# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:24:05 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-yloxy)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(cc1NC(=O)Nc2ccc(Oc3ccncc3)cc2)C(C)(C)C
#
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
 N61  N61  1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-yloxy)phenyl]urea  ligand  50  27  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N61
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
 N61  O1   O  O     0  -0.486   1.1189  -0.8230  -0.6878
 N61  C9   C  C     0   0.737   1.1080   0.3155  -0.2621
 N61  N3   N  NH1   0  -0.801   2.2390   0.9689   0.1537
 N61  C8   C  CR5   0   0.662   3.5086   0.4242   0.1240
 N61  C7   C  CR15  0  -0.550   3.9851  -0.8651   0.0038
 N61  C2   C  CR5   0   0.339   5.3855  -0.7261   0.0998
 N61  C3   C  CT    0  -0.181   6.4186  -1.8191  -0.0013
 N61  C6   C  CH3   0  -0.641   5.9373  -3.0542   0.7655
 N61  C5   C  CH3   0  -0.629   6.6057  -2.1865  -1.4795
 N61  C4   C  CH3   0  -0.638   7.7596  -1.3568   0.5702
 N61  N2   N  N     0  -0.322   5.7271   0.5354   0.2644
 N61  N1   N  NR5   0  -0.336   4.5808   1.2298   0.2646
 N61  C1   C  CH3   0  -0.556   4.5851   2.6607   0.4463
 N61  N4   N  NH1   0  -0.793  -0.0147   1.0861  -0.1370
 N61  C10  C  CR6   0   0.379  -1.3274   0.7141  -0.4312
 N61  C20  C  CR16  0  -0.305  -1.7818  -0.6051  -0.4286
 N61  C19  C  CR16  0  -0.295  -3.1181  -0.8787  -0.6826
 N61  C13  C  CR6   0   0.281  -4.0057   0.1514  -0.9361
 N61  C12  C  CR16  0  -0.287  -3.5706   1.4663  -0.9383
 N61  C11  C  CR16  0  -0.343  -2.2372   1.7409  -0.6926
 N61  O2   O  O2    0  -0.501  -5.3226  -0.1387  -1.2225
 N61  C14  C  CR6   0   0.456  -6.2382  -0.0740  -0.2348
 N61  C18  C  CR16  0  -0.409  -5.9413   0.2001   1.0952
 N61  C17  C  CR16  0  -0.064  -6.9931   0.2352   1.9989
 N61  N5   N  N     0  -0.419  -8.2638   0.0253   1.6811
 N61  C16  C  CR16  0  -0.063  -8.5260  -0.2380   0.4033
 N61  C15  C  CR16  0  -0.400  -7.5655  -0.3009  -0.5882
 N61  H1   H  HNH1  0   0.428   2.1425   1.8862   0.5626
 N61  H2   H  HCR5  0   0.262   3.4151  -1.7668  -0.1254
 N61  H3   H  HCH3  0   0.227   5.0089  -3.4512   0.3510
 N61  H4   H  HCH3  0   0.228   6.6846  -3.8483   0.7123
 N61  H5   H  HCH3  0   0.228   5.7632  -2.8284   1.8189
 N61  H6   H  HCH3  0   0.226   6.9583  -1.3293  -2.0562
 N61  H7   H  HCH3  0   0.224   7.3418  -2.9868  -1.5863
 N61  H8   H  HCH3  0   0.227   5.6719  -2.5311  -1.9270
 N61  H9   H  HCH3  0   0.223   7.6748  -1.0732   1.6204
 N61  H10  H  HCH3  0   0.224   8.4891  -2.1653   0.4995
 N61  H11  H  HCH3  0   0.226   8.1551  -0.5015   0.0225
 N61  H12  H  HCH3  0   0.259   4.2108   2.9435   1.4310
 N61  H13  H  HCH3  0   0.279   5.6090   3.0076   0.3509
 N61  H14  H  HCH3  0   0.260   3.9813   3.1487  -0.3179
 N61  H15  H  HNH1  0   0.417   0.1136   2.0679   0.0583
 N61  H16  H  HCR6  0   0.281  -1.1124  -1.4249  -0.2245
 N61  H17  H  HCR6  0   0.277  -3.4628  -1.9051  -0.6792
 N61  H18  H  HCR6  0   0.281  -4.2619   2.2750  -1.1388
 N61  H19  H  HCR6  0   0.278  -1.8983   2.7698  -0.7014
 N61  H20  H  HCR6  0   0.290  -4.9334   0.3847   1.4397
 N61  H21  H  HCR6  0   0.268  -6.7814   0.4467   3.0412
 N61  H22  H  HCR6  0   0.268  -9.5656  -0.4077   0.1461
 N61  H23  H  HCR6  0   0.283  -7.8412  -0.5173  -1.6116

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
 N61  C17  N5   aromatic  1.327  0.020  1.327
 N61  C17  C18  aromatic  1.387  0.020  1.387
