# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 10:42:55 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2c1[nH]c(C(O)=O)c2c3c[nH]nc3
#
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
 Y6P  Y6P  '7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid'  ligand  28  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y6P
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
 Y6P  C10  C  CR5    0  -0.157  -48.0070  -3.6472  27.5347
 Y6P  N12  N  NR15   0  -0.435  -48.4161  -5.7977  27.5608
 Y6P  C15  C  C      0   0.351  -49.4341  -0.6103  27.3382
 Y6P  C01  C  C1     0  -0.254  -43.7040  -2.4681  26.4911
 Y6P  C02  C  C1     0  -0.401  -44.9299  -3.0061  26.8219
 Y6P  C03  C  CR5    0   0.046  -46.0427  -2.1555  26.8853
 Y6P  C04  C  CR5    0   0.319  -45.8635  -0.7817  26.6218
 Y6P  C05  C  C      0   0.058  -44.6272  -0.2189  26.2794
 Y6P  C06  C  C1     0  -0.347  -43.5594  -1.0953  26.2202
 Y6P  C07  C  CR5    0   0.011  -47.4292  -2.3493  27.2088
 Y6P  C08  C  CR5    0   0.082  -48.0212  -1.1034  27.1378
 Y6P  C11  C  CR15   0  -0.036  -47.7055  -4.8516  26.9261
 Y6P  C14  C  CR15   0  -0.114  -48.9254  -4.0142  28.5429
 Y6P  N09  N  NR15   0  -0.719  -47.0714  -0.1840  26.7832
 Y6P  N13  N  N      0  -0.275  -49.1607  -5.3121  28.5474
 Y6P  O16  O  OC    -1  -0.596  -49.6018   0.6050  27.1082
 Y6P  O17  O  O      0  -0.566  -50.2824  -1.4392  27.7064
 Y6P  H1   H  HNR5   0   0.414  -48.4291  -6.7842  27.3589
 Y6P  H2   H  H      0   0.238  -42.8320  -3.1079  26.4422
 Y6P  H3   H  H      0   0.236  -45.0235  -4.0632  27.0372
 Y6P  H4   H  H      0   0.236  -42.5794  -0.7098  25.9630
 Y6P  H5   H  HCR5   0   0.279  -47.0617  -5.0881  26.0945
 Y6P  H6   H  HCR5   0   0.238  -49.4115  -3.3693  29.2557
 Y6P  H7   H  HCH3   0   0.243  -45.0901   1.5518  25.1422
 Y6P  H8   H  HCH3   0   0.241  -44.8342   1.8458  26.8534
 Y6P  H9   H  HCH3   0   0.249  -43.4578   1.5169  25.8034
 Y6P  H10  H  HNR5   0   0.393  -47.2923   0.7904  26.6566
 Y6P  C18  C  CH3    0  -0.733  -44.4934   1.2477  26.0053

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
 Y6P  C18  C05  single    1.498  0.020  1.498
 Y6P  C06  C05  aromatic  1.383  0.020  1.383
 Y6P  C06  C01  aromatic  1.407  0.020  1.407
 Y6P  C05  C04  aromatic  1.401  0.020  1.401
 Y6P  C01  C02  aromatic  1.379  0.020  1.379
 Y6P  C04  N09  aromatic  1.357  0.020  1.357
 Y6P  C04  C03  aromatic  1.410  0.020  1.410
 Y6P  N09  C08  aromatic  1.369  0.020  1.369
 Y6P  O17  C15  deloc     1.242  0.020  1.242
 Y6P  C02  C03  aromatic  1.402  0.020  1.402
 Y6P  C03  C07  aromatic  1.437  0.020  1.437
 Y6P  C11  N12  aromatic  1.343  0.020  1.343
 Y6P  C11  C10  aromatic  1.383  0.020  1.383
 Y6P  C08  C07  aromatic  1.381  0.020  1.381
