# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:10:32 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-[5-[4-fluoranyl-2-(2-imidazol-1-ylethoxy)phenyl]-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1n[nH]c2ccc(cc12)c3ccc(F)cc3OCCn4ccnc4
#
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
 NZE  NZE  1-[5-[4-fluoranyl-2-(2-imidazol-1-ylethoxy)phenyl]-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine  ligand  50  28  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NZE
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
 NZE  C2   C  CH2   0  -0.403  28.1696  42.2177  68.0612
 NZE  C4   C  CR56  0   0.401  28.9143  43.4426  64.6359
 NZE  C5   C  CR16  0  -0.277  28.5849  43.7777  63.3179
 NZE  C1   C  CH3   0  -0.522  27.3701  40.0592  67.2910
 NZE  C3   C  CR5   0   0.203  28.6773  42.7519  66.7539
 NZE  C8   C  CR16  0  -0.383  26.6242  42.8157  65.1328
 NZE  C14  C  CR16  0  -0.542  22.8340  43.8442  62.4124
 NZE  C15  C  CR6   0   0.384  24.1492  44.0327  62.8272
 NZE  C16  C  CH2   0  -0.196  24.1508  46.2956  62.0888
 NZE  C18  C  CR15  0  -0.108  26.4793  46.8483  60.0165
 NZE  C13  C  CR6   0   0.547  22.2623  42.5937  62.5632
 NZE  C12  C  CR16  0  -0.433  22.9382  41.5256  63.1084
 NZE  C11  C  CR16  0  -0.268  24.2515  41.7370  63.5108
 NZE  O    O  O2    0  -0.456  24.7775  45.2175  62.7529
 NZE  C17  C  CH2   0  -0.340  25.1290  47.4491  62.0522
 NZE  N3   N  NR5   0  -0.394  26.3502  47.1226  61.3503
 NZE  C20  C  CR15  0   0.112  27.5708  46.9669  61.9040
 NZE  N4   N  N     0  -0.455  28.4710  46.6223  61.0199
 NZE  C19  C  CR15  0  -0.213  27.7975  46.5429  59.8335
 NZE  C10  C  CR6   0  -0.063  24.8824  42.9677  63.3796
 NZE  C7   C  CR6   0   0.077  26.2788  43.1456  63.8373
 NZE  C6   C  CR16  0  -0.286  27.2726  43.6197  62.9440
 NZE  C9   C  CR56  0  -0.077  27.9561  42.9604  65.5409
 NZE  N2   N  NR15  0  -0.552  30.0780  43.4895  65.3227
 NZE  N1   N  N     0  -0.241  29.9371  43.0822  66.5864
 NZE  N    N  NT    0  -0.385  28.2128  40.7743  68.2225
 NZE  C    C  CH3   0  -0.516  29.5558  40.2419  68.2542
 NZE  H1   H  HCH2  0   0.252  28.7502  42.6644  68.8721
 NZE  H2   H  HCH2  0   0.248  27.1341  42.5424  68.1970
 NZE  H3   H  HCR6  0   0.263  29.3215  44.1535  62.6205
 NZE  H4   H  HCH3  0   0.234  27.3195  39.0071  67.5770
 NZE  H5   H  HCH3  0   0.231  26.3551  40.4590  67.3191
 NZE  H6   H  HCH3  0   0.196  27.7180  40.0998  66.2483
 NZE  H7   H  HCR6  0   0.253  25.8703  42.4633  65.8266
 NZE  H8   H  HCR6  0   0.300  22.2409  44.6448  61.9908
 NZE  H9   H  HCH2  0   0.251  23.2485  46.6190  62.6184
 NZE  H10  H  HCH2  0   0.244  23.8599  46.0091  61.0723