 N61  N5   C16  aromatic  1.331  0.020  1.331
 N61  C18  C14  aromatic  1.390  0.020  1.390
 N61  C16  C15  aromatic  1.382  0.020  1.382
 N61  C14  C15  aromatic  1.392  0.020  1.392
 N61  C14  O2   single    1.348  0.020  1.348
 N61  O2   C13  single    1.379  0.020  1.379
 N61  C13  C12  aromatic  1.385  0.020  1.385
 N61  C13  C19  aromatic  1.383  0.020  1.383
 N61  C12  C11  aromatic  1.383  0.020  1.383
 N61  C19  C20  aromatic  1.387  0.020  1.387
 N61  C11  C10  aromatic  1.397  0.020  1.397
 N61  C20  C10  aromatic  1.395  0.020  1.395
 N61  C10  N4   single    1.396  0.020  1.396
 N61  N4   C9   single    1.367  0.020  1.367
 N61  C9   O1   double    1.216  0.020  1.216
 N61  C9   N3   single    1.371  0.020  1.371
 N61  N3   C8   single    1.382  0.020  1.382
 N61  C7   C8   aromatic  1.380  0.020  1.380
 N61  C7   C2   aromatic  1.411  0.020  1.411
 N61  C8   N1   aromatic  1.348  0.020  1.348
 N61  C4   C3   single    1.529  0.020  1.529
 N61  N1   C1   single    1.442  0.020  1.442
 N61  N1   N2   aromatic  1.340  0.020  1.340
 N61  C2   C3   single    1.507  0.020  1.507
 N61  C2   N2   aromatic  1.317  0.020  1.317
 N61  C6   C3   single    1.531  0.020  1.531
 N61  C3   C5   single    1.535  0.020  1.535
 N61  N3   H1   single    0.860  0.020  1.020
 N61  C7   H2   single    0.930  0.020  1.080
 N61  C6   H3   single    0.970  0.020  1.090
 N61  C6   H4   single    0.970  0.020  1.090
 N61  C6   H5   single    0.970  0.020  1.090
 N61  C5   H6   single    0.970  0.020  1.090
 N61  C5   H7   single    0.970  0.020  1.090
 N61  C5   H8   single    0.970  0.020  1.090
 N61  C4   H9   single    0.970  0.020  1.090
 N61  C4   H10  single    0.970  0.020  1.090
 N61  C4   H11  single    0.970  0.020  1.090
 N61  C1   H12  single    0.970  0.020  1.090
 N61  C1   H13  single    0.970  0.020  1.090
 N61  C1   H14  single    0.970  0.020  1.090
 N61  N4   H15  single    0.860  0.020  1.020
 N61  C20  H16  single    0.930  0.020  1.080
 N61  C19  H17  single    0.930  0.020  1.080
 N61  C12  H18  single    0.930  0.020  1.080
 N61  C11  H19  single    0.930  0.020  1.080
 N61  C18  H20  single    0.930  0.020  1.080
 N61  C17  H21  single    0.930  0.020  1.080
 N61  C16  H22  single    0.930  0.020  1.080
 N61  C15  H23  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
 N61  N4   C9   N3   112.40  3.000
 N61  N3   C9   O1   123.05  3.000
 N61  N4   C9   O1   124.56  3.000
 N61  H1   N3   C8   117.06  3.000
 N61  H1   N3   C9   118.51  3.000
 N61  C8   N3   C9   124.31  3.000
 N61  N1   C8   C7   107.03  3.000
 N61  N1   C8   N3   119.52  3.000
 N61  C7   C8   N3   133.43  3.000
 N61  H2   C7   C2   128.13  3.000
 N61  H2   C7   C8   127.70  3.000
 N61  C2   C7   C8   104.17  3.000
 N61  N2   C2   C3   121.68  3.000
 N61  N2   C2   C7   111.11  3.000
 N61  C3   C2   C7   127.19  3.000
 N61  C4   C3   C5   108.99  3.000
 N61  C5   C3   C6   109.12  3.000
 N61  C4   C3   C6   109.41  3.000
 N61  C5   C3   C2   108.77  3.000
 N61  C6   C3   C2   109.62  3.000
 N61  C4   C3   C2   110.90  3.000
 N61  H5   C6   H4   107.86  3.000
 N61  H5   C6   H3   107.83  3.000
 N61  H4   C6   H3   107.41  3.000
 N61  H5   C6   C3   111.50  3.000
 N61  H4   C6   C3   110.31  3.000
 N61  H3   C6   C3   111.75  3.000
 N61  H8   C5   H7   107.76  3.000
 N61  H8   C5   H6   107.92  3.000
 N61  H7   C5   H6   107.81  3.000
 N61  H8   C5   C3   111.49  3.000
 N61  H7   C5   C3   110.59  3.000
 N61  H6   C5   C3   111.12  3.000
 N61  H11  C4   H10  107.83  3.000