 Y6P  C08  C15  single    1.510  0.020  1.510
 Y6P  C07  C10  single    1.458  0.020  1.458
 Y6P  C15  O16  deloc     1.248  0.020  1.248
 Y6P  N12  N13  aromatic  1.328  0.020  1.328
 Y6P  C10  C14  aromatic  1.412  0.020  1.412
 Y6P  N13  C14  aromatic  1.319  0.020  1.319
 Y6P  N12  H1   single    0.860  0.020  1.020
 Y6P  C01  H2   single    0.930  0.020  1.080
 Y6P  C02  H3   single    0.930  0.020  1.080
 Y6P  C06  H4   single    0.930  0.020  1.080
 Y6P  C11  H5   single    0.930  0.020  1.080
 Y6P  C14  H6   single    0.930  0.020  1.080
 Y6P  C18  H7   single    0.970  0.020  1.090
 Y6P  C18  H8   single    0.970  0.020  1.090
 Y6P  C18  H9   single    0.970  0.020  1.090
 Y6P  N09  H10  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
 Y6P  C14  C10  C11  103.28  3.000
 Y6P  C14  C10  C07  130.45  3.000
 Y6P  C11  C10  C07  126.21  3.000
 Y6P  H1   N12  N13  119.99  3.000
 Y6P  H1   N12  C11  127.04  3.000
 Y6P  N13  N12  C11  112.97  3.000
 Y6P  O17  C15  O16  127.79  3.000
 Y6P  O16  C15  C08  114.79  3.000
 Y6P  O17  C15  C08  117.43  3.000
 Y6P  H2   C01  C06  119.03  3.000
 Y6P  H2   C01  C02  119.75  3.000
 Y6P  C06  C01  C02  121.22  3.000
 Y6P  H3   C02  C03  120.98  3.000
 Y6P  H3   C02  C01  120.35  3.000
 Y6P  C03  C02  C01  118.66  3.000
 Y6P  C07  C03  C04  107.22  3.000
 Y6P  C07  C03  C02  133.96  3.000
 Y6P  C04  C03  C02  118.80  3.000
 Y6P  N09  C04  C05  129.61  3.000
 Y6P  N09  C04  C03  107.08  3.000
 Y6P  C05  C04  C03  123.31  3.000
 Y6P  C18  C05  C06  122.94  3.000
 Y6P  C06  C05  C04  115.94  3.000
 Y6P  C18  C05  C04  121.13  3.000
 Y6P  H4   C06  C05  118.88  3.000
 Y6P  H4   C06  C01  119.05  3.000
 Y6P  C05  C06  C01  122.07  3.000
 Y6P  C08  C07  C03  106.29  3.000
 Y6P  C08  C07  C10  130.15  3.000
 Y6P  C03  C07  C10  123.57  3.000
 Y6P  N09  C08  C07  108.77  3.000
 Y6P  C07  C08  C15  133.54  3.000
 Y6P  N09  C08  C15  117.68  3.000
 Y6P  H5   C11  N12  121.75  3.000
 Y6P  H5   C11  C10  131.37  3.000
 Y6P  N12  C11  C10  106.88  3.000
 Y6P  H6   C14  N13  120.42  3.000
 Y6P  H6   C14  C10  127.61  3.000
 Y6P  N13  C14  C10  111.97  3.000
 Y6P  H10  N09  C08  122.02  3.000
 Y6P  H10  N09  C04  127.32  3.000
 Y6P  C08  N09  C04  110.65  3.000
 Y6P  C14  N13  N12  104.91  3.000
 Y6P  H9   C18  H8   107.78  3.000
 Y6P  H9   C18  H7   107.71  3.000
 Y6P  H8   C18  H7   106.89  3.000
 Y6P  H9   C18  C05  111.16  3.000
 Y6P  H8   C18  C05  111.47  3.000
 Y6P  H7   C18  C05  111.61  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
 Y6P  CONST_01  N13  N12  C11  C10    0.00   0.0  0
 Y6P  CONST_02  C04  C03  C07  C10  180.00   0.0  0
 Y6P  CONST_03  C02  C03  C07  C10    0.00   0.0  0
 Y6P  CONST_04  N09  C08  C07  C10  180.00   0.0  0
