# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 21:02:19 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: 5-[methyl-[(2-propoxypyridin-3-yl)methyl]amino]-2~{H}-indazole-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1ncccc1CN(C)c2ccc3n[nH]c(C(O)=O)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
 SLJ  SLJ  '5-[methyl-[(2-propoxypyridin-3-yl)methyl]amino]-2~{H}-indazole-3-carboxylic acid'  ligand  44  25  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SLJ
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
 SLJ  C1   C  CH2    0  -0.462  -31.4825  5.9916  -12.3766
 SLJ  C2   C  CH2    0  -0.145  -31.6322  4.6356  -13.0341
 SLJ  C3   C  CR6    0   0.514  -32.6263  3.7465  -15.0057
 SLJ  C7   C  CR6    0  -0.081  -33.3839  3.9869  -16.1684
 SLJ  C8   C  CH2    0  -0.380  -33.8481  5.3879  -16.4981
 SLJ  C9   C  CH3    0  -0.545  -36.1005  5.3051  -17.5026
 SLJ  C10  C  CR6    0   0.389  -34.1157  5.5743  -18.9246
 SLJ  C11  C  CR16   0  -0.467  -32.7525  5.4715  -19.1383
 SLJ  C12  C  CR56   0  -0.058  -32.2555  5.5962  -20.4526
 SLJ  C13  C  CR56   0   0.201  -33.1298  5.8108  -21.5508
 SLJ  C14  C  CR5    0   0.154  -30.9838  5.5463  -21.0353
 SLJ  C15  C  C      0   0.360  -29.5987  5.3450  -20.4958
 SLJ  C16  C  CR16   0  -0.280  -34.5189  5.9038  -21.3284
 SLJ  O2   O  OC    -1  -0.577  -29.5070  5.1900  -19.2647
 SLJ  O1   O  O      0  -0.597  -28.6863  5.3540  -21.3452
 SLJ  N3   N  NR15   0  -0.446  -31.2032  5.7286  -22.3494
 SLJ  N2   N  N      0  -0.311  -32.4589  5.8905  -22.7094
 SLJ  C17  C  CR16   0  -0.351  -34.9833  5.7882  -20.0509
 SLJ  N1   N  NT     0  -0.515  -34.6768  5.4917  -17.6659
 SLJ  C6   C  CR16   0  -0.172  -33.6776  2.8864  -16.9448
 SLJ  C5   C  CR16   0  -0.342  -33.2255  1.6204  -16.5702
 SLJ  C4   C  CR16   0  -0.070  -32.4902  1.5138  -15.4111
 SLJ  N    N  N      0  -0.462  -32.1962  2.5610  -14.6379
 SLJ  O    O  O2     0  -0.477  -32.3523  4.8144  -14.2506
 SLJ  C    C  CH3    0  -0.671  -30.7272  5.8795  -11.0595
 SLJ  H1   H  HCH2   0   0.229  -30.9537  6.6703  -13.0506
 SLJ  H2   H  HCH2   0   0.228  -32.4708  6.4239  -12.2008
 SLJ  H3   H  HCH2   0   0.218  -32.1702  3.9466  -12.3758
 SLJ  H4   H  HCH2   0   0.218  -30.6511  4.1948  -13.2349
 SLJ  H5   H  HCH2   0   0.262  -32.9822  6.0495  -16.6003
 SLJ  H6   H  HCH2   0   0.275  -34.4079  5.7856  -15.6480
 SLJ  H7   H  HCH3   0   0.259  -36.3126  5.1049  -16.4553
 SLJ  H8   H  HCH3   0   0.236  -36.6744  6.1905  -17.7897
 SLJ  H9   H  HCH3   0   0.233  -36.4793  4.4569  -18.0794
 SLJ  H10  H  HCR6   0   0.243  -32.0597  5.2793  -18.3325
 SLJ  H11  H  HCR6   0   0.250  -35.2060  6.0664  -22.1492
 SLJ  H13  H  HNR5   0   0.406  -30.4708  5.7458  -23.0450
 SLJ  H14  H  HCR6   0   0.265  -36.0491  5.8701  -19.8908
 SLJ  H15  H  HCR6   0   0.268  -34.2611  3.0049  -17.8493
 SLJ  H16  H  HCR6   0   0.260  -33.4445  0.7471  -17.1683
