# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:50:03 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc(c1)c2ccc3ccn(Cc4ccc(CN5CCCC5)cc4)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
 JFH  JFH  3-[1-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine  ligand  53  28  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JFH
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
 JFH  C10  C  CR56  0   0.418  -1.9645  -2.0781  -0.2518
 JFH  C13  C  CR6   0   0.113   1.1248  -1.5622  -0.9006
 JFH  C15  C  CR16  0  -0.299   2.8003  -1.4485   0.8314
 JFH  C20  C  CH2   0  -0.466   6.8721   2.7658   0.1084
 JFH  C21  C  CH2   0  -0.463   6.8571   1.6330  -0.9414
 JFH  C22  C  CH2   0  -0.272   5.8546   0.6186  -0.3894
 JFH  C24  C  CR16  0  -0.300   1.4006  -0.2362  -1.2158
 JFH  C26  C  CR15  0  -0.431  -2.1061  -4.2026   0.5656
 JFH  C28  C  CR15  0  -0.585  -4.7663   1.9145   0.6929
 JFH  C02  C  CR5   0   0.547  -4.7247   3.1760   0.1294
 JFH  C05  C  CR5   0   0.280  -3.7517   1.1922   0.0259
 JFH  C06  C  CR6   0   0.044  -3.3671  -0.2094   0.2244
 JFH  C07  C  CR16  0  -0.350  -4.1134  -1.0293   1.0970
 JFH  C08  C  CR16  0  -0.325  -3.7974  -2.3564   1.2976
 JFH  C09  C  CR56  0   0.042  -2.7068  -2.9081   0.6177
 JFH  C14  C  CR16  0  -0.270   1.8367  -2.1608   0.1335
 JFH  C16  C  CR6   0   0.085   3.0759  -0.1203   0.5199
 JFH  C19  C  CH2   0  -0.275   5.8767   2.3041   1.1738
 JFH  C23  C  CR16  0  -0.270   2.3649   0.4765  -0.5163
 JFH  C25  C  CR15  0  -0.027  -1.0609  -4.1096  -0.3064
 JFH  C27  C  CR16  0  -0.364  -2.2769  -0.7387  -0.4539
 JFH  N01  N  NH2   0  -0.856  -5.4291   4.3201   0.4166
 JFH  N03  N  NR15  0  -0.481  -3.7407   3.1400  -0.7876
 JFH  N04  N  N     0  -0.329  -3.1405   1.9439  -0.8719
 JFH  N11  N  NR5   0  -0.519  -0.9729  -2.8385  -0.8090
 JFH  N18  N  NT    0  -0.422   4.9808   1.4219   0.4477
 JFH  H1   H  HCR6  0   0.248   3.3527  -1.9373   1.6255
 JFH  H2   H  HCH2  0   0.251   3.5913   1.3524   1.9711
 JFH  H3   H  HCH2  0   0.206   4.6668  -0.0385   1.9493
 JFH  H5   H  HCH2  0   0.234   6.5528   3.7088  -0.3363
 JFH  H6   H  HCH2  0   0.234   6.5308   2.0095  -1.9112
 JFH  H7   H  HCH2  0   0.233   7.8387   1.1826  -1.0854
 JFH  H8   H  HCH2  0   0.235   5.2930   0.1027  -1.1699
 JFH  H9   H  HCH2  0   0.191   6.3779  -0.1517   0.2031
 JFH  H10  H  HCR6  0   0.251   0.8567   0.2482  -2.0189
 JFH  H11  H  HCR5  0   0.247  -2.4126  -5.0885   1.0984
 JFH  H12  H  HCR5  0   0.260  -5.4349   1.5807   1.4690
 JFH  H13  H  HCR6  0   0.242  -4.9634  -0.6108   1.6203
 JFH  H14  H  HCR6  0   0.246  -4.3907  -2.9619   1.9714
 JFH  H17  H  HCR6  0   0.248   1.6475  -3.1950   0.3968
 JFH  H18  H  HCH2  0   0.190   6.4067   1.7681   1.9798
 JFH  H19  H  HCH2  0   0.233   5.3261   3.1256   1.6374
 JFH  H20  H  HCR6  0   0.245   2.5717   1.5055  -0.7828
