# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:25:01 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 3-[1-(phenylmethyl)indol-6-yl]-1~{H}-pyrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c1)c2ccc3ccn(Cc4ccccc4)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
 JDQ  JDQ  3-[1-(phenylmethyl)indol-6-yl]-1~{H}-pyrazol-5-amine  ligand  38  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 OK
;

data_comp_JDQ
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
 JDQ  C10  C  CR56  0   0.043  -0.5991   2.7715   0.2181
 JDQ  C15  C  CR6   0   0.104  -2.8147  -0.8761  -0.6366
 JDQ  C17  C  CR16  0  -0.242  -2.7920  -3.2578  -0.2373
 JDQ  C20  C  CR16  0  -0.282  -3.3154  -0.6819   0.6477
 JDQ  C21  C  CR15  0  -0.028  -2.6608   2.6153  -0.6370
 JDQ  C22  C  CR15  0  -0.431  -1.8374   3.4616   0.0460
 JDQ  C02  C  CR5   0   0.551   4.5359  -1.0902   0.4517
 JDQ  N03  N  NR15  0  -0.482   3.6288  -1.8797  -0.1517
 JDQ  N04  N  N     0  -0.330   2.4393  -1.2843  -0.3217
 JDQ  C05  C  CR5   0   0.283   2.5866  -0.0766   0.1923
 JDQ  C06  C  CR15  0  -0.587   3.8929   0.1087   0.6980
 JDQ  C07  C  CR6   0   0.040   1.4797   0.8863   0.1883
 JDQ  C08  C  CR16  0  -0.350   1.6403   2.1487   0.7976
 JDQ  C09  C  CR16  0  -0.326   0.6257   3.0824   0.8176
 JDQ  C11  C  CR56  0   0.415  -0.7490   1.5053  -0.3897
 JDQ  C12  C  CR16  0  -0.359   0.2702   0.5604  -0.4119
 JDQ  N13  N  NR5   0  -0.528  -2.0134   1.4393  -0.9095
 JDQ  C14  C  CH2   0  -0.385  -2.5855   0.2907  -1.5669
 JDQ  C16  C  CR16  0  -0.307  -2.5511  -2.1710  -1.0687
 JDQ  C18  C  CR16  0  -0.267  -3.2933  -3.0576   1.0410
 JDQ  C19  C  CR16  0  -0.241  -3.5528  -1.7652   1.4815
 JDQ  H1   H  HCR6  0   0.257  -2.5807  -4.2595  -0.5882
 JDQ  H2   H  HCR6  0   0.253  -3.5202   0.3202   1.0056
 JDQ  H3   H  HCR5  0   0.287  -3.6790   2.7595  -0.9642
 JDQ  H4   H  HCR5  0   0.248  -2.0853   4.4559   0.3813
 JDQ  H5   H  HNH2  0   0.390   6.4500  -0.7744   0.9423
 JDQ  H6   H  HNH2  0   0.386   6.1917  -2.2089   0.1527
 JDQ  H7   H  HNR5  0   0.412   3.7621  -2.8273  -0.4662
 JDQ  H8   H  HCR5  0   0.261   4.3197   0.9803   1.1656
 JDQ  H9   H  HCR6  0   0.242   2.5836   2.3960   1.2673
 JDQ  H10  H  HCR6  0   0.246   0.7798   4.0427   1.2942
 JDQ  H11  H  HCR6  0   0.254   0.1360  -0.4072  -0.8793
 JDQ  H12  H  HCH2  0   0.274  -1.9428  -0.0141  -2.3962
 JDQ  H13  H  HCH2  0   0.288  -3.5311   0.6079  -2.0104
 JDQ  H14  H  HCR6  0   0.254  -2.1518  -2.3360  -2.0628
 JDQ  H15  H  HCR6  0   0.256  -3.4774  -3.9023   1.6921
 JDQ  H16  H  HCR6  0   0.256  -3.9422  -1.5992   2.4778
 JDQ  N01  N  NH2   0  -0.857   5.7964  -1.5240   0.7791

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
 JDQ  N03  C02  aromatic  1.345  0.020  1.345
