# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 21:48:23 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 7,8-dimethoxy-1-methyl-2H-pyrazolo[3,4-c]cinnoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2nnc3n[nH]c(C)c3c2cc1OC
#
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
 JY4  JY4  7,8-dimethoxy-1-methyl-2H-pyrazolo[3,4-c]cinnoline  ligand  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JY4
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
 JY4  C4   C  CR56  0  -0.080   1.8107  -0.1195  -0.0039
 JY4  C5   C  CR66  0   0.113  -0.1001   1.2731   0.0119
 JY4  C6   C  CR6   0   0.367  -1.8572  -0.8954   0.0156
 JY4  C7   C  CR6   0   0.315  -2.3661   0.4412   0.0242
 JY4  C8   C  CR5   0   0.341   2.7938  -1.1034  -0.0110
 JY4  C10  C  CH3   0  -0.763   2.7250  -2.5857  -0.0114
 JY4  C1   C  CR16  0  -0.529  -0.4994  -1.1231   0.0059
 JY4  C11  C  CH3   0  -0.446  -2.3781  -3.2011   0.0089
 JY4  C12  C  CH3   0  -0.441  -4.2723   1.8303   0.0335
 JY4  C2   C  CR16  0  -0.429  -1.4937   1.4961   0.0221
 JY4  C3   C  CR66  0   0.153   0.3965  -0.0426   0.0045
 JY4  C9   C  CR56  0   0.298   2.5278   1.0960  -0.0057
 JY4  N13  N  N     0  -0.282   0.6913   2.3969   0.0095
 JY4  N14  N  NR15  0  -0.453   3.9477  -0.4175  -0.0167
 JY4  N15  N  N     0  -0.266   1.9598   2.3302   0.0007
 JY4  N16  N  N     0  -0.277   3.8426   0.9006  -0.0139
 JY4  O17  O  O2    0  -0.451  -2.7912  -1.8460   0.0176
 JY4  O18  O  O2    0  -0.457  -3.7031   0.5351   0.0342
 JY4  H1   H  HCH3  0   0.267   2.2120  -2.9528   0.8781
 JY4  H2   H  HCH3  0   0.267   2.1829  -2.9510  -0.8840
 JY4  H3   H  HCH3  0   0.275   3.7199  -3.0280  -0.0283
 JY4  H4   H  HCR6  0   0.282  -0.1112  -2.1322  -0.0016
 JY4  H5   H  HCH3  0   0.237  -1.7966  -3.4396  -0.8848
 JY4  H6   H  HCH3  0   0.236  -1.7898  -3.4489   0.8958
 JY4  H7   H  HCH3  0   0.269  -3.2862  -3.7977   0.0091
 JY4  H8   H  HCH3  0   0.232  -3.9816   2.3994   0.9202
 JY4  H9   H  HCH3  0   0.233  -3.9881   2.3958  -0.8575
 JY4  H10  H  HCH3  0   0.265  -5.3505   1.6944   0.0381
 JY4  H11  H  HCR6  0   0.291  -1.8387   2.5215   0.0282
 JY4  H12  H  HNR5  0   0.433   4.8701  -0.8307  -0.0220

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
 JY4  C11  O17  single    1.417  0.020  1.417
 JY4  C10  C8   single    1.484  0.020  1.484
 JY4  O17  C6   single    1.333  0.020  1.333
 JY4  C8   N14  aromatic  1.342  0.020  1.342
 JY4  C8   C4   aromatic  1.391  0.020  1.391
 JY4  N14  N16  aromatic  1.322  0.020  1.322
 JY4  C1   C6   aromatic  1.377  0.020  1.377
 JY4  C1   C3   aromatic  1.404  0.020  1.404
 JY4  C6   C7   aromatic  1.430  0.020  1.430
 JY4  C4   C3   aromatic  1.416  0.020  1.416
 JY4  C4   C9   aromatic  1.411  0.020  1.411
 JY4  C3   C5   aromatic  1.406  0.020  1.406