 JFH  H21  H  HCR5  0   0.287  -0.3589  -4.8653  -0.6248
 JFH  H22  H  HCR6  0   0.250  -1.6953  -0.1146  -1.1201
 JFH  H23  H  HNH2  0   0.390  -6.2867   4.1411   0.9146
 JFH  H24  H  HNH2  0   0.387  -5.6045   4.9214  -0.3749
 JFH  H25  H  HNR5  0   0.413  -3.4431   3.8918  -1.3883
 JFH  C12  C  CH2   0  -0.419   0.0816  -2.3416  -1.6629
 JFH  C17  C  CH2   0  -0.325   4.1051   0.6561   1.2998
 JFH  H4   H  HCH2  0   0.233   7.8616   2.9302   0.5336
 JFH  H15  H  HCH2  0   0.278  -0.3553  -1.7210  -2.4476
 JFH  H16  H  HCH2  0   0.289   0.5314  -3.2031  -2.1582

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
 JFH  N03  N04  aromatic  1.341  0.020  1.341
 JFH  N03  C02  aromatic  1.346  0.020  1.346
 JFH  N04  C05  aromatic  1.321  0.020  1.321
 JFH  N01  C02  single    1.374  0.020  1.374
 JFH  C02  C28  aromatic  1.382  0.020  1.382
 JFH  C05  C28  aromatic  1.413  0.020  1.413
 JFH  C05  C06  single    1.467  0.020  1.467
 JFH  C06  C27  aromatic  1.389  0.020  1.389
 JFH  C06  C07  aromatic  1.411  0.020  1.411
 JFH  C27  C10  aromatic  1.390  0.020  1.390
 JFH  C07  C08  aromatic  1.379  0.020  1.379
 JFH  C08  C09  aromatic  1.399  0.020  1.399
 JFH  C10  C09  aromatic  1.413  0.020  1.413
 JFH  C10  N11  aromatic  1.368  0.020  1.368
 JFH  C12  N11  single    1.445  0.020  1.445
 JFH  C12  C13  single    1.509  0.020  1.509
 JFH  C09  C26  aromatic  1.428  0.020  1.428
 JFH  N11  C25  aromatic  1.370  0.020  1.370
 JFH  C26  C25  aromatic  1.364  0.020  1.364
 JFH  C24  C13  aromatic  1.391  0.020  1.391
 JFH  C24  C23  aromatic  1.388  0.020  1.388
 JFH  C13  C14  aromatic  1.391  0.020  1.391
 JFH  C23  C16  aromatic  1.391  0.020  1.391
 JFH  C14  C15  aromatic  1.387  0.020  1.387
 JFH  C16  C15  aromatic  1.392  0.020  1.392
 JFH  C16  C17  single    1.507  0.020  1.507
 JFH  C19  C20  single    1.529  0.020  1.529
 JFH  C19  N18  single    1.452  0.020  1.452
 JFH  C17  N18  single    1.442  0.020  1.442
 JFH  C20  C21  single    1.545  0.020  1.545
 JFH  N18  C22  single    1.452  0.020  1.452
 JFH  C21  C22  single    1.529  0.020  1.529
 JFH  C15  H1   single    0.930  0.020  1.080
 JFH  C17  H2   single    0.970  0.020  1.090
 JFH  C17  H3   single    0.970  0.020  1.090
 JFH  C20  H4   single    0.970  0.020  1.090
 JFH  C20  H5   single    0.970  0.020  1.090
 JFH  C21  H6   single    0.970  0.020  1.090
 JFH  C21  H7   single    0.970  0.020  1.090
 JFH  C22  H8   single    0.970  0.020  1.090
 JFH  C22  H9   single    0.970  0.020  1.090
 JFH  C24  H10  single    0.930  0.020  1.080
 JFH  C26  H11  single    0.930  0.020  1.080
 JFH  C28  H12  single    0.930  0.020  1.080
 JFH  C07  H13  single    0.930  0.020  1.080
 JFH  C08  H14  single    0.930  0.020  1.080
 JFH  C12  H15  single    0.970  0.020  1.090
 JFH  C12  H16  single    0.970  0.020  1.090
