# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:24:34 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 1-[5-(4-fluoranyl-2-methyl-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)cc3C
#
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
 9K2  9K2  1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine  ligand  39  21  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9K2
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
 9K2  N1   N  N     0  -0.242  -3.8297   1.1002   0.0990
 9K2  C2   C  CH2   0  -0.359  -3.3943  -1.1460   0.9833
 9K2  C3   C  CR5   0   0.204  -2.9642   0.1663   0.4131
 9K2  C6   C  CR16  0  -0.297   0.5243   2.0977  -0.7301
 9K2  C8   C  CR16  0  -0.384  -0.3588   0.0551   0.2211
 9K2  C9   C  CR56  0  -0.078  -1.6423   0.6039   0.1111
 9K2  C10  C  CR6   0   0.033   2.0922   0.2301  -0.1209
 9K2  C11  C  CR16  0  -0.272   2.3584  -0.9683  -0.7816
 9K2  C12  C  CR16  0  -0.419   3.6117  -1.5607  -0.7489
 9K2  C13  C  CR6   0   0.533   4.6038  -0.9233  -0.0341
 9K2  F    F  F     0  -0.318   5.8312  -1.4687   0.0122
 9K2  C14  C  CR16  0  -0.454   4.3772   0.2583   0.6426
 9K2  C15  C  CR6   0   0.088   3.1174   0.8510   0.6097
 9K2  C7   C  CR6   0   0.029   0.7262   0.8008  -0.1950
 9K2  C5   C  CR16  0  -0.281  -0.7230   2.6615  -0.8520
 9K2  C4   C  CR56  0   0.404  -1.8094   1.8927  -0.4199
 9K2  N2   N  NR15  0  -0.547  -3.1406   2.1278  -0.4003
 9K2  N    N  NT    0  -0.402  -3.9891  -2.0208  -0.0137
 9K2  C1   C  CH3   0  -0.524  -3.0430  -2.4085  -1.0370
 9K2  C    C  CH3   0  -0.524  -4.5790  -3.1832   0.6138
 9K2  H2   H  HCH2  0   0.213  -2.5296  -1.6177   1.4807
 9K2  H3   H  HCH2  0   0.256  -4.1392  -0.9721   1.7637
 9K2  H4   H  HCR6  0   0.257   1.3846   2.6594  -1.0719
 9K2  H5   H  HCR6  0   0.250  -0.2137  -0.9356   0.6359
 9K2  H6   H  HCR6  0   0.259   1.5691  -1.4454  -1.3489
 9K2  H7   H  HCR6  0   0.277   3.8067  -2.4888  -1.2697
 9K2  H8   H  HCH3  0   0.252   2.9215   2.9968   0.7285
 9K2  H9   H  HCH3  0   0.249   1.9257   2.1251   1.8805
 9K2  H10  H  HCH3  0   0.255   3.6662   2.2556   2.1346
 9K2  H11  H  HCR6  0   0.271   5.1784   0.7153   1.2107
 9K2  H12  H  HCR6  0   0.270  -0.8542   3.6493  -1.2732
 9K2  H14  H  HCH3  0   0.191  -2.1846  -2.9757  -0.6416
 9K2  H15  H  HCH3  0   0.237  -3.5401  -3.0346  -1.7789
 9K2  H16  H  HCH3  0   0.239  -2.6506  -1.5318  -1.5535
 9K2  H17  H  HCH3  0   0.234  -5.3368  -2.8768   1.3368
 9K2  H18  H  HCH3  0   0.235  -5.0669  -3.8032  -0.1394
 9K2  H19  H  HCH3  0   0.193  -3.8471  -3.8145   1.1421
 9K2  H1   H  HNR5  0   0.416  -3.6276   2.9561  -0.7010
 9K2  C16  C  CH3   0  -0.745   2.8933   2.1212   1.3792

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
 9K2  C16  C15  single    1.502  0.020  1.502
 9K2  C14  C15  aromatic  1.393  0.020  1.393
 9K2  C14  C13  aromatic  1.380  0.020  1.380
 9K2  C6   C5   aromatic  1.374  0.020  1.374
 9K2  C6   C7   aromatic  1.417  0.020  1.417
 9K2  C15  C10  aromatic  1.404  0.020  1.404
 9K2  F    C13  single    1.344  0.020  1.344
 9K2  C5   C4   aromatic  1.399  0.020  1.399
 9K2  C13  C12  aromatic  1.379  0.020  1.379
 9K2  C10  C7   single    1.482  0.020  1.482
 9K2  C10  C11  aromatic  1.394  0.020  1.394
 9K2  C7   C8   aromatic  1.381  0.020  1.381
 9K2  C12  C11  aromatic  1.387  0.020  1.387
 9K2  C4   N2   aromatic  1.352  0.020  1.352
 9K2  C4   C9   aromatic  1.404  0.020  1.404
 9K2  N2   N1   aromatic  1.334  0.020  1.334