 Y6P  CONST_05  N12  N13  C14  C10    0.00   0.0  0
 Y6P  CONST_06  C07  C10  C11  N12  180.00   0.0  0
 Y6P  CONST_07  C14  C10  C11  N12    0.00   0.0  0
 Y6P  CONST_08  C04  C05  C06  C01    0.00   0.0  0
 Y6P  CONST_09  C04  C03  C02  C01    0.00   0.0  0
 Y6P  CONST_10  C07  C03  C02  C01  180.00   0.0  0
 Y6P  CONST_11  C05  C06  C01  C02    0.00   0.0  0
 Y6P  CONST_12  C05  C04  C03  C02    0.00   0.0  0
 Y6P  CONST_13  N09  C04  C03  C02  180.00   0.0  0
 Y6P  CONST_14  C08  C07  C03  C02  180.00   0.0  0
 Y6P  CONST_15  C06  C05  C04  C03    0.00   0.0  0
 Y6P  CONST_16  C08  N09  C04  C03    0.00   0.0  0
 Y6P  CONST_17  C06  C01  C02  C03    0.00   0.0  0
 Y6P  CONST_18  N09  C08  C07  C03    0.00   0.0  0
 Y6P  CONST_21  C07  C08  N09  C04    0.00   0.0  0
 Y6P  CONST_22  C08  C07  C03  C04    0.00   0.0  0
 Y6P  CONST_23  C08  N09  C04  C05  180.00   0.0  0
 Y6P  CONST_24  C07  C03  C04  C05  180.00   0.0  0
 Y6P  CONST_25  N09  C04  C05  C06  180.00   0.0  0
 Y6P  CONST_26  N09  C04  C03  C07    0.00   0.0  0
 Y6P  CONST_27  N13  C14  C10  C07  180.00   0.0  0
 Y6P  CONST_30  C14  N13  N12  C11    0.00   0.0  0
 Y6P  CONST_31  N13  C14  C10  C11    0.00   0.0  0
 Y6P  CONST_32  C15  C08  C07  C10    0.00   0.0  0
 Y6P  CONST_33  C04  N09  C08  C15  180.00   0.0  0
 Y6P  CONST_34  C03  C07  C08  C15  180.00   0.0  0
 Y6P  CONST_35  C18  C05  C06  C01  180.00   0.0  0
 Y6P  CONST_36  C18  C05  C04  C03  180.00   0.0  0
 Y6P  CONST_37  N09  C04  C05  C18    0.00   0.0  0
 Y6P  CONST_38  H1   N12  C11  C10  180.00   0.0  0
 Y6P  CONST_39  H6   C14  N13  N12  180.00   0.0  0
 Y6P  CONST_40  H4   C06  C01  C02  180.00   0.0  0
 Y6P  CONST_41  H10  N09  C04  C03  180.00   0.0  0
 Y6P  CONST_42  H2   C01  C02  C03  180.00   0.0  0
 Y6P  CONST_43  H3   C02  C03  C04  180.00   0.0  0
 Y6P  CONST_44  H5   C11  C10  C07    0.00   0.0  0
 Y6P  Var_01    O17  C15  C08  C07    4.05  30.0  2
 Y6P  Var_02    H7   C18  C05  C04  -62.49  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
 Y6P  plan-1  C10  0.020
 Y6P  plan-1  N12  0.020
 Y6P  plan-1  C07  0.020
 Y6P  plan-1  C11  0.020
 Y6P  plan-1  C14  0.020
 Y6P  plan-1  N13  0.020
 Y6P  plan-1  H1   0.020
 Y6P  plan-1  H5   0.020
 Y6P  plan-1  H6   0.020
 Y6P  plan-2  C10  0.020
 Y6P  plan-2  C15  0.020
 Y6P  plan-2  C01  0.020
 Y6P  plan-2  C02  0.020
 Y6P  plan-2  C03  0.020
 Y6P  plan-2  C04  0.020
 Y6P  plan-2  C05  0.020
 Y6P  plan-2  C06  0.020
 Y6P  plan-2  C07  0.020
 Y6P  plan-2  C08  0.020
 Y6P  plan-2  N09  0.020
 Y6P  plan-2  H2   0.020
 Y6P  plan-2  H3   0.020
 Y6P  plan-2  H4   0.020
 Y6P  plan-2  H10  0.020
 Y6P  plan-2  C18  0.020
 Y6P  plan-3  C15  0.020
 Y6P  plan-3  C08  0.020
 Y6P  plan-3  O16  0.020
 Y6P  plan-3  O17  0.020