 NZE  H12  H  HCR6  0   0.275  22.4681  40.5571  63.2106
 NZE  H13  H  HCR6  0   0.264  24.8102  40.9092  63.9292
 NZE  H14  H  HCH2  0   0.279  25.3939  47.7571  63.0635
 NZE  H15  H  HCH2  0   0.281  24.6427  48.2977  61.5697
 NZE  H16  H  HCR5  0   0.278  27.7413  47.1193  62.9593
 NZE  H17  H  HCR5  0   0.248  28.2924  46.2778  58.9118
 NZE  H18  H  HCR6  0   0.249  26.9930  43.8574  61.9261
 NZE  H19  H  HNR5  0   0.413  30.9780  43.8006  64.9950
 NZE  H21  H  HCH3  0   0.229  30.1482  40.7631  69.0081
 NZE  H22  H  HCH3  0   0.229  29.5210  39.1867  68.5306
 NZE  H23  H  HCH3  0   0.194  30.0929  40.3141  67.2975
 NZE  F    F  F     0  -0.315  20.9922  42.4312  62.1601
 NZE  H11  H  HCR5  0   0.289  25.6479  46.8996  59.3328

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
 NZE  C19  C18  aromatic  1.365  0.020  1.365
 NZE  C19  N4   aromatic  1.366  0.020  1.366
 NZE  C18  N3   aromatic  1.368  0.020  1.368
 NZE  N4   C20  aromatic  1.308  0.020  1.308
 NZE  N3   C17  single    1.446  0.020  1.446
 NZE  N3   C20  aromatic  1.349  0.020  1.349
 NZE  C16  C17  single    1.513  0.020  1.513
 NZE  C16  O    single    1.413  0.020  1.413
 NZE  C14  C15  aromatic  1.392  0.020  1.392
 NZE  C14  C13  aromatic  1.383  0.020  1.383
 NZE  F    C13  single    1.342  0.020  1.342
 NZE  O    C15  single    1.343  0.020  1.343
 NZE  C6   C5   aromatic  1.374  0.020  1.374
 NZE  C6   C7   aromatic  1.418  0.020  1.418
 NZE  C15  C10  aromatic  1.406  0.020  1.406
 NZE  C13  C12  aromatic  1.377  0.020  1.377
 NZE  C5   C4   aromatic  1.399  0.020  1.399
 NZE  C10  C11  aromatic  1.389  0.020  1.389
 NZE  C10  C7   single    1.480  0.020  1.480
 NZE  C12  C11  aromatic  1.390  0.020  1.390
 NZE  C7   C8   aromatic  1.381  0.020  1.381
 NZE  C4   N2   aromatic  1.352  0.020  1.352
 NZE  C4   C9   aromatic  1.403  0.020  1.403
 NZE  N2   N1   aromatic  1.335  0.020  1.335
 NZE  C8   C9   aromatic  1.400  0.020  1.400
 NZE  C9   C3   aromatic  1.427  0.020  1.427
 NZE  N1   C3   aromatic  1.313  0.020  1.313
 NZE  C3   C2   single    1.501  0.020  1.501
 NZE  C1   N    single    1.445  0.020  1.445
 NZE  C2   N    single    1.453  0.020  1.453
 NZE  C    N    single    1.445  0.020  1.445
 NZE  C2   H1   single    0.970  0.020  1.090
 NZE  C2   H2   single    0.970  0.020  1.090
 NZE  C5   H3   single    0.930  0.020  1.080
 NZE  C1   H4   single    0.970  0.020  1.090
 NZE  C1   H5   single    0.970  0.020  1.090
 NZE  C1   H6   single    0.970  0.020  1.090
 NZE  C8   H7   single    0.930  0.020  1.080
 NZE  C14  H8   single    0.930  0.020  1.080
 NZE  C16  H9   single    0.970  0.020  1.090