 9K2  C8   C9   aromatic  1.400  0.020  1.400
 9K2  C9   C3   aromatic  1.425  0.020  1.425
 9K2  N1   C3   aromatic  1.311  0.020  1.311
 9K2  C3   C2   single    1.494  0.020  1.494
 9K2  C    N    single    1.447  0.020  1.447
 9K2  C2   N    single    1.454  0.020  1.454
 9K2  N    C1   single    1.447  0.020  1.447
 9K2  C2   H2   single    0.970  0.020  1.090
 9K2  C2   H3   single    0.970  0.020  1.090
 9K2  C6   H4   single    0.930  0.020  1.080
 9K2  C8   H5   single    0.930  0.020  1.080
 9K2  C11  H6   single    0.930  0.020  1.080
 9K2  C12  H7   single    0.930  0.020  1.080
 9K2  C16  H8   single    0.970  0.020  1.090
 9K2  C16  H9   single    0.970  0.020  1.090
 9K2  C16  H10  single    0.970  0.020  1.090
 9K2  C14  H11  single    0.930  0.020  1.080
 9K2  C5   H12  single    0.930  0.020  1.080
 9K2  C1   H14  single    0.970  0.020  1.090
 9K2  C1   H15  single    0.970  0.020  1.090
 9K2  C1   H16  single    0.970  0.020  1.090
 9K2  C    H17  single    0.970  0.020  1.090
 9K2  C    H18  single    0.970  0.020  1.090
 9K2  C    H19  single    0.970  0.020  1.090
 9K2  N2   H1   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
 9K2  N2   N1   C3   107.29  3.000
 9K2  H3   C2   H2   106.27  3.000
 9K2  H3   C2   N    107.86  3.000
 9K2  H2   C2   N    111.88  3.000
 9K2  H3   C2   C3   109.21  3.000
 9K2  H2   C2   C3   108.78  3.000
 9K2  N    C2   C3   112.62  3.000
 9K2  C9   C3   C2   128.15  3.000
 9K2  C2   C3   N1   121.79  3.000
 9K2  C9   C3   N1   110.05  3.000
 9K2  H4   C6   C5   118.71  3.000
 9K2  H4   C6   C7   118.73  3.000
 9K2  C5   C6   C7   122.56  3.000
 9K2  H5   C8   C7   120.25  3.000
 9K2  H5   C8   C9   120.74  3.000
 9K2  C7   C8   C9   119.01  3.000
 9K2  C4   C9   C8   119.91  3.000
 9K2  C8   C9   C3   135.51  3.000
 9K2  C4   C9   C3   104.58  3.000
 9K2  C7   C10  C15  121.92  3.000
 9K2  C7   C10  C11  118.90  3.000
 9K2  C15  C10  C11  119.17  3.000
 9K2  H6   C11  C12  118.88  3.000
 9K2  H6   C11  C10  119.20  3.000
 9K2  C12  C11  C10  121.91  3.000
 9K2  H7   C12  C13  121.09  3.000
 9K2  H7   C12  C11  121.20  3.000
 9K2  C13  C12  C11  117.71  3.000
 9K2  C14  C13  F    118.72  3.000
 9K2  F    C13  C12  119.16  3.000
 9K2  C14  C13  C12  122.12  3.000
 9K2  H11  C14  C15  120.13  3.000
 9K2  H11  C14  C13  119.78  3.000
 9K2  C15  C14  C13  120.08  3.000
 9K2  C14  C15  C16  118.87  3.000
 9K2  C14  C15  C10  118.99  3.000
 9K2  C16  C15  C10  122.13  3.000
 9K2  C10  C7   C8   120.08  3.000
 9K2  C8   C7   C6   119.73  3.000
 9K2  C10  C7   C6   120.16  3.000
 9K2  H12  C5   C4   121.85  3.000
 9K2  H12  C5   C6   121.28  3.000
 9K2  C4   C5   C6   116.87  3.000
 9K2  N2   C4   C5   132.33  3.000
 9K2  N2   C4   C9   105.74  3.000
 9K2  C5   C4   C9   121.92  3.000
 9K2  H1   N2   C4   127.95  3.000
 9K2  H1   N2   N1   119.71  3.000
 9K2  C4   N2   N1   112.34  3.000
 9K2  C    N    C1   110.99  3.000
 9K2  C1   N    C2   112.26  3.000
 9K2  C    N    C2   110.66  3.000
 9K2  H16  C1   H15  107.65  3.000
 9K2  H16  C1   H14  107.66  3.000
 9K2  H15  C1   H14  107.67  3.000
 9K2  H16  C1   N    110.79  3.000
 9K2  H15  C1   N    109.69  3.000
 9K2  H14  C1   N    113.18  3.000
 9K2  H19  C    H18  107.61  3.000
 9K2  H19  C    H17  107.74  3.000
 9K2  H18  C    H17  107.85  3.000
 9K2  H19  C    N    113.43  3.000
 9K2  H18  C    N    109.85  3.000
 9K2  H17  C    N    110.18  3.000
 9K2  H10  C16  H9   108.09  3.000
