# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 07:27:54 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-[3-(2-methylpyridin-4-yl)-1~{H}-pyrazolo[4,3-c]pyridin-6-yl]-3-(phenylmethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(ccn1)c2n[nH]c3cc(NC(=O)NCc4ccccc4)ncc23
#
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
 6S9  6S9  1-[3-(2-methylpyridin-4-yl)-1~{H}-pyrazolo[4,3-c]pyridin-6-yl]-3-(phenylmethyl)urea  ligand  45  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6S9
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
 6S9  O    O  O     0  -0.507   2.4195   1.6337   0.1592
 6S9  C5   C  C     0   0.723   2.7247   0.6715   0.8419
 6S9  N2   N  NH1   0  -0.664   3.9586   0.4777   1.3644
 6S9  C6   C  CH2   0  -0.371   5.0904   1.3215   1.0683
 6S9  C7   C  CR6   0   0.119   6.1079   0.6503   0.1778
 6S9  C12  C  CR16  0  -0.294   5.7345   0.1343  -1.0625
 6S9  C11  C  CR16  0  -0.240   6.6694  -0.4780  -1.8831
 6S9  C10  C  CR16  0  -0.268   7.9950  -0.5837  -1.4754
 6S9  C9   C  CR16  0  -0.241   8.3760  -0.0713  -0.2440
 6S9  C8   C  CR16  0  -0.312   7.4349   0.5402   0.5771
 6S9  N1   N  NH1   0  -0.768   1.8428  -0.3439   1.1669
 6S9  C3   C  CR6   0   0.501   0.4933  -0.3720   0.8356
 6S9  N    N  N     0  -0.430  -0.1887   0.7806   0.9434
 6S9  C2   C  CR16  0  -0.129  -1.4768   0.8007   0.6871
 6S9  C4   C  CR16  0  -0.442  -0.0768  -1.5794   0.4724
 6S9  C    C  CR56  0   0.528  -1.4473  -1.5452   0.2330
 6S9  N4   N  NR15  0  -0.543  -2.3293  -2.4904  -0.1458
 6S9  N3   N  N     0  -0.239  -3.5625  -2.0053  -0.2925
 6S9  C13  C  CR5   0   0.217  -3.5190  -0.7262  -0.0089
 6S9  C1   C  CR56  0  -0.186  -2.1819  -0.3525   0.3371
 6S9  C14  C  CR6   0   0.166  -4.7281   0.0923  -0.0849
 6S9  C18  C  CR16  0  -0.378  -5.7932  -0.2851  -0.9005
 6S9  C17  C  CR6   0   0.248  -6.9367   0.5016  -0.9538
 6S9  C19  C  CH3   0  -0.718  -8.0930   0.1285  -1.8300
 6S9  N5   N  N     0  -0.427  -7.0559   1.6255  -0.2443
 6S9  C16  C  CR16  0  -0.067  -6.0455   1.9835   0.5342
 6S9  C15  C  CR16  0  -0.411  -4.8683   1.2624   0.6547
 6S9  H4   H  HNH1  0   0.399   4.1362  -0.3377   1.9290
 6S9  H6   H  HCH2  0   0.269   4.7211   2.2310   0.5957
 6S9  H5   H  HCH2  0   0.265   5.5647   1.6252   2.0036
 6S9  H11  H  HCR6  0   0.250   4.7061   0.2159  -1.3950
 6S9  H10  H  HCR6  0   0.256   6.3654  -0.8727  -2.8440
 6S9  H9   H  HCR6  0   0.256   8.7242  -1.0636  -2.1155
 6S9  H8   H  HCR6  0   0.255   9.4052  -0.1498   0.0824
 6S9  H7   H  HCR6  0   0.253   7.7384   0.9339   1.5401
 6S9  H3   H  HNH1  0   0.413   2.2401  -1.2317   1.4332
 6S9  H1   H  HCR6  0   0.264  -1.9666   1.7645   0.7707
 6S9  H2   H  HCR6  0   0.291   0.5108  -2.4818   0.3702
 6S9  H    H  HNR5  0   0.426  -2.1568  -3.4700  -0.3060
 6S9  H14  H  HCR6  0   0.263  -5.7298  -1.1814  -1.5030
 6S9  H16  H  HCH3  0   0.252  -9.0163   0.0802  -1.2520
 6S9  H17  H  HCH3  0   0.253  -8.2400   0.8773  -2.6098
 6S9  H15  H  HCH3  0   0.245  -7.9400  -0.8353  -2.3120
 6S9  H13  H  HCR6  0   0.265  -6.1735   2.8975   1.1040
 6S9  H12  H  HCR6  0   0.262  -4.1016   1.6072   1.3338