 JFH  C14  H17  single    0.930  0.020  1.080
 JFH  C19  H18  single    0.970  0.020  1.090
 JFH  C19  H19  single    0.970  0.020  1.090
 JFH  C23  H20  single    0.930  0.020  1.080
 JFH  C25  H21  single    0.930  0.020  1.080
 JFH  C27  H22  single    0.930  0.020  1.080
 JFH  N01  H23  single    0.890  0.020  1.040
 JFH  N01  H24  single    0.890  0.020  1.040
 JFH  N03  H25  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
 JFH  N11  C10  C27  129.73  3.000
 JFH  N11  C10  C09  107.75  3.000
 JFH  C27  C10  C09  122.51  3.000
 JFH  C14  C13  C12  120.48  3.000
 JFH  C14  C13  C24  118.52  3.000
 JFH  C12  C13  C24  121.01  3.000
 JFH  H1   C15  C16  119.57  3.000
 JFH  H1   C15  C14  119.42  3.000
 JFH  C16  C15  C14  121.01  3.000
 JFH  H5   C20  H4   107.14  3.000
 JFH  H5   C20  C19  110.77  3.000
 JFH  H4   C20  C19  111.40  3.000
 JFH  H5   C20  C21  110.75  3.000
 JFH  H4   C20  C21  112.62  3.000
 JFH  C19  C20  C21  104.23  3.000
 JFH  H7   C21  H6   107.15  3.000
 JFH  H7   C21  C22  111.35  3.000
 JFH  H6   C21  C22  110.73  3.000
 JFH  H7   C21  C20  112.60  3.000
 JFH  H6   C21  C20  110.74  3.000
 JFH  C22  C21  C20  104.33  3.000
 JFH  H9   C22  H8   107.33  3.000
 JFH  H9   C22  N18  111.22  3.000
 JFH  H8   C22  N18  111.35  3.000
 JFH  H9   C22  C21  110.24  3.000
 JFH  H8   C22  C21  113.13  3.000
 JFH  N18  C22  C21  103.63  3.000
 JFH  H10  C24  C23  119.50  3.000
 JFH  H10  C24  C13  119.64  3.000
 JFH  C23  C24  C13  120.87  3.000
 JFH  H11  C26  C25  126.13  3.000
 JFH  H11  C26  C09  127.38  3.000
 JFH  C25  C26  C09  106.48  3.000
 JFH  H12  C28  C05  128.85  3.000
 JFH  H12  C28  C02  126.52  3.000
 JFH  C05  C28  C02  104.63  3.000
 JFH  N03  C02  N01  122.67  3.000
 JFH  N01  C02  C28  131.25  3.000
 JFH  N03  C02  C28  105.98  3.000
 JFH  N04  C05  C06  120.96  3.000
 JFH  C06  C05  C28  127.80  3.000
 JFH  N04  C05  C28  111.23  3.000
 JFH  C27  C06  C07  119.72  3.000
 JFH  C07  C06  C05  120.01  3.000
 JFH  C27  C06  C05  120.26  3.000
 JFH  H13  C07  C08  118.80  3.000
 JFH  H13  C07  C06  119.33  3.000
 JFH  C08  C07  C06  121.87  3.000
 JFH  H14  C08  C09  120.60  3.000
 JFH  H14  C08  C07  120.21  3.000
 JFH  C09  C08  C07  119.18  3.000
 JFH  C08  C09  C26  134.69  3.000
 JFH  C26  C09  C10  106.80  3.000
 JFH  C08  C09  C10  118.50  3.000
 JFH  H17  C14  C15  119.28  3.000
 JFH  H17  C14  C13  120.13  3.000
 JFH  C15  C14  C13  120.59  3.000
 JFH  C23  C16  C17  120.90  3.000
 JFH  C17  C16  C15  120.74  3.000
 JFH  C23  C16  C15  118.35  3.000
 JFH  H19  C19  H18  107.31  3.000
 JFH  H19  C19  N18  110.99  3.000
 JFH  H18  C19  N18  111.50  3.000
 JFH  H19  C19  C20  113.37  3.000
 JFH  H18  C19  C20  110.05  3.000
 JFH  N18  C19  C20  103.69  3.000
 JFH  H20  C23  C16  119.56  3.000
 JFH  H20  C23  C24  119.77  3.000
