326   0.2230   1.8007
 JFE  H11  H  HCR6  0   0.238   3.1251   1.9743   1.7059
 JFE  H12  H  HCR6  0   0.246   1.6051   3.8882   1.7052
 JFE  H13  H  HCR6  0   0.255   0.6398  -0.1327  -1.0947
 JFE  H14  H  HCH2  0   0.275  -1.0823   0.8157  -2.8561
 JFE  H15  H  HCH2  0   0.289  -2.6214   1.5905  -2.5586
 JFE  H16  H  HCR6  0   0.250  -1.5907  -1.4851  -2.9104
 JFE  H17  H  HCR6  0   0.279  -3.6051  -3.3608   0.3591
 JFE  H18  H  HCR5  0   0.287  -2.5942   3.6162  -1.2829
 JFE  N01  N  NH2   0  -0.857   5.7563  -2.3534   1.1242

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
 JFE  O21  C22  single    1.414  0.020  1.414
 JFE  O21  C19  single    1.347  0.020  1.347
 JFE  C18  C19  aromatic  1.394  0.020  1.394
 JFE  C18  C17  aromatic  1.389  0.020  1.389
 JFE  C19  C20  aromatic  1.395  0.020  1.395
 JFE  C17  C16  aromatic  1.385  0.020  1.385
 JFE  C20  C15  aromatic  1.386  0.020  1.386
 JFE  C16  C15  aromatic  1.392  0.020  1.392
 JFE  C15  C14  single    1.510  0.020  1.510
 JFE  C23  C24  aromatic  1.364  0.020  1.364
 JFE  C23  N13  aromatic  1.370  0.020  1.370
 JFE  C24  C10  aromatic  1.428  0.020  1.428
 JFE  C14  N13  single    1.442  0.020  1.442
 JFE  N13  C11  aromatic  1.369  0.020  1.369
 JFE  C10  C11  aromatic  1.412  0.020  1.412
 JFE  C10  C09  aromatic  1.399  0.020  1.399
 JFE  C11  C12  aromatic  1.390  0.020  1.390
 JFE  C09  C08  aromatic  1.379  0.020  1.379
 JFE  C12  C07  aromatic  1.389  0.020  1.389
 JFE  C08  C07  aromatic  1.411  0.020  1.411
 JFE  C07  C05  single    1.467  0.020  1.467
 JFE  C06  C05  aromatic  1.413  0.020  1.413
 JFE  C06  C02  aromatic  1.383  0.020  1.383
 JFE  C05  N04  aromatic  1.321  0.020  1.321
 JFE  C02  N01  single    1.373  0.020  1.373
 JFE  C02  N03  aromatic  1.345  0.020  1.345
 JFE  N04  N03  aromatic  1.341  0.020  1.341
 JFE  C17  H1   single    0.930  0.020  1.080
 JFE  C20  H2   single    0.930  0.020  1.080
 JFE  C22  H3   single    0.970  0.020  1.090
 JFE  C22  H4   single    0.970  0.020  1.090
 JFE  C22  H5   single    0.970  0.020  1.090
 JFE  C24  H6   single    0.930  0.020  1.080
 JFE  N01  H7   single    0.890  0.020  1.040
 JFE  N01  H8   single    0.890  0.020  1.040
 JFE  N03  H9   single    0.860  0.020  1.020
 JFE  C06  H10  single    0.930  0.020  1.080
 JFE  C08  H11  single    0.930  0.020  1.080
 JFE  C09  H12  single    0.930  0.020  1.080
 JFE  C12  H13  single    0.930  0.020  1.080
 JFE  C14  H14  single    0.970  0.020  1.090
 JFE  C14  H15  single    0.970  0.020  1.090
 JFE  C16  H16  single    0.930  0.020  1.080
 JFE  C18  H17  single    0.930  0.020  1.080
 JFE  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
 JFE  C11  C10  C09  118.46  3.000
 JFE  C09  C10  C24  134.73  3.000
 JFE  C11  C10  C24  106.82  3.000
 JFE  C16  C15  C14  119.86  3.000
 JFE  C14  C15  C20  120.41  3.000
 JFE  C16  C15  C20  119.72  3.000
 JFE  H1   C17  C18  119.03  3.000
 JFE  H1   C17  C16  119.83  3.000
 JFE  C18  C17  C16  121.13  3.000
 JFE  H2   C20  C19  118.89  3.000
 JFE  H2   C20  C15  120.51  3.000
 JFE  C19  C20  C15  120.60  3.000
 JFE  H5   C22  H4   108.75  3.000
 JFE  H5   C22  H3   108.78  3.000
 JFE  H4   C22  H3   108.80  3.000