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
 6S9  N4   N3   aromatic  1.333  0.020  1.333
 6S9  N4   C    aromatic  1.347  0.020  1.347
 6S9  C4   C    aromatic  1.392  0.020  1.392
 6S9  C4   C3   aromatic  1.384  0.020  1.384
 6S9  N3   C13  aromatic  1.311  0.020  1.311
 6S9  C    C1   aromatic  1.405  0.020  1.405
 6S9  C9   C10  aromatic  1.387  0.020  1.387
 6S9  C9   C8   aromatic  1.391  0.020  1.391
 6S9  N1   C3   single    1.390  0.020  1.390
 6S9  N1   C5   single    1.384  0.020  1.384
 6S9  C3   N    aromatic  1.344  0.020  1.344
 6S9  C19  C17  single    1.498  0.020  1.498
 6S9  C13  C1   aromatic  1.431  0.020  1.431
 6S9  C13  C14  single    1.462  0.020  1.462
 6S9  C18  C17  aromatic  1.389  0.020  1.389
 6S9  C18  C14  aromatic  1.394  0.020  1.394
 6S9  C10  C11  aromatic  1.391  0.020  1.391
 6S9  C1   C2   aromatic  1.396  0.020  1.396
 6S9  O    C5   double    1.219  0.020  1.219
 6S9  C8   C7   aromatic  1.390  0.020  1.390
 6S9  C5   N2   single    1.354  0.020  1.354
 6S9  N    C2   aromatic  1.314  0.020  1.314
 6S9  C17  N5   aromatic  1.334  0.020  1.334
 6S9  C14  C15  aromatic  1.391  0.020  1.391
 6S9  C11  C12  aromatic  1.386  0.020  1.386
 6S9  N2   C6   single    1.442  0.020  1.442
 6S9  C7   C12  aromatic  1.394  0.020  1.394
 6S9  C7   C6   single    1.510  0.020  1.510
 6S9  N5   C16  aromatic  1.325  0.020  1.325
 6S9  C15  C16  aromatic  1.386  0.020  1.386
 6S9  N2   H4   single    0.860  0.020  1.020
 6S9  C6   H6   single    0.970  0.020  1.090
 6S9  C6   H5   single    0.970  0.020  1.090
 6S9  C12  H11  single    0.930  0.020  1.080
 6S9  C11  H10  single    0.930  0.020  1.080
 6S9  C10  H9   single    0.930  0.020  1.080
 6S9  C9   H8   single    0.930  0.020  1.080
 6S9  C8   H7   single    0.930  0.020  1.080
 6S9  N1   H3   single    0.860  0.020  1.020
 6S9  C2   H1   single    0.930  0.020  1.080
 6S9  C4   H2   single    0.930  0.020  1.080
 6S9  N4   H    single    0.860  0.020  1.020
 6S9  C18  H14  single    0.930  0.020  1.080
 6S9  C19  H16  single    0.970  0.020  1.090
 6S9  C19  H17  single    0.970  0.020  1.090
 6S9  C19  H15  single    0.970  0.020  1.090
 6S9  C16  H13  single    0.930  0.020  1.080
 6S9  C15  H12  single    0.930  0.020  1.080

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
 6S9  N1   C5   N2   112.66  3.000
 6S9  N2   C5   O    123.88  3.000
 6S9  N1   C5   O    123.46  3.000
 6S9  H4   N2   C6   116.75  3.000
 6S9  H4   N2   C5   119.52  3.000
 6S9  C6   N2   C5   123.52  3.000
 6S9  H5   C6   H6   106.66  3.000
 6S9  H5   C6   C7   109.65  3.000
 6S9  H6   C6   C7   110.11  3.000
 6S9  H5   C6   N2   109.13  3.000
 6S9  H6   C6   N2   108.15  3.000
 6S9  C7   C6   N2   112.95  3.000
 6S9  C8   C7   C12  118.81  3.000
 6S9  C12  C7   C6   120.58  3.000
 6S9  C8   C7   C6   120.61  3.000
 6S9  H11  C12  C11  119.44  3.000
 6S9  H11  C12  C7   119.94  3.000
 6S9  C11  C12  C7   120.62  3.000
 6S9  H10  C11  C10  120.01  3.000
 6S9  H10  C11  C12  119.81  3.000
 6S9  C10  C11  C12  120.18  3.000
 6S9  H9   C10  C9   120.25  3.000
 6S9  H9   C10  C11  120.15  3.000
 6S9  C9   C10  C11  119.60  3.000