 JFH  C16  C23  C24  120.67  3.000
 JFH  H21  C25  N11  119.98  3.000
 JFH  H21  C25  C26  129.71  3.000
 JFH  N11  C25  C26  110.30  3.000
 JFH  H22  C27  C06  120.17  3.000
 JFH  H22  C27  C10  121.62  3.000
 JFH  C06  C27  C10  118.21  3.000
 JFH  H24  N01  H23  110.21  3.000
 JFH  H24  N01  C02  114.91  3.000
 JFH  H23  N01  C02  113.06  3.000
 JFH  H25  N03  N04  119.74  3.000
 JFH  H25  N03  C02  127.04  3.000
 JFH  N04  N03  C02  113.21  3.000
 JFH  N03  N04  C05  104.94  3.000
 JFH  C25  N11  C12  125.65  3.000
 JFH  C25  N11  C10  108.65  3.000
 JFH  C12  N11  C10  125.34  3.000
 JFH  C19  N18  C22  104.66  3.000
 JFH  C22  N18  C17  114.34  3.000
 JFH  C19  N18  C17  113.69  3.000
 JFH  H16  C12  H15  106.72  3.000
 JFH  H16  C12  N11  107.32  3.000
 JFH  H15  C12  N11  109.16  3.000
 JFH  H16  C12  C13  110.63  3.000
 JFH  H15  C12  C13  110.25  3.000
 JFH  N11  C12  C13  112.55  3.000
 JFH  H3   C17  H2   106.14  3.000
 JFH  H3   C17  N18  111.88  3.000
 JFH  H2   C17  N18  108.03  3.000
 JFH  H3   C17  C16  109.13  3.000
 JFH  H2   C17  C16  108.93  3.000
 JFH  N18  C17  C16  112.49  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
 JFH  CONST_01  C05  C06  C27  C10   180.00   0.0  0
 JFH  CONST_02  C07  C06  C27  C10     0.00   0.0  0
 JFH  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 JFH  CONST_04  C25  C26  C09  C10     0.00   0.0  0
 JFH  CONST_05  C26  C25  N11  C10     0.00   0.0  0
 JFH  CONST_06  C16  C23  C24  C13     0.00   0.0  0
 JFH  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 JFH  CONST_08  C24  C13  C14  C15     0.00   0.0  0
 JFH  CONST_09  C24  C23  C16  C15     0.00   0.0  0
 JFH  CONST_10  C07  C08  C09  C26   180.00   0.0  0
 JFH  CONST_11  C27  C10  C09  C26   180.00   0.0  0
 JFH  CONST_12  N11  C10  C09  C26     0.00   0.0  0
 JFH  CONST_13  N04  N03  C02  C28     0.00   0.0  0
 JFH  CONST_14  N03  N04  C05  C28     0.00   0.0  0
 JFH  CONST_15  C27  C06  C05  C28   180.00   0.0  0
 JFH  CONST_16  C07  C06  C05  C28     0.00   0.0  0
 JFH  CONST_17  C05  N04  N03  C02     0.00   0.0  0
 JFH  CONST_18  N04  C05  C28  C02     0.00   0.0  0
 JFH  CONST_19  C06  C05  C28  C02   180.00   0.0  0
 JFH  CONST_20  N03  C02  C28  C05     0.00   0.0  0
 JFH  CONST_21  C08  C07  C06  C05   180.00   0.0  0
 JFH  CONST_22  N03  N04  C05  C06   180.00   0.0  0
 JFH  CONST_23  C09  C10  C27  C06     0.00   0.0  0
 JFH  CONST_24  N11  C10  C27  C06   180.00   0.0  0
 JFH  CONST_25  C09  C08  C07  C06     0.00   0.0  0
 JFH  CONST_26  N04  C05  C06  C07   180.00   0.0  0
 JFH  CONST_27  C27  C06  C07  C08     0.00   0.0  0
 JFH  CONST_28  C27  C10  C09  C08     0.00   0.0  0
 JFH  CONST_29  N11  C10  C09  C08   180.00   0.0  0
 JFH  CONST_30  C25  C26  C09  C08   180.00   0.0  0
 JFH  CONST_31  C25  N11  C10  C09     0.00   0.0  0
 JFH  CONST_32  N11  C25  C26  C09     0.00   0.0  0