 JFE  H5   C22  O21  106.56  3.000
 JFE  H4   C22  O21  111.98  3.000
 JFE  H3   C22  O21  111.87  3.000
 JFE  H6   C24  C23  126.05  3.000
 JFE  H6   C24  C10  127.45  3.000
 JFE  C23  C24  C10  106.50  3.000
 JFE  C06  C02  N03  105.97  3.000
 JFE  N03  C02  N01  122.69  3.000
 JFE  C06  C02  N01  131.23  3.000
 JFE  H9   N03  N04  119.64  3.000
 JFE  H9   N03  C02  127.16  3.000
 JFE  N04  N03  C02  113.20  3.000
 JFE  C05  N04  N03  104.98  3.000
 JFE  C07  C05  C06  127.91  3.000
 JFE  C06  C05  N04  111.21  3.000
 JFE  C07  C05  N04  120.88  3.000
 JFE  H10  C06  C05  129.03  3.000
 JFE  H10  C06  C02  126.34  3.000
 JFE  C05  C06  C02  104.64  3.000
 JFE  C12  C07  C08  119.70  3.000
 JFE  C08  C07  C05  120.09  3.000
 JFE  C12  C07  C05  120.21  3.000
 JFE  H11  C08  C09  118.78  3.000
 JFE  H11  C08  C07  119.30  3.000
 JFE  C09  C08  C07  121.92  3.000
 JFE  H12  C09  C08  120.13  3.000
 JFE  H12  C09  C10  120.70  3.000
 JFE  C08  C09  C10  119.16  3.000
 JFE  N13  C11  C12  129.64  3.000
 JFE  C12  C11  C10  122.60  3.000
 JFE  N13  C11  C10  107.75  3.000
 JFE  H13  C12  C11  121.38  3.000
 JFE  H13  C12  C07  120.46  3.000
 JFE  C11  C12  C07  118.16  3.000
 JFE  C23  N13  C14  126.08  3.000
 JFE  C14  N13  C11  125.24  3.000
 JFE  C23  N13  C11  108.65  3.000
 JFE  H15  C14  H14  106.37  3.000
 JFE  H15  C14  N13  107.43  3.000
 JFE  H14  C14  N13  109.62  3.000
 JFE  H15  C14  C15  109.89  3.000
 JFE  H14  C14  C15  109.97  3.000
 JFE  N13  C14  C15  113.30  3.000
 JFE  H16  C16  C17  120.25  3.000
 JFE  H16  C16  C15  120.14  3.000
 JFE  C17  C16  C15  119.61  3.000
 JFE  H17  C18  C19  121.65  3.000
 JFE  H17  C18  C17  119.14  3.000
 JFE  C19  C18  C17  119.22  3.000
 JFE  O21  C19  C18  124.26  3.000
 JFE  C18  C19  C20  119.72  3.000
 JFE  O21  C19  C20  116.02  3.000
 JFE  C19  O21  C22  118.55  3.000
 JFE  H18  C23  N13  119.99  3.000
 JFE  H18  C23  C24  129.73  3.000
 JFE  N13  C23  C24  110.28  3.000
 JFE  H8   N01  H7   110.48  3.000
 JFE  H8   N01  C02  113.38  3.000
 JFE  H7   N01  C02  115.15  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
 JFE  CONST_01  N13  C23  C24  C10     0.00   0.0  0
 JFE  CONST_02  C23  N13  C11  C10     0.00   0.0  0
 JFE  CONST_03  C07  C12  C11  C10     0.00   0.0  0
 JFE  CONST_04  C07  C08  C09  C10     0.00   0.0  0
 JFE  CONST_05  C18  C19  C20  C15     0.00   0.0  0
 JFE  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 JFE  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 JFE  CONST_08  C20  C15  C16  C17     0.00   0.0  0
 JFE  CONST_09  C11  N13  C23  C24     0.00   0.0  0
 JFE  CONST_10  N13  C11  C10  C24     0.00   0.0  0
 JFE  CONST_11  C12  C11  C10  C24   180.00   0.0  0
 JFE  CONST_12  C08  C09  C10  C24   180.00   0.0  0
 JFE  CONST_13  C07  C05  C06  C02   180.00   0.0  0
 JFE  CONST_14  N04  C05  C06  C02     0.00   0.0  0
 JFE  CONST_15  C05  N04  N03  C02     0.00   0.0  0
 JFE  CONST_16  C05  C06  C02  N03     0.00   0.0  0
 JFE  CONST_17  C07  C05  N04  N03   180.00   0.0  0
 JFE  CONST_18  C06  C05  N04  N03     0.00   0.0  0
 JFE  CONST_19  C12  C07  C05  N04     0.00   0.0  0
 JFE  CONST_20  C08  C07  C05  N04   180.00   0.0  0