 JY4  N16  C9   aromatic  1.329  0.020  1.329
 JY4  C7   O18  single    1.340  0.020  1.340
 JY4  C7   C2   aromatic  1.369  0.020  1.369
 JY4  C9   N15  aromatic  1.359  0.020  1.359
 JY4  O18  C12  single    1.415  0.020  1.415
 JY4  C5   C2   aromatic  1.411  0.020  1.411
 JY4  C5   N13  aromatic  1.375  0.020  1.375
 JY4  N15  N13  aromatic  1.270  0.020  1.270
 JY4  C10  H1   single    0.970  0.020  1.090
 JY4  C10  H2   single    0.970  0.020  1.090
 JY4  C10  H3   single    0.970  0.020  1.090
 JY4  C1   H4   single    0.930  0.020  1.080
 JY4  C11  H5   single    0.970  0.020  1.090
 JY4  C11  H6   single    0.970  0.020  1.090
 JY4  C11  H7   single    0.970  0.020  1.090
 JY4  C12  H8   single    0.970  0.020  1.090
 JY4  C12  H9   single    0.970  0.020  1.090
 JY4  C12  H10  single    0.970  0.020  1.090
 JY4  C2   H11  single    0.930  0.020  1.080
 JY4  N14  H12  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
 JY4  C9   C4   C3   117.43  3.000
 JY4  C9   C4   C8   104.48  3.000
 JY4  C3   C4   C8   138.09  3.000
 JY4  N13  C5   C3   124.16  3.000
 JY4  N13  C5   C2   116.06  3.000
 JY4  C3   C5   C2   119.77  3.000
 JY4  O17  C6   C1   124.97  3.000
 JY4  C1   C6   C7   120.36  3.000
 JY4  O17  C6   C7   114.66  3.000
 JY4  O18  C7   C2   125.57  3.000
 JY4  C2   C7   C6   119.57  3.000
 JY4  O18  C7   C6   114.86  3.000
 JY4  N14  C8   C10  123.39  3.000
 JY4  N14  C8   C4   104.25  3.000
 JY4  C10  C8   C4   132.36  3.000
 JY4  H3   C10  H2   107.80  3.000
 JY4  H3   C10  H1   107.80  3.000
 JY4  H2   C10  H1   107.83  3.000
 JY4  H3   C10  C8   111.31  3.000
 JY4  H2   C10  C8   110.98  3.000
 JY4  H1   C10  C8   110.98  3.000
 JY4  H4   C1   C3   119.29  3.000
 JY4  H4   C1   C6   120.57  3.000
 JY4  C3   C1   C6   120.14  3.000
 JY4  H7   C11  H6   108.98  3.000
 JY4  H7   C11  H5   108.97  3.000
 JY4  H6   C11  H5   109.14  3.000
 JY4  H7   C11  O17  106.35  3.000
 JY4  H6   C11  O17  111.65  3.000
 JY4  H5   C11  O17  111.66  3.000
 JY4  H10  C12  H9   109.03  3.000
 JY4  H10  C12  H8   109.00  3.000
 JY4  H9   C12  H8   108.84  3.000
 JY4  H10  C12  O18  106.54  3.000
 JY4  H9   C12  O18  111.68  3.000
 JY4  H8   C12  O18  111.67  3.000
 JY4  H11  C2   C7   121.81  3.000
 JY4  H11  C2   C5   117.69  3.000
 JY4  C7   C2   C5   120.50  3.000
 JY4  C1   C3   C5   119.66  3.000
 JY4  C5   C3   C4   113.79  3.000
 JY4  C1   C3   C4   126.55  3.000
 JY4  N16  C9   N15  123.17  3.000
 JY4  N15  C9   C4   124.75  3.000
 JY4  N16  C9   C4   112.09  3.000
 JY4  N15  N13  C5   122.14  3.000
 JY4  H12  N14  N16  118.69  3.000
 JY4  H12  N14  C8   125.14  3.000
 JY4  N16  N14  C8   116.17  3.000
 JY4  N13  N15  C9   117.73  3.000
 JY4  N14  N16  C9   103.01  3.000
 JY4  C11  O17  C6   118.55  3.000
 JY4  C12  O18  C7   117.74  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