 6S9  H8   C9   C8   119.81  3.000
 6S9  H8   C9   C10  120.14  3.000
 6S9  C8   C9   C10  120.05  3.000
 6S9  H7   C8   C9   119.66  3.000
 6S9  H7   C8   C7   119.59  3.000
 6S9  C9   C8   C7   120.75  3.000
 6S9  H3   N1   C3   115.32  3.000
 6S9  H3   N1   C5   117.19  3.000
 6S9  C3   N1   C5   125.29  3.000
 6S9  C4   C3   N    124.09  3.000
 6S9  N    C3   N1   117.15  3.000
 6S9  C4   C3   N1   118.70  3.000
 6S9  C2   N    C3   119.69  3.000
 6S9  H1   C2   C1   121.69  3.000
 6S9  H1   C2   N    116.20  3.000
 6S9  C1   C2   N    122.10  3.000
 6S9  H2   C4   C    122.63  3.000
 6S9  H2   C4   C3   121.94  3.000
 6S9  C    C4   C3   115.43  3.000
 6S9  C1   C    N4   105.91  3.000
 6S9  C1   C    C4   121.55  3.000
 6S9  N4   C    C4   132.52  3.000
 6S9  H    N4   N3   119.64  3.000
 6S9  H    N4   C    127.94  3.000
 6S9  N3   N4   C    112.41  3.000
 6S9  C13  N3   N4   107.49  3.000
 6S9  C14  C13  C1   129.73  3.000
 6S9  C14  C13  N3   120.50  3.000
 6S9  C1   C13  N3   109.76  3.000
 6S9  C13  C1   C    104.42  3.000
 6S9  C13  C1   C2   138.44  3.000
 6S9  C    C1   C2   117.12  3.000
 6S9  C15  C14  C18  117.50  3.000
 6S9  C15  C14  C13  121.77  3.000
 6S9  C18  C14  C13  120.72  3.000
 6S9  H14  C18  C17  119.75  3.000
 6S9  H14  C18  C14  120.36  3.000
 6S9  C17  C18  C14  119.89  3.000
 6S9  N5   C17  C19  116.86  3.000
 6S9  N5   C17  C18  122.02  3.000
 6S9  C19  C17  C18  121.12  3.000
 6S9  H15  C19  H17  108.07  3.000
 6S9  H15  C19  H16  108.34  3.000
 6S9  H17  C19  H16  107.17  3.000
 6S9  H15  C19  C17  111.78  3.000
 6S9  H17  C19  C17  110.56  3.000
 6S9  H16  C19  C17  110.77  3.000
 6S9  C16  N5   C17  118.16  3.000
 6S9  H13  C16  C15  119.54  3.000
 6S9  H13  C16  N5   116.51  3.000
 6S9  C15  C16  N5   123.94  3.000
 6S9  H12  C15  C16  119.43  3.000
 6S9  H12  C15  C14  122.06  3.000
 6S9  C16  C15  C14  118.49  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
 6S9  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 6S9  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 6S9  CONST_03  C9   C10  C11  C12     0.00   0.0  0
 6S9  CONST_04  C9   C8   C7   C12     0.00   0.0  0
 6S9  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 6S9  CONST_06  C8   C7   C12  C11     0.00   0.0  0
 6S9  CONST_07  N4   C    C4   C3    180.00   0.0  0
 6S9  CONST_08  C1   C    C4   C3      0.00   0.0  0
 6S9  CONST_09  C1   C2   N    C3      0.00   0.0  0
 6S9  CONST_10  C    C4   C3   N       0.00   0.0  0
 6S9  CONST_11  C    C1   C2   N       0.00   0.0  0
 6S9  CONST_12  C13  C1   C2   N     180.00   0.0  0
 6S9  CONST_13  N4   C    C1   C2    180.00   0.0  0
 6S9  CONST_14  C4   C    C1   C2      0.00   0.0  0
 6S9  CONST_15  N3   C13  C1   C2    180.00   0.0  0
 6S9  CONST_16  C14  C13  C1   C2      0.00   0.0  0
 6S9  CONST_17  C4   C3   N    C2      0.00   0.0  0
 6S9  CONST_18  N3   N4   C    C4    180.00   0.0  0
 6S9  CONST_19  C13  C1   C    C4    180.00   0.0  0
 6S9  CONST_20  C13  N3   N4   C       0.00   0.0  0
 6S9  CONST_21  N3   C13  C1   C       0.00   0.0  0
 6S9  CONST_22  C14  C13  C1   C     180.00   0.0  0