 9K2  H10  C16  H8   107.23  3.000
 9K2  H9   C16  H8   107.12  3.000
 9K2  H10  C16  C15  110.72  3.000
 9K2  H9   C16  C15  111.79  3.000
 9K2  H8   C16  C15  111.67  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
 9K2  CONST_01  C5   C4   N2   N1    180.00   0.0  0
 9K2  CONST_02  C9   C4   N2   N1      0.00   0.0  0
 9K2  CONST_03  C4   C9   C3   N1      0.00   0.0  0
 9K2  CONST_04  C8   C9   C3   N1    180.00   0.0  0
 9K2  CONST_05  C5   C4   C9   C3    180.00   0.0  0
 9K2  CONST_06  N2   C4   C9   C3      0.00   0.0  0
 9K2  CONST_07  C7   C8   C9   C3    180.00   0.0  0
 9K2  CONST_08  C4   N2   N1   C3      0.00   0.0  0
 9K2  CONST_09  N2   C4   C5   C6    180.00   0.0  0
 9K2  CONST_10  C9   C4   C5   C6      0.00   0.0  0
 9K2  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 9K2  CONST_14  C5   C6   C7   C8      0.00   0.0  0
 9K2  CONST_17  C5   C4   C9   C8      0.00   0.0  0
 9K2  CONST_18  N2   C4   C9   C8    180.00   0.0  0
 9K2  CONST_19  C10  C7   C8   C9    180.00   0.0  0
 9K2  CONST_20  N2   N1   C3   C9      0.00   0.0  0
 9K2  CONST_21  C13  C14  C15  C10     0.00   0.0  0
 9K2  CONST_22  C5   C6   C7   C10   180.00   0.0  0
 9K2  CONST_23  C13  C12  C11  C10     0.00   0.0  0
 9K2  CONST_24  C14  C15  C10  C11     0.00   0.0  0
 9K2  CONST_25  C14  C13  C12  C11     0.00   0.0  0
 9K2  CONST_26  C15  C14  C13  C12     0.00   0.0  0
 9K2  CONST_27  C15  C10  C11  C12     0.00   0.0  0
 9K2  CONST_28  C7   C10  C11  C12   180.00   0.0  0
 9K2  CONST_29  C7   C10  C15  C14   180.00   0.0  0
 9K2  CONST_30  C4   C5   C6   C7      0.00   0.0  0
 9K2  CONST_31  C4   C9   C8   C7      0.00   0.0  0
 9K2  CONST_32  C4   C9   C3   C2    180.00   0.0  0
 9K2  CONST_33  C8   C9   C3   C2      0.00   0.0  0
 9K2  CONST_34  N2   N1   C3   C2    180.00   0.0  0
 9K2  CONST_35  C16  C15  C10  C11   180.00   0.0  0
 9K2  CONST_36  F    C13  C12  C11   180.00   0.0  0
 9K2  CONST_37  C16  C15  C14  C13   180.00   0.0  0
 9K2  CONST_38  C7   C10  C15  C16     0.00   0.0  0
 9K2  CONST_39  C15  C14  C13  F     180.00   0.0  0
 9K2  CONST_40  H5   C8   C9   C3      0.00   0.0  0
 9K2  CONST_41  H1   N2   N1   C3    180.00   0.0  0
 9K2  CONST_42  H4   C6   C7   C8    180.00   0.0  0
 9K2  CONST_43  H12  C5   C4   C9    180.00   0.0  0
 9K2  CONST_44  H11  C14  C15  C10   180.00   0.0  0
 9K2  CONST_45  H7   C12  C11  C10   180.00   0.0  0
 9K2  CONST_46  H6   C11  C12  C13   180.00   0.0  0
 9K2  Var_01    N    C2   C3   N1     74.59  30.0  2
 9K2  Var_02    H8   C16  C15  C10   -80.28  30.0  2
 9K2  Var_03    C    N    C2   C3   -170.94  30.0  3
 9K2  Var_04    H17  C    N    C2     58.35  30.0  3
 9K2  Var_05    H14  C1   N    C2     61.64  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
 9K2  plan-1  C10  0.020
 9K2  plan-1  C11  0.020
 9K2  plan-1  C12  0.020
 9K2  plan-1  C13  0.020
 9K2  plan-1  F    0.020
 9K2  plan-1  C14  0.020
 9K2  plan-1  C15  0.020
 9K2  plan-1  C7   0.020
 9K2  plan-1  H6   0.020
 9K2  plan-1  H7   0.020
 9K2  plan-1  H11  0.020
 9K2  plan-1  C16  0.020
 9K2  plan-2  N1   0.020
 9K2  plan-2  C2   0.020
 9K2  plan-2  C3   0.020
 9K2  plan-2  C6   0.020
 9K2  plan-2  C8   0.020
 9K2  plan-2  C9   0.020
 9K2  plan-2  C10  0.020
 9K2  plan-2  C7   0.020
 9K2  plan-2  C5   0.020
 9K2  plan-2  C4   0.020
 9K2  plan-2  N2   0.020
 9K2  plan-2  H4   0.020
 9K2  plan-2  H5   0.020
 9K2  plan-2  H12  0.020
 9K2  plan-2  H1   0.020