 NZE  C16  H10  single    0.970  0.020  1.090
 NZE  C18  H11  single    0.930  0.020  1.080
 NZE  C12  H12  single    0.930  0.020  1.080
 NZE  C11  H13  single    0.930  0.020  1.080
 NZE  C17  H14  single    0.970  0.020  1.090
 NZE  C17  H15  single    0.970  0.020  1.090
 NZE  C20  H16  single    0.930  0.020  1.080
 NZE  C19  H17  single    0.930  0.020  1.080
 NZE  C6   H18  single    0.930  0.020  1.080
 NZE  N2   H19  single    0.860  0.020  1.020
 NZE  C    H21  single    0.970  0.020  1.090
 NZE  C    H22  single    0.970  0.020  1.090
 NZE  C    H23  single    0.970  0.020  1.090

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
 NZE  H2   C2   H1   106.83  3.000
 NZE  H2   C2   N    108.02  3.000
 NZE  H1   C2   N    107.93  3.000
 NZE  H2   C2   C3   108.83  3.000
 NZE  H1   C2   C3   108.73  3.000
 NZE  N    C2   C3   116.12  3.000
 NZE  N2   C4   C9   105.78  3.000
 NZE  C9   C4   C5   121.93  3.000
 NZE  N2   C4   C5   132.29  3.000
 NZE  H3   C5   C6   121.00  3.000
 NZE  H3   C5   C4   122.01  3.000
 NZE  C6   C5   C4   116.99  3.000
 NZE  H6   C1   H5   107.76  3.000
 NZE  H6   C1   H4   107.37  3.000
 NZE  H5   C1   H4   107.66  3.000
 NZE  H6   C1   N    114.10  3.000
 NZE  H5   C1   N    110.15  3.000
 NZE  H4   C1   N    109.58  3.000
 NZE  N1   C3   C9   109.87  3.000
 NZE  N1   C3   C2   121.68  3.000
 NZE  C9   C3   C2   128.44  3.000
 NZE  H7   C8   C9   120.58  3.000
 NZE  H7   C8   C7   120.29  3.000
 NZE  C9   C8   C7   119.12  3.000
 NZE  H8   C14  C13  119.01  3.000
 NZE  H8   C14  C15  122.26  3.000
 NZE  C13  C14  C15  118.72  3.000
 NZE  C10  C15  O    116.48  3.000
 NZE  C10  C15  C14  120.48  3.000
 NZE  O    C15  C14  123.03  3.000
 NZE  H10  C16  H9   107.90  3.000
 NZE  H10  C16  C17  110.40  3.000
 NZE  H9   C16  C17  108.62  3.000
 NZE  H10  C16  O    110.76  3.000
 NZE  H9   C16  O    111.31  3.000
 NZE  C17  C16  O    107.84  3.000
 NZE  H11  C18  C19  132.10  3.000
 NZE  H11  C18  N3   122.43  3.000
 NZE  C19  C18  N3   105.47  3.000
 NZE  C12  C13  F    119.31  3.000
 NZE  C12  C13  C14  122.80  3.000
 NZE  F    C13  C14  117.89  3.000
 NZE  H12  C12  C11  121.31  3.000
 NZE  H12  C12  C13  121.26  3.000
 NZE  C11  C12  C13  117.43  3.000
 NZE  H13  C11  C10  118.65  3.000
 NZE  H13  C11  C12  118.89  3.000
 NZE  C10  C11  C12  122.45  3.000
 NZE  C16  O    C15  119.44  3.000
 NZE  H15  C17  H14  107.40  3.000
 NZE  H15  C17  N3   109.73  3.000
 NZE  H14  C17  N3   108.00  3.000
 NZE  H15  C17  C16  108.40  3.000
 NZE  H14  C17  C16  110.49  3.000
 NZE  N3   C17  C16  112.68  3.000
 NZE  C20  N3   C17  126.22  3.000
 NZE  C20  N3   C18  106.95  3.000
 NZE  C17  N3   C18  126.76  3.000