 6S9  CONST_23  C1   C13  N3   N4      0.00   0.0  0
 6S9  CONST_24  C14  C13  N3   N4    180.00   0.0  0
 6S9  CONST_25  C13  C1   C    N4      0.00   0.0  0
 6S9  CONST_26  C1   C    N4   N3      0.00   0.0  0
 6S9  CONST_29  C17  C18  C14  C13   180.00   0.0  0
 6S9  CONST_30  C16  C15  C14  C13   180.00   0.0  0
 6S9  CONST_33  N5   C17  C18  C14     0.00   0.0  0
 6S9  CONST_34  N5   C16  C15  C14     0.00   0.0  0
 6S9  CONST_35  C16  N5   C17  C18     0.00   0.0  0
 6S9  CONST_36  C16  C15  C14  C18     0.00   0.0  0
 6S9  CONST_37  C15  C14  C18  C17     0.00   0.0  0
 6S9  CONST_38  C15  C16  N5   C17     0.00   0.0  0
 6S9  CONST_39  C9   C8   C7   C6    180.00   0.0  0
 6S9  CONST_40  C11  C12  C7   C6    180.00   0.0  0
 6S9  CONST_41  C    C4   C3   N1    180.00   0.0  0
 6S9  CONST_42  C2   N    C3   N1    180.00   0.0  0
 6S9  CONST_43  C19  C17  C18  C14   180.00   0.0  0
 6S9  CONST_44  C16  N5   C17  C19   180.00   0.0  0
 6S9  CONST_45  H8   C9   C8   C7    180.00   0.0  0
 6S9  CONST_46  H10  C11  C12  C7    180.00   0.0  0
 6S9  CONST_47  H9   C10  C11  C12   180.00   0.0  0
 6S9  CONST_48  H7   C8   C7   C12   180.00   0.0  0
 6S9  CONST_49  H11  C12  C11  C10   180.00   0.0  0
 6S9  CONST_50  H1   C2   N    C3    180.00   0.0  0
 6S9  CONST_51  H2   C4   C3   N     180.00   0.0  0
 6S9  CONST_52  H    N4   C    C4      0.00   0.0  0
 6S9  CONST_53  H14  C18  C14  C13     0.00   0.0  0
 6S9  CONST_54  H12  C15  C14  C13     0.00   0.0  0
 6S9  CONST_55  H13  C16  C15  C14   180.00   0.0  0
 6S9  CONST_59  C3   N1   C5   O       0.00   0.0  0
 6S9  CONST_60  C3   N1   C5   N2    180.00   0.0  0
 6S9  CONST_61  C6   N2   C5   O       0.00   0.0  0
 6S9  CONST_62  N1   C5   N2   C6    180.00   0.0  0
 6S9  CONST_63  H4   N2   C5   O     180.00   0.0  0
 6S9  Var_01    C8   C7   C6   N2   -124.18  30.0  2
 6S9  Var_02    H16  C19  C17  C18   125.82  30.0  2
 6S9  Var_03    C7   C6   N2   C5   -107.82  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
 6S9  plan-1  C6   0.020
 6S9  plan-1  C7   0.020
 6S9  plan-1  C12  0.020
 6S9  plan-1  C11  0.020
 6S9  plan-1  C10  0.020
 6S9  plan-1  C9   0.020
 6S9  plan-1  C8   0.020
 6S9  plan-1  H11  0.020
 6S9  plan-1  H10  0.020
 6S9  plan-1  H9   0.020
 6S9  plan-1  H8   0.020
 6S9  plan-1  H7   0.020
 6S9  plan-2  C13  0.020
 6S9  plan-2  C14  0.020
 6S9  plan-2  C18  0.020
 6S9  plan-2  C17  0.020
 6S9  plan-2  C19  0.020
 6S9  plan-2  N5   0.020
 6S9  plan-2  C16  0.020
 6S9  plan-2  C15  0.020
 6S9  plan-2  H14  0.020
 6S9  plan-2  H13  0.020
 6S9  plan-2  H12  0.020
 6S9  plan-3  N1   0.020
 6S9  plan-3  C3   0.020
 6S9  plan-3  N    0.020
 6S9  plan-3  C2   0.020
 6S9  plan-3  C4   0.020
 6S9  plan-3  C    0.020
 6S9  plan-3  N4   0.020
 6S9  plan-3  N3   0.020
 6S9  plan-3  C13  0.020
 6S9  plan-3  C1   0.020
 6S9  plan-3  C14  0.020
 6S9  plan-3  H1   0.020
 6S9  plan-3  H2   0.020
 6S9  plan-3  H    0.020
 6S9  plan-4  O    0.020
 6S9  plan-4  C5   0.020
 6S9  plan-4  N2   0.020
 6S9  plan-4  C6   0.020
 6S9  plan-4  N1   0.020
 6S9  plan-4  C3   0.020
 6S9  plan-4  H4   0.020
 6S9  plan-4  H3   0.020