 JFH  CONST_33  C23  C24  C13  C14     0.00   0.0  0
 JFH  CONST_34  C23  C16  C15  C14     0.00   0.0  0
 JFH  CONST_35  C27  C10  N11  C25   180.00   0.0  0
 JFH  CONST_36  N04  C05  C06  C27     0.00   0.0  0
 JFH  CONST_37  C12  C13  C14  C15   180.00   0.0  0
 JFH  CONST_38  C24  C23  C16  C17   180.00   0.0  0
 JFH  CONST_39  C14  C15  C16  C17   180.00   0.0  0
 JFH  CONST_40  C12  N11  C25  C26   180.00   0.0  0
 JFH  CONST_41  N01  C02  C28  C05   180.00   0.0  0
 JFH  CONST_42  C12  N11  C10  C09   180.00   0.0  0
 JFH  CONST_43  C27  C10  N11  C12     0.00   0.0  0
 JFH  CONST_44  C23  C24  C13  C12   180.00   0.0  0
 JFH  CONST_45  N04  N03  C02  N01   180.00   0.0  0
 JFH  CONST_46  H14  C08  C09  C10   180.00   0.0  0
 JFH  CONST_47  H11  C26  C09  C10   180.00   0.0  0
 JFH  CONST_48  H21  C25  N11  C10   180.00   0.0  0
 JFH  CONST_49  H20  C23  C24  C13   180.00   0.0  0
 JFH  CONST_50  H1   C15  C14  C13   180.00   0.0  0
 JFH  CONST_51  H17  C14  C13  C24   180.00   0.0  0
 JFH  CONST_52  H25  N03  C02  C28   180.00   0.0  0
 JFH  CONST_53  H22  C27  C06  C05     0.00   0.0  0
 JFH  CONST_54  H13  C07  C06  C05     0.00   0.0  0
 JFH  CONST_55  H12  C28  C05  C06     0.00   0.0  0
 JFH  CONST_56  H10  C24  C13  C14   180.00   0.0  0
 JFH  Var_01    C22  N18  C19  C20    43.14  30.0  1
 JFH  Var_02    N18  C22  C21  C20    25.50  30.0  1
 JFH  Var_03    N18  C19  C20  C21   -25.56  30.0  1
 JFH  Var_04    C19  N18  C22  C21   -43.09  30.0  1
 JFH  Var_05    C19  C20  C21  C22     0.02  30.0  1
 JFH  Var_06    C13  C12  N11  C10    73.52  30.0  1
 JFH  Var_07    N18  C17  C16  C15   135.23  30.0  2
 JFH  Var_08    C16  C17  N18  C22   -66.91  30.0  1
 JFH  Var_09    N11  C12  C13  C24  -121.11  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
 JFH  plan-1  C28  0.020
 JFH  plan-1  C02  0.020
 JFH  plan-1  C05  0.020
 JFH  plan-1  C06  0.020
 JFH  plan-1  N01  0.020
 JFH  plan-1  N03  0.020
 JFH  plan-1  N04  0.020
 JFH  plan-1  H12  0.020
 JFH  plan-1  H25  0.020
 JFH  plan-2  C13  0.020
 JFH  plan-2  C15  0.020
 JFH  plan-2  C24  0.020
 JFH  plan-2  C14  0.020
 JFH  plan-2  C16  0.020
 JFH  plan-2  C23  0.020
 JFH  plan-2  H1   0.020
 JFH  plan-2  H10  0.020
 JFH  plan-2  H17  0.020
 JFH  plan-2  H20  0.020
 JFH  plan-2  C12  0.020
 JFH  plan-2  C17  0.020
 JFH  plan-3  C10  0.020
 JFH  plan-3  C26  0.020
 JFH  plan-3  C05  0.020
 JFH  plan-3  C06  0.020
 JFH  plan-3  C07  0.020
 JFH  plan-3  C08  0.020
 JFH  plan-3  C09  0.020
 JFH  plan-3  C25  0.020
 JFH  plan-3  C27  0.020
 JFH  plan-3  N11  0.020
 JFH  plan-3  H11  0.020
 JFH  plan-3  H13  0.020
 JFH  plan-3  H14  0.020
 JFH  plan-3  H21  0.020
 JFH  plan-3  H22  0.020
 JFH  plan-3  C12  0.020
 JFH  plan-4  C02  0.020
 JFH  plan-4  N01  0.020
 JFH  plan-4  H23  0.020
 JFH  plan-4  H24  0.020