 JFE  CONST_21  C06  C02  N03  N04     0.00   0.0  0
 JFE  CONST_22  C11  C12  C07  C05   180.00   0.0  0
 JFE  CONST_23  C09  C08  C07  C05   180.00   0.0  0
 JFE  CONST_24  C12  C07  C05  C06   180.00   0.0  0
 JFE  CONST_25  C08  C07  C05  C06     0.00   0.0  0
 JFE  CONST_26  N13  C11  C12  C07   180.00   0.0  0
 JFE  CONST_27  C11  C10  C09  C08     0.00   0.0  0
 JFE  CONST_28  C11  C12  C07  C08     0.00   0.0  0
 JFE  CONST_29  C23  C24  C10  C09   180.00   0.0  0
 JFE  CONST_30  N13  C11  C10  C09   180.00   0.0  0
 JFE  CONST_31  C12  C11  C10  C09     0.00   0.0  0
 JFE  CONST_32  C12  C07  C08  C09     0.00   0.0  0
 JFE  CONST_33  C23  C24  C10  C11     0.00   0.0  0
 JFE  CONST_34  C23  N13  C11  C12   180.00   0.0  0
 JFE  CONST_35  C19  C18  C17  C16     0.00   0.0  0
 JFE  CONST_36  C19  C20  C15  C16     0.00   0.0  0
 JFE  CONST_37  C14  N13  C11  C10   180.00   0.0  0
 JFE  CONST_38  O21  C19  C20  C15   180.00   0.0  0
 JFE  CONST_39  O21  C19  C18  C17   180.00   0.0  0
 JFE  CONST_40  C14  C15  C16  C17   180.00   0.0  0
 JFE  CONST_41  C14  N13  C23  C24   180.00   0.0  0
 JFE  CONST_42  C05  C06  C02  N01   180.00   0.0  0
 JFE  CONST_43  N04  N03  C02  N01   180.00   0.0  0
 JFE  CONST_44  C14  N13  C11  C12     0.00   0.0  0
 JFE  CONST_45  C19  C20  C15  C14   180.00   0.0  0
 JFE  CONST_46  H18  C23  C24  C10   180.00   0.0  0
 JFE  CONST_47  H13  C12  C11  C10   180.00   0.0  0
 JFE  CONST_48  H11  C08  C09  C10   180.00   0.0  0
 JFE  CONST_49  H1   C17  C16  C15   180.00   0.0  0
 JFE  CONST_50  H17  C18  C19  C20   180.00   0.0  0
 JFE  CONST_51  H16  C16  C15  C20   180.00   0.0  0
 JFE  CONST_52  H12  C09  C10  C24     0.00   0.0  0
 JFE  CONST_53  H10  C06  C02  N03   180.00   0.0  0
 JFE  CONST_54  H9   N03  N04  C05   180.00   0.0  0
 JFE  CONST_55  H6   C24  C10  C09     0.00   0.0  0
 JFE  CONST_56  H2   C20  C15  C16   180.00   0.0  0
 JFE  Var_01    C23  N13  C14  C15  -111.92  30.0  2
 JFE  Var_02    N13  C14  C15  C20    41.79  30.0  2
 JFE  Var_03    C18  C19  O21  C22    -1.87  30.0  2
 JFE  Var_04    H3   C22  O21  C19   -59.82  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
 JFE  plan-1  C02  0.020
 JFE  plan-1  N03  0.020
 JFE  plan-1  N04  0.020
 JFE  plan-1  C05  0.020
 JFE  plan-1  C06  0.020
 JFE  plan-1  C07  0.020
 JFE  plan-1  H9   0.020
 JFE  plan-1  H10  0.020
 JFE  plan-1  N01  0.020
 JFE  plan-2  C15  0.020
 JFE  plan-2  C17  0.020
 JFE  plan-2  C20  0.020
 JFE  plan-2  C14  0.020
 JFE  plan-2  C16  0.020
 JFE  plan-2  C18  0.020
 JFE  plan-2  C19  0.020
 JFE  plan-2  O21  0.020
 JFE  plan-2  H1   0.020
 JFE  plan-2  H2   0.020
 JFE  plan-2  H16  0.020
 JFE  plan-2  H17  0.020
 JFE  plan-3  C10  0.020
 JFE  plan-3  C24  0.020
 JFE  plan-3  C05  0.020
 JFE  plan-3  C07  0.020
 JFE  plan-3  C08  0.020
 JFE  plan-3  C09  0.020
 JFE  plan-3  C11  0.020
 JFE  plan-3  C12  0.020
 JFE  plan-3  N13  0.020
 JFE  plan-3  C14  0.020
 JFE  plan-3  C23  0.020
 JFE  plan-3  H6   0.020
 JFE  plan-3  H11  0.020
 JFE  plan-3  H12  0.020
 JFE  plan-3  H13  0.020
 JFE  plan-3  H18  0.020
 JFE  plan-4  C02  0.020
 JFE  plan-4  H7   0.020
 JFE  plan-4  H8   0.020
 JFE  plan-4  N01  0.020