 JY4  CONST_01  N16  N14  C8   C4     0.00   0.0  0
 JY4  CONST_02  C6   C1   C3   C4   180.00   0.0  0
 JY4  CONST_03  C2   C5   C3   C4   180.00   0.0  0
 JY4  CONST_04  N13  C5   C3   C4     0.00   0.0  0
 JY4  CONST_05  N14  N16  C9   C4     0.00   0.0  0
 JY4  CONST_06  N13  N15  C9   C4     0.00   0.0  0
 JY4  CONST_07  C6   C1   C3   C5     0.00   0.0  0
 JY4  CONST_08  C8   C4   C3   C5   180.00   0.0  0
 JY4  CONST_09  C9   C4   C3   C5     0.00   0.0  0
 JY4  CONST_10  C6   C7   C2   C5     0.00   0.0  0
 JY4  CONST_11  C9   N15  N13  C5     0.00   0.0  0
 JY4  CONST_12  C3   C1   C6   C7     0.00   0.0  0
 JY4  CONST_13  C3   C5   C2   C7     0.00   0.0  0
 JY4  CONST_14  N13  C5   C2   C7   180.00   0.0  0
 JY4  CONST_15  C9   N16  N14  C8     0.00   0.0  0
 JY4  CONST_16  C1   C3   C4   C8     0.00   0.0  0
 JY4  CONST_17  N16  C9   C4   C8     0.00   0.0  0
 JY4  CONST_18  N15  C9   C4   C8   180.00   0.0  0
 JY4  CONST_19  C2   C7   C6   C1     0.00   0.0  0
 JY4  CONST_20  C9   C4   C3   C1   180.00   0.0  0
 JY4  CONST_21  C2   C5   C3   C1     0.00   0.0  0
 JY4  CONST_22  N13  C5   C3   C1   180.00   0.0  0
 JY4  CONST_23  N15  N13  C5   C2   180.00   0.0  0
 JY4  CONST_24  N14  C8   C4   C3   180.00   0.0  0
 JY4  CONST_25  N16  C9   C4   C3   180.00   0.0  0
 JY4  CONST_26  N15  C9   C4   C3     0.00   0.0  0
 JY4  CONST_27  N15  N13  C5   C3     0.00   0.0  0
 JY4  CONST_28  N14  C8   C4   C9     0.00   0.0  0
 JY4  CONST_29  N16  C9   N15  N13  180.00   0.0  0
 JY4  CONST_30  N15  C9   N16  N14  180.00   0.0  0
 JY4  CONST_31  O18  C7   C2   C5   180.00   0.0  0
 JY4  CONST_32  N16  N14  C8   C10  180.00   0.0  0
 JY4  CONST_33  C3   C4   C8   C10    0.00   0.0  0
 JY4  CONST_34  C9   C4   C8   C10  180.00   0.0  0
 JY4  CONST_35  O18  C7   C6   C1   180.00   0.0  0
 JY4  CONST_36  O17  C6   C7   C2   180.00   0.0  0
 JY4  CONST_37  O17  C6   C1   C3   180.00   0.0  0
 JY4  CONST_38  H12  N14  C8   C4   180.00   0.0  0
 JY4  CONST_39  H4   C1   C3   C4     0.00   0.0  0
 JY4  CONST_40  H11  C2   C7   C6   180.00   0.0  0
 JY4  Var_01    C2   C7   O18  C12    0.45  30.0  1
 JY4  Var_02    H1   C10  C8   C4   -60.50  30.0  2
 JY4  Var_03    H5   C11  O17  C6   -61.08  30.0  3
 JY4  Var_04    H8   C12  O18  C7   -61.32  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
 JY4  plan-1  C4   0.020
 JY4  plan-1  C5   0.020
 JY4  plan-1  C6   0.020
 JY4  plan-1  C7   0.020
 JY4  plan-1  C8   0.020
 JY4  plan-1  C10  0.020
 JY4  plan-1  C1   0.020
 JY4  plan-1  C2   0.020
 JY4  plan-1  C3   0.020
 JY4  plan-1  C9   0.020
 JY4  plan-1  N13  0.020
 JY4  plan-1  N14  0.020
 JY4  plan-1  N15  0.020
 JY4  plan-1  N16  0.020
 JY4  plan-1  O17  0.020
 JY4  plan-1  O18  0.020
 JY4  plan-1  H4   0.020
 JY4  plan-1  H11  0.020
 JY4  plan-1  H12  0.020