 NZE  H16  C20  N4   126.10  3.000
 NZE  H16  C20  N3   121.84  3.000
 NZE  N4   C20  N3   112.06  3.000
 NZE  C19  N4   C20  105.24  3.000
 NZE  H17  C19  N4   121.99  3.000
 NZE  H17  C19  C18  127.74  3.000
 NZE  N4   C19  C18  110.27  3.000
 NZE  C7   C10  C11  120.38  3.000
 NZE  C7   C10  C15  121.49  3.000
 NZE  C11  C10  C15  118.12  3.000
 NZE  C6   C7   C10  120.44  3.000
 NZE  C10  C7   C8   119.83  3.000
 NZE  C6   C7   C8   119.71  3.000
 NZE  H18  C6   C7   119.01  3.000
 NZE  H18  C6   C5   118.53  3.000
 NZE  C7   C6   C5   122.45  3.000
 NZE  C8   C9   C3   135.52  3.000
 NZE  C3   C9   C4   104.68  3.000
 NZE  C8   C9   C4   119.80  3.000
 NZE  H19  N2   N1   119.77  3.000
 NZE  H19  N2   C4   127.92  3.000
 NZE  N1   N2   C4   112.30  3.000
 NZE  N2   N1   C3   107.38  3.000
 NZE  C    N    C1   111.95  3.000
 NZE  C    N    C2   113.34  3.000
 NZE  C1   N    C2   113.74  3.000
 NZE  H23  C    H22  107.42  3.000
 NZE  H23  C    H21  107.73  3.000
 NZE  H22  C    H21  107.71  3.000
 NZE  H23  C    N    114.25  3.000
 NZE  H22  C    N    109.40  3.000
 NZE  H21  C    N    110.10  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
 NZE  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 NZE  CONST_02  C3   N1   N2   C4      0.00   0.0  0
 NZE  CONST_03  C7   C8   C9   C4      0.00   0.0  0
 NZE  CONST_04  N1   C3   C9   C4      0.00   0.0  0
 NZE  CONST_05  C10  C7   C6   C5    180.00   0.0  0
 NZE  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 NZE  CONST_07  N1   N2   C4   C5    180.00   0.0  0
 NZE  CONST_08  C8   C9   C4   C5      0.00   0.0  0
 NZE  CONST_09  C3   C9   C4   C5    180.00   0.0  0
 NZE  CONST_10  N2   C4   C9   C3      0.00   0.0  0
 NZE  CONST_11  C7   C8   C9   C3    180.00   0.0  0
 NZE  CONST_14  N2   C4   C9   C8    180.00   0.0  0
 NZE  CONST_15  N1   C3   C9   C8    180.00   0.0  0
 NZE  CONST_16  C11  C10  C15  C14     0.00   0.0  0
 NZE  CONST_17  C7   C10  C15  C14   180.00   0.0  0
 NZE  CONST_18  C11  C12  C13  C14     0.00   0.0  0
 NZE  CONST_19  C12  C13  C14  C15     0.00   0.0  0
 NZE  CONST_20  C12  C11  C10  C15     0.00   0.0  0
 NZE  CONST_22  C20  N4   C19  C18     0.00   0.0  0
 NZE  CONST_23  N4   C20  N3   C18     0.00   0.0  0
 NZE  CONST_24  C10  C15  C14  C13     0.00   0.0  0
 NZE  CONST_25  C10  C11  C12  C13     0.00   0.0  0
 NZE  CONST_26  C7   C10  C11  C12   180.00   0.0  0
 NZE  CONST_28  N4   C19  C18  N3      0.00   0.0  0
 NZE  CONST_29  C19  N4   C20  N3      0.00   0.0  0
 NZE  CONST_30  C19  C18  N3   C20     0.00   0.0  0
 NZE  CONST_31  C9   C8   C7   C10   180.00   0.0  0
 NZE  CONST_32  N2   C4   C5   C6    180.00   0.0  0