 SLJ  H17  H  HCR6   0   0.258  -32.1165  0.5526  -15.0768
 SLJ  H18  H  HCH3   0   0.237  -30.6268  6.8546  -10.5839
 SLJ  H19  H  HCH3   0   0.223  -31.2445  5.2223  -10.3588
 SLJ  H20  H  HCH3   0   0.223  -29.7227  5.4802  -11.2083

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
 SLJ  N2   N3   aromatic  1.316  0.020  1.316
 SLJ  N2   C13  aromatic  1.341  0.020  1.341
 SLJ  N3   C14  aromatic  1.345  0.020  1.345
 SLJ  C13  C16  aromatic  1.410  0.020  1.410
 SLJ  C13  C12  aromatic  1.420  0.020  1.420
 SLJ  C16  C17  aromatic  1.364  0.020  1.364
 SLJ  O1   C15  deloc     1.247  0.020  1.247
 SLJ  C14  C12  aromatic  1.400  0.020  1.400
 SLJ  C14  C15  single    1.500  0.020  1.500
 SLJ  C12  C11  aromatic  1.411  0.020  1.411
 SLJ  C15  O2   deloc     1.244  0.020  1.244
 SLJ  C17  C10  aromatic  1.438  0.020  1.438
 SLJ  C11  C10  aromatic  1.384  0.020  1.384
 SLJ  C10  N1   single    1.381  0.020  1.381
 SLJ  N1   C9   single    1.445  0.020  1.445
 SLJ  N1   C8   single    1.436  0.020  1.436
 SLJ  C6   C5   aromatic  1.396  0.020  1.396
 SLJ  C6   C7   aromatic  1.378  0.020  1.378
 SLJ  C5   C4   aromatic  1.377  0.020  1.377
 SLJ  C8   C7   single    1.512  0.020  1.512
 SLJ  C7   C3   aromatic  1.408  0.020  1.408
 SLJ  C4   N    aromatic  1.335  0.020  1.335
 SLJ  C3   N    aromatic  1.314  0.020  1.314
 SLJ  C3   O    single    1.336  0.020  1.336
 SLJ  O    C2   single    1.425  0.020  1.425
 SLJ  C2   C1   single    1.514  0.020  1.514
 SLJ  C1   C    single    1.522  0.020  1.522
 SLJ  C1   H1   single    0.970  0.020  1.090
 SLJ  C1   H2   single    0.970  0.020  1.090
 SLJ  C2   H3   single    0.970  0.020  1.090
 SLJ  C2   H4   single    0.970  0.020  1.090
 SLJ  C8   H5   single    0.970  0.020  1.090
 SLJ  C8   H6   single    0.970  0.020  1.090
 SLJ  C9   H7   single    0.970  0.020  1.090
 SLJ  C9   H8   single    0.970  0.020  1.090
 SLJ  C9   H9   single    0.970  0.020  1.090
 SLJ  C11  H10  single    0.930  0.020  1.080
 SLJ  C16  H11  single    0.930  0.020  1.080
 SLJ  N3   H13  single    0.860  0.020  1.020
 SLJ  C17  H14  single    0.930  0.020  1.080
 SLJ  C6   H15  single    0.930  0.020  1.080
 SLJ  C5   H16  single    0.930  0.020  1.080
 SLJ  C4   H17  single    0.930  0.020  1.080
 SLJ  C    H18  single    0.970  0.020  1.090
 SLJ  C    H19  single    0.970  0.020  1.090
 SLJ  C    H20  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
 SLJ  H2   C1   H1   106.92  3.000
 SLJ  H2   C1   C    109.79  3.000
 SLJ  H1   C1   C    109.83  3.000
 SLJ  H2   C1   C2   109.55  3.000
 SLJ  H1   C1   C2   109.64  3.000
 SLJ  C    C1   C2   111.02  3.000
 SLJ  H4   C2   H3   107.32  3.000
 SLJ  H4   C2   O    110.31  3.000
 SLJ  H3   C2   O    110.13  3.000
 SLJ  H4   C2   C1   110.59  3.000
 SLJ  H3   C2   C1   110.55  3.000
 SLJ  O    C2   C1   107.95  3.000
 SLJ  O    C3   N    119.73  3.000
 SLJ  O    C3   C7   116.13  3.000
 SLJ  N    C3   C7   124.14  3.000