 JDQ  N03  N04  aromatic  1.341  0.020  1.341
 JDQ  N01  C02  single    1.373  0.020  1.373
 JDQ  C02  C06  aromatic  1.383  0.020  1.383
 JDQ  N04  C05  aromatic  1.321  0.020  1.321
 JDQ  C05  C06  aromatic  1.413  0.020  1.413
 JDQ  C05  C07  single    1.467  0.020  1.467
 JDQ  C07  C08  aromatic  1.411  0.020  1.411
 JDQ  C07  C12  aromatic  1.389  0.020  1.389
 JDQ  C08  C09  aromatic  1.379  0.020  1.379
 JDQ  C12  C11  aromatic  1.390  0.020  1.390
 JDQ  C09  C10  aromatic  1.399  0.020  1.399
 JDQ  C11  C10  aromatic  1.413  0.020  1.413
 JDQ  C11  N13  aromatic  1.369  0.020  1.369
 JDQ  C10  C22  aromatic  1.428  0.020  1.428
 JDQ  N13  C14  single    1.442  0.020  1.442
 JDQ  N13  C21  aromatic  1.370  0.020  1.370
 JDQ  C14  C15  single    1.510  0.020  1.510
 JDQ  C22  C21  aromatic  1.364  0.020  1.364
 JDQ  C15  C20  aromatic  1.392  0.020  1.392
 JDQ  C15  C16  aromatic  1.390  0.020  1.390
 JDQ  C20  C19  aromatic  1.387  0.020  1.387
 JDQ  C16  C17  aromatic  1.389  0.020  1.389
 JDQ  C19  C18  aromatic  1.390  0.020  1.390
 JDQ  C17  C18  aromatic  1.388  0.020  1.388
 JDQ  C17  H1   single    0.930  0.020  1.080
 JDQ  C20  H2   single    0.930  0.020  1.080
 JDQ  C21  H3   single    0.930  0.020  1.080
 JDQ  C22  H4   single    0.930  0.020  1.080
 JDQ  N01  H5   single    0.890  0.020  1.040
 JDQ  N01  H6   single    0.890  0.020  1.040
 JDQ  N03  H7   single    0.860  0.020  1.020
 JDQ  C06  H8   single    0.930  0.020  1.080
 JDQ  C08  H9   single    0.930  0.020  1.080
 JDQ  C09  H10  single    0.930  0.020  1.080
 JDQ  C12  H11  single    0.930  0.020  1.080
 JDQ  C14  H12  single    0.970  0.020  1.090
 JDQ  C14  H13  single    0.970  0.020  1.090
 JDQ  C16  H14  single    0.930  0.020  1.080
 JDQ  C18  H15  single    0.930  0.020  1.080
 JDQ  C19  H16  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
 JDQ  C11  C10  C09  118.47  3.000
 JDQ  C11  C10  C22  106.81  3.000
 JDQ  C09  C10  C22  134.72  3.000
 JDQ  C16  C15  C14  119.97  3.000
 JDQ  C16  C15  C20  119.01  3.000
 JDQ  C14  C15  C20  121.02  3.000
 JDQ  H1   C17  C18  120.18  3.000
 JDQ  H1   C17  C16  119.75  3.000
 JDQ  C18  C17  C16  120.07  3.000
 JDQ  H2   C20  C19  119.42  3.000
 JDQ  H2   C20  C15  120.11  3.000
 JDQ  C19  C20  C15  120.47  3.000
 JDQ  H3   C21  N13  120.02  3.000
 JDQ  H3   C21  C22  129.68  3.000
 JDQ  N13  C21  C22  110.30  3.000
 JDQ  H4   C22  C21  126.09  3.000
 JDQ  H4   C22  C10  127.41  3.000
 JDQ  C21  C22  C10  106.50  3.000
 JDQ  C06  C02  N03  105.97  3.000
 JDQ  C06  C02  N01  131.19  3.000
 JDQ  N03  C02  N01  122.73  3.000
 JDQ  H7   N03  N04  119.71  3.000
 JDQ  H7   N03  C02  127.07  3.000
 JDQ  N04  N03  C02  113.22  3.000
 JDQ  C05  N04  N03  104.94  3.000
 JDQ  C07  C05  C06  127.77  3.000