 NZE  CONST_33  C9   C4   C5   C6      0.00   0.0  0
 NZE  CONST_34  C9   C8   C7   C6      0.00   0.0  0
 NZE  CONST_35  N1   N2   C4   C9      0.00   0.0  0
 NZE  CONST_36  N2   N1   C3   C9      0.00   0.0  0
 NZE  CONST_37  C4   C9   C3   C2    180.00   0.0  0
 NZE  CONST_38  C8   C9   C3   C2      0.00   0.0  0
 NZE  CONST_39  N2   N1   C3   C2    180.00   0.0  0
 NZE  CONST_40  F    C13  C14  C15   180.00   0.0  0
 NZE  CONST_41  C11  C12  C13  F     180.00   0.0  0
 NZE  CONST_42  O    C15  C14  C13   180.00   0.0  0
 NZE  CONST_43  O    C15  C10  C11   180.00   0.0  0
 NZE  CONST_44  C7   C10  C15  O       0.00   0.0  0
 NZE  CONST_45  C19  C18  N3   C17   180.00   0.0  0
 NZE  CONST_46  N4   C20  N3   C17   180.00   0.0  0
 NZE  CONST_47  H18  C6   C5   C4    180.00   0.0  0
 NZE  CONST_48  H7   C8   C9   C4    180.00   0.0  0
 NZE  CONST_49  H19  N2   C4   C5      0.00   0.0  0
 NZE  CONST_50  H12  C12  C13  C14   180.00   0.0  0
 NZE  CONST_51  H13  C11  C10  C15   180.00   0.0  0
 NZE  CONST_52  H16  C20  N3   C18   180.00   0.0  0
 NZE  CONST_53  H8   C14  C13  C12   180.00   0.0  0
 NZE  CONST_54  H17  C19  C18  N3    180.00   0.0  0
 NZE  CONST_55  H11  C18  N3   C20   180.00   0.0  0
 NZE  CONST_56  H3   C5   C6   C7    180.00   0.0  0
 NZE  Var_01    C18  N3   C17  C16    66.14  30.0  2
 NZE  Var_02    C10  C15  O    C16   173.71  30.0  2
 NZE  Var_03    N    C2   C3   C9     88.45  30.0  2
 NZE  Var_04    C3   C2   N    C1    -63.62  30.0  2
 NZE  Var_05    C17  C16  O    C15  -174.98  30.0  2
 NZE  Var_06    N3   C17  C16  O      60.17  30.0  3
 NZE  Var_07    H4   C1   N    C2   -170.39  30.0  3
 NZE  Var_08    H21  C    N    C2     53.10  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
 NZE  plan-1  C18  0.020
 NZE  plan-1  C17  0.020
 NZE  plan-1  N3   0.020
 NZE  plan-1  C20  0.020
 NZE  plan-1  N4   0.020
 NZE  plan-1  C19  0.020
 NZE  plan-1  H16  0.020
 NZE  plan-1  H17  0.020
 NZE  plan-1  H11  0.020
 NZE  plan-2  C14  0.020
 NZE  plan-2  C15  0.020
 NZE  plan-2  C13  0.020
 NZE  plan-2  C12  0.020
 NZE  plan-2  C11  0.020
 NZE  plan-2  O    0.020
 NZE  plan-2  C10  0.020
 NZE  plan-2  C7   0.020
 NZE  plan-2  H8   0.020
 NZE  plan-2  H12  0.020
 NZE  plan-2  H13  0.020
 NZE  plan-2  F    0.020
 NZE  plan-3  C2   0.020
 NZE  plan-3  C4   0.020
 NZE  plan-3  C5   0.020
 NZE  plan-3  C3   0.020
 NZE  plan-3  C8   0.020
 NZE  plan-3  C10  0.020
 NZE  plan-3  C7   0.020
 NZE  plan-3  C6   0.020
 NZE  plan-3  C9   0.020
 NZE  plan-3  N2   0.020
 NZE  plan-3  N1   0.020
 NZE  plan-3  H3   0.020
 NZE  plan-3  H7   0.020
 NZE  plan-3  H18  0.020
 NZE  plan-3  H19  0.020