 SLJ  C6   C7   C8   123.46  3.000
 SLJ  C8   C7   C3   120.21  3.000
 SLJ  C6   C7   C3   116.32  3.000
 SLJ  H6   C8   H5   104.95  3.000
 SLJ  H6   C8   N1   108.10  3.000
 SLJ  H5   C8   N1   109.69  3.000
 SLJ  H6   C8   C7   108.96  3.000
 SLJ  H5   C8   C7   109.72  3.000
 SLJ  N1   C8   C7   114.93  3.000
 SLJ  H9   C9   H8   107.93  3.000
 SLJ  H9   C9   H7   107.32  3.000
 SLJ  H8   C9   H7   107.43  3.000
 SLJ  H9   C9   N1   112.45  3.000
 SLJ  H8   C9   N1   112.51  3.000
 SLJ  H7   C9   N1   108.96  3.000
 SLJ  N1   C10  C17  118.55  3.000
 SLJ  N1   C10  C11  122.46  3.000
 SLJ  C17  C10  C11  118.99  3.000
 SLJ  H10  C11  C12  119.01  3.000
 SLJ  H10  C11  C10  122.01  3.000
 SLJ  C12  C11  C10  118.97  3.000
 SLJ  C14  C12  C13  104.06  3.000
 SLJ  C14  C12  C11  134.81  3.000
 SLJ  C13  C12  C11  121.13  3.000
 SLJ  N2   C13  C16  128.70  3.000
 SLJ  C16  C13  C12  119.65  3.000
 SLJ  N2   C13  C12  111.66  3.000
 SLJ  N3   C14  C15  121.35  3.000
 SLJ  C15  C14  C12  133.95  3.000
 SLJ  N3   C14  C12  104.70  3.000
 SLJ  O1   C15  O2   128.40  3.000
 SLJ  O2   C15  C14  116.14  3.000
 SLJ  O1   C15  C14  115.46  3.000
 SLJ  H11  C16  C17  120.44  3.000
 SLJ  H11  C16  C13  121.04  3.000
 SLJ  C17  C16  C13  118.52  3.000
 SLJ  H13  N3   N2   120.08  3.000
 SLJ  H13  N3   C14  123.84  3.000
 SLJ  N2   N3   C14  116.08  3.000
 SLJ  N3   N2   C13  103.51  3.000
 SLJ  H14  C17  C16  117.90  3.000
 SLJ  H14  C17  C10  119.36  3.000
 SLJ  C16  C17  C10  122.74  3.000
 SLJ  C10  N1   C9   120.74  3.000
 SLJ  C9   N1   C8   117.87  3.000
 SLJ  C10  N1   C8   120.75  3.000
 SLJ  H15  C6   C5   119.87  3.000
 SLJ  H15  C6   C7   119.87  3.000
 SLJ  C5   C6   C7   120.27  3.000
 SLJ  H16  C5   C4   120.76  3.000
 SLJ  H16  C5   C6   121.25  3.000
 SLJ  C4   C5   C6   117.98  3.000
 SLJ  H17  C4   N    116.18  3.000
 SLJ  H17  C4   C5   120.82  3.000
 SLJ  N    C4   C5   123.00  3.000
 SLJ  C4   N    C3   118.28  3.000
 SLJ  C3   O    C2   119.06  3.000
 SLJ  H20  C    H19  107.67  3.000
 SLJ  H20  C    H18  107.59  3.000
 SLJ  H19  C    H18  107.61  3.000
 SLJ  H20  C    C1   111.45  3.000
 SLJ  H19  C    C1   111.39  3.000
 SLJ  H18  C    C1   110.95  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
 SLJ  CONST_01  C5   C6   C7   C3      0.00   0.0  0
 SLJ  CONST_02  C5   C4   N    C3      0.00   0.0  0
 SLJ  CONST_03  C4   C5   C6   C7      0.00   0.0  0
 SLJ  CONST_04  C4   N    C3   C7      0.00   0.0  0
 SLJ  CONST_05  C13  C16  C17  C10     0.00   0.0  0
 SLJ  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 SLJ  CONST_07  C14  C12  C11  C10   180.00   0.0  0
 SLJ  CONST_08  N2   C13  C12  C11   180.00   0.0  0
 SLJ  CONST_09  C16  C13  C12  C11     0.00   0.0  0
 SLJ  CONST_10  N3   C14  C12  C11   180.00   0.0  0
 SLJ  CONST_11  C16  C17  C10  C11     0.00   0.0  0
 SLJ  CONST_12  N3   N2   C13  C12     0.00   0.0  0
 SLJ  CONST_13  C17  C16  C13  C12     0.00   0.0  0