 JDQ  C07  C05  N04  120.99  3.000
 JDQ  C06  C05  N04  111.24  3.000
 JDQ  H8   C06  C05  128.88  3.000
 JDQ  H8   C06  C02  126.49  3.000
 JDQ  C05  C06  C02  104.63  3.000
 JDQ  C12  C07  C08  119.71  3.000
 JDQ  C12  C07  C05  120.28  3.000
 JDQ  C08  C07  C05  120.01  3.000
 JDQ  H9   C08  C09  118.70  3.000
 JDQ  H9   C08  C07  119.41  3.000
 JDQ  C09  C08  C07  121.89  3.000
 JDQ  H10  C09  C08  120.13  3.000
 JDQ  H10  C09  C10  120.69  3.000
 JDQ  C08  C09  C10  119.18  3.000
 JDQ  N13  C11  C12  129.68  3.000
 JDQ  N13  C11  C10  107.74  3.000
 JDQ  C12  C11  C10  122.57  3.000
 JDQ  H11  C12  C11  121.56  3.000
 JDQ  H11  C12  C07  120.27  3.000
 JDQ  C11  C12  C07  118.17  3.000
 JDQ  C14  N13  C11  125.32  3.000
 JDQ  C14  N13  C21  125.95  3.000
 JDQ  C11  N13  C21  108.64  3.000
 JDQ  H13  C14  H12  106.39  3.000
 JDQ  H13  C14  N13  107.31  3.000
 JDQ  H12  C14  N13  109.56  3.000
 JDQ  H13  C14  C15  110.09  3.000
 JDQ  H12  C14  C15  109.96  3.000
 JDQ  N13  C14  C15  113.26  3.000
 JDQ  H14  C16  C17  119.57  3.000
 JDQ  H14  C16  C15  119.79  3.000
 JDQ  C17  C16  C15  120.64  3.000
 JDQ  H15  C18  C19  120.22  3.000
 JDQ  H15  C18  C17  120.20  3.000
 JDQ  C19  C18  C17  119.58  3.000
 JDQ  H16  C19  C18  120.10  3.000
 JDQ  H16  C19  C20  119.66  3.000
 JDQ  C18  C19  C20  120.24  3.000
 JDQ  H6   N01  H5   110.57  3.000
 JDQ  H6   N01  C02  115.23  3.000
 JDQ  H5   N01  C02  113.52  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
 JDQ  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 JDQ  CONST_02  C07  C12  C11  C10    0.00   0.0  0
 JDQ  CONST_03  C21  N13  C11  C10    0.00   0.0  0
 JDQ  CONST_04  N13  C21  C22  C10    0.00   0.0  0
 JDQ  CONST_05  C18  C19  C20  C15    0.00   0.0  0
 JDQ  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 JDQ  CONST_07  C20  C15  C16  C17    0.00   0.0  0
 JDQ  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 JDQ  CONST_09  C12  C11  N13  C21  180.00   0.0  0
 JDQ  CONST_10  C09  C10  C22  C21  180.00   0.0  0
 JDQ  CONST_11  C11  C10  C22  C21    0.00   0.0  0
 JDQ  CONST_12  C08  C09  C10  C22  180.00   0.0  0
 JDQ  CONST_13  C12  C11  C10  C22  180.00   0.0  0
 JDQ  CONST_14  N13  C11  C10  C22    0.00   0.0  0
 JDQ  CONST_15  C11  N13  C21  C22    0.00   0.0  0
 JDQ  CONST_16  C05  N04  N03  C02    0.00   0.0  0
 JDQ  CONST_17  N04  C05  C06  C02    0.00   0.0  0
 JDQ  CONST_18  C07  C05  C06  C02  180.00   0.0  0
 JDQ  CONST_19  C05  C06  C02  N03    0.00   0.0  0
 JDQ  CONST_20  C06  C05  N04  N03    0.00   0.0  0
 JDQ  CONST_21  C07  C05  N04  N03  180.00   0.0  0
 JDQ  CONST_22  C06  C02  N03  N04    0.00   0.0  0
 JDQ  CONST_23  C08  C07  C05  N04  180.00   0.0  0
 JDQ  CONST_24  C12  C07  C05  N04    0.00   0.0  0