 SLJ  CONST_14  N2   N3   C14  C12     0.00   0.0  0
 SLJ  CONST_15  C17  C10  C11  C12     0.00   0.0  0
 SLJ  CONST_16  C14  N3   N2   C13     0.00   0.0  0
 SLJ  CONST_17  N3   C14  C12  C13     0.00   0.0  0
 SLJ  CONST_18  N2   C13  C12  C14     0.00   0.0  0
 SLJ  CONST_19  C16  C13  C12  C14   180.00   0.0  0
 SLJ  CONST_20  N3   N2   C13  C16   180.00   0.0  0
 SLJ  CONST_21  C17  C16  C13  N2    180.00   0.0  0
 SLJ  CONST_22  N    C4   C5   C6      0.00   0.0  0
 SLJ  CONST_23  N    C3   C7   C6      0.00   0.0  0
 SLJ  CONST_24  C5   C6   C7   C8    180.00   0.0  0
 SLJ  CONST_25  N    C3   C7   C8    180.00   0.0  0
 SLJ  CONST_26  C15  C14  C12  C11     0.00   0.0  0
 SLJ  CONST_27  N1   C10  C11  C12   180.00   0.0  0
 SLJ  CONST_28  C15  C14  C12  C13   180.00   0.0  0
 SLJ  CONST_29  N2   N3   C14  C15   180.00   0.0  0
 SLJ  CONST_30  N1   C10  C17  C16   180.00   0.0  0
 SLJ  CONST_31  O    C3   C7   C6    180.00   0.0  0
 SLJ  CONST_32  O    C3   N    C4    180.00   0.0  0
 SLJ  CONST_33  H15  C6   C7   C3    180.00   0.0  0
 SLJ  CONST_34  H17  C4   N    C3    180.00   0.0  0
 SLJ  CONST_35  H16  C5   C6   C7    180.00   0.0  0
 SLJ  CONST_36  H11  C16  C17  C10   180.00   0.0  0
 SLJ  CONST_37  H14  C17  C10  C11   180.00   0.0  0
 SLJ  CONST_38  H13  N3   C14  C12   180.00   0.0  0
 SLJ  CONST_39  H10  C11  C12  C13   180.00   0.0  0
 SLJ  CONST_40  C17  C10  N1   C8    180.00   0.0  0
 SLJ  CONST_41  C11  C10  N1   C8      0.00   0.0  0
 SLJ  CONST_42  C17  C10  N1   C9      0.00   0.0  0
 SLJ  CONST_43  C11  C10  N1   C9    180.00   0.0  0
 SLJ  Var_01    C7   C3   O    C2    177.69  30.0  2
 SLJ  Var_02    N1   C8   C7   C3   -176.53  30.0  2
 SLJ  Var_03    C10  N1   C8   C7    -83.65  30.0  1
 SLJ  Var_04    O1   C15  C14  C12   179.54  30.0  2
 SLJ  Var_05    H3   C2   O    C3    -58.31  30.0  3
 SLJ  Var_06    H7   C9   N1   C10   170.86  30.0  3
 SLJ  Var_07    C    C1   C2   O     179.62  30.0  3
 SLJ  Var_08    H18  C    C1   C2   -179.58  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
 SLJ  plan-1  C3   0.020
 SLJ  plan-1  C7   0.020
 SLJ  plan-1  C8   0.020
 SLJ  plan-1  C6   0.020
 SLJ  plan-1  C5   0.020
 SLJ  plan-1  C4   0.020
 SLJ  plan-1  N    0.020
 SLJ  plan-1  O    0.020
 SLJ  plan-1  H15  0.020
 SLJ  plan-1  H16  0.020
 SLJ  plan-1  H17  0.020
 SLJ  plan-2  C10  0.020
 SLJ  plan-2  C11  0.020
 SLJ  plan-2  C12  0.020
 SLJ  plan-2  C13  0.020
 SLJ  plan-2  C14  0.020
 SLJ  plan-2  C15  0.020
 SLJ  plan-2  C16  0.020
 SLJ  plan-2  N3   0.020
 SLJ  plan-2  N2   0.020
 SLJ  plan-2  C17  0.020
 SLJ  plan-2  N1   0.020
 SLJ  plan-2  H10  0.020
 SLJ  plan-2  H11  0.020
 SLJ  plan-2  H13  0.020
 SLJ  plan-2  H14  0.020
 SLJ  plan-3  C8   0.020
 SLJ  plan-3  C9   0.020
 SLJ  plan-3  C10  0.020
 SLJ  plan-3  N1   0.020
 SLJ  plan-4  C14  0.020
 SLJ  plan-4  C15  0.020
 SLJ  plan-4  O2   0.020
 SLJ  plan-4  O1   0.020