 JDQ  CONST_25  C09  C08  C07  C05  180.00   0.0  0
 JDQ  CONST_26  C11  C12  C07  C05  180.00   0.0  0
 JDQ  CONST_27  C08  C07  C05  C06    0.00   0.0  0
 JDQ  CONST_28  C12  C07  C05  C06  180.00   0.0  0
 JDQ  CONST_29  N13  C11  C12  C07  180.00   0.0  0
 JDQ  CONST_30  C11  C12  C07  C08    0.00   0.0  0
 JDQ  CONST_31  C11  C10  C09  C08    0.00   0.0  0
 JDQ  CONST_32  C12  C07  C08  C09    0.00   0.0  0
 JDQ  CONST_33  C12  C11  C10  C09    0.00   0.0  0
 JDQ  CONST_34  N13  C11  C10  C09  180.00   0.0  0
 JDQ  CONST_35  C19  C20  C15  C16    0.00   0.0  0
 JDQ  CONST_36  C19  C18  C17  C16    0.00   0.0  0
 JDQ  CONST_37  C14  N13  C11  C10  180.00   0.0  0
 JDQ  CONST_38  C14  C15  C16  C17  180.00   0.0  0
 JDQ  CONST_39  C14  N13  C21  C22  180.00   0.0  0
 JDQ  CONST_40  N04  N03  C02  N01  180.00   0.0  0
 JDQ  CONST_41  C05  C06  C02  N01  180.00   0.0  0
 JDQ  CONST_42  C14  N13  C11  C12    0.00   0.0  0
 JDQ  CONST_43  C19  C20  C15  C14  180.00   0.0  0
 JDQ  CONST_44  H9   C08  C09  C10  180.00   0.0  0
 JDQ  CONST_45  H11  C12  C11  C10  180.00   0.0  0
 JDQ  CONST_46  H3   C21  C22  C10  180.00   0.0  0
 JDQ  CONST_47  H16  C19  C20  C15  180.00   0.0  0
 JDQ  CONST_48  H1   C17  C16  C15  180.00   0.0  0
 JDQ  CONST_49  H14  C16  C15  C20  180.00   0.0  0
 JDQ  CONST_50  H15  C18  C19  C20  180.00   0.0  0
 JDQ  CONST_51  H10  C09  C10  C22    0.00   0.0  0
 JDQ  CONST_52  H8   C06  C02  N03  180.00   0.0  0
 JDQ  CONST_53  H7   N03  N04  C05  180.00   0.0  0
 JDQ  CONST_54  H4   C22  C10  C09    0.00   0.0  0
 JDQ  CONST_55  H2   C20  C15  C16  180.00   0.0  0
 JDQ  Var_01    C11  N13  C14  C15   67.66  30.0  2
 JDQ  Var_02    N13  C14  C15  C20   41.18  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
 JDQ  plan-1  C02  0.020
 JDQ  plan-1  N03  0.020
 JDQ  plan-1  N04  0.020
 JDQ  plan-1  C05  0.020
 JDQ  plan-1  C06  0.020
 JDQ  plan-1  C07  0.020
 JDQ  plan-1  H7   0.020
 JDQ  plan-1  H8   0.020
 JDQ  plan-1  N01  0.020
 JDQ  plan-2  C15  0.020
 JDQ  plan-2  C17  0.020
 JDQ  plan-2  C20  0.020
 JDQ  plan-2  C14  0.020
 JDQ  plan-2  C16  0.020
 JDQ  plan-2  C18  0.020
 JDQ  plan-2  C19  0.020
 JDQ  plan-2  H1   0.020
 JDQ  plan-2  H2   0.020
 JDQ  plan-2  H14  0.020
 JDQ  plan-2  H15  0.020
 JDQ  plan-2  H16  0.020
 JDQ  plan-3  C10  0.020
 JDQ  plan-3  C21  0.020
 JDQ  plan-3  C22  0.020
 JDQ  plan-3  C05  0.020
 JDQ  plan-3  C07  0.020
 JDQ  plan-3  C08  0.020
 JDQ  plan-3  C09  0.020
 JDQ  plan-3  C11  0.020
 JDQ  plan-3  C12  0.020
 JDQ  plan-3  N13  0.020
 JDQ  plan-3  C14  0.020
 JDQ  plan-3  H3   0.020
 JDQ  plan-3  H4   0.020
 JDQ  plan-3  H9   0.020
 JDQ  plan-3  H10  0.020
 JDQ  plan-3  H11  0.020
 JDQ  plan-4  C02  0.020
 JDQ  plan-4  H5   0.020
 JDQ  plan-4  H6   0.020
 JDQ  plan-4  N01  0.020