 N61  H11  C4   H9   107.93  3.000
 N61  H10  C4   H9   107.88  3.000
 N61  H11  C4   C3   111.57  3.000
 N61  H10  C4   C3   109.75  3.000
 N61  H9   C4   C3   111.72  3.000
 N61  N1   N2   C2   105.93  3.000
 N61  C1   N1   N2   120.76  3.000
 N61  N2   N1   C8   111.75  3.000
 N61  C1   N1   C8   127.46  3.000
 N61  H14  C1   H13  108.55  3.000
 N61  H14  C1   H12  109.08  3.000
 N61  H13  C1   H12  108.68  3.000
 N61  H14  C1   N1   110.75  3.000
 N61  H13  C1   N1   107.99  3.000
 N61  H12  C1   N1   111.71  3.000
 N61  H15  N4   C10  114.82  3.000
 N61  H15  N4   C9   117.49  3.000
 N61  C10  N4   C9   127.06  3.000
 N61  C11  C10  C20  118.90  3.000
 N61  C20  C10  N4   123.91  3.000
 N61  C11  C10  N4   117.14  3.000
 N61  H16  C20  C19  118.87  3.000
 N61  H16  C20  C10  121.14  3.000
 N61  C19  C20  C10  119.98  3.000
 N61  H17  C19  C13  120.15  3.000
 N61  H17  C19  C20  119.54  3.000
 N61  C13  C19  C20  120.31  3.000
 N61  O2   C13  C12  119.97  3.000
 N61  C12  C13  C19  120.38  3.000
 N61  O2   C13  C19  119.62  3.000
 N61  H18  C12  C11  120.01  3.000
 N61  H18  C12  C13  120.59  3.000
 N61  C11  C12  C13  119.40  3.000
 N61  H19  C11  C12  119.25  3.000
 N61  H19  C11  C10  119.74  3.000
 N61  C12  C11  C10  121.01  3.000
 N61  C14  O2   C13  119.10  3.000
 N61  C15  C14  C18  118.60  3.000
 N61  C15  C14  O2   116.98  3.000
 N61  C18  C14  O2   124.43  3.000
 N61  H20  C18  C17  119.68  3.000
 N61  H20  C18  C14  122.53  3.000
 N61  C17  C18  C14  117.80  3.000
 N61  H21  C17  N5   116.63  3.000
 N61  H21  C17  C18  118.88  3.000
 N61  N5   C17  C18  124.49  3.000
 N61  C16  N5   C17  116.75  3.000
 N61  H22  C16  C15  119.29  3.000
 N61  H22  C16  N5   116.59  3.000
 N61  C15  C16  N5   124.12  3.000
 N61  H23  C15  C16  120.71  3.000
 N61  H23  C15  C14  121.05  3.000
 N61  C16  C15  C14  118.24  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
 N61  CONST_01  N2   C2   C7   C8      0.00   0.0  0
 N61  CONST_02  C2   N2   N1   C8      0.00   0.0  0
 N61  CONST_03  N2   N1   C8   C7      0.00   0.0  0
 N61  CONST_04  N1   N2   C2   C7      0.00   0.0  0
 N61  CONST_05  N1   C8   C7   C2      0.00   0.0  0
 N61  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 N61  CONST_07  C13  C19  C20  C10     0.00   0.0  0
 N61  CONST_08  C12  C13  C19  C20     0.00   0.0  0
 N61  CONST_09  C12  C11  C10  C20     0.00   0.0  0
 N61  CONST_10  C11  C12  C13  C19     0.00   0.0  0
 N61  CONST_11  C11  C10  C20  C19     0.00   0.0  0
 N61  CONST_12  N5   C17  C18  C14     0.00   0.0  0
 N61  CONST_13  N5   C16  C15  C14     0.00   0.0  0
 N61  CONST_14  C16  N5   C17  C18     0.00   0.0  0
 N61  CONST_15  C16  C15  C14  C18     0.00   0.0  0
 N61  CONST_16  C15  C16  N5   C17     0.00   0.0  0
 N61  CONST_17  C15  C14  C18  C17     0.00   0.0  0
 N61  CONST_18  C2   C7   C8   N3    180.00   0.0  0
 N61  CONST_19  N2   N1   C8   N3    180.00   0.0  0
 N61  CONST_20  C3   C2   C7   C8    180.00   0.0  0
 N61  CONST_21  C1   N1   C8   C7    180.00   0.0  0
 N61  CONST_22  C1   N1   N2   C2    180.00   0.0  0
 N61  CONST_23  N1   N2   C2   C3    180.00   0.0  0
 N61  CONST_24  C12  C11  C10  N4    180.00   0.0  0
 N61  CONST_25  C19  C20  C10  N4    180.00   0.0  0
 N61  CONST_26  O2   C13  C19  C20   180.00   0.0  0
 N61  CONST_27  O2   C13  C12  C11   180.00   0.0  0
 N61  CONST_28  C17  C18  C14  O2    180.00   0.0  0
 N61  CONST_29  C16  C15  C14  O2    180.00   0.0  0
 N61  CONST_30  H2   C7   C2   N2    180.00   0.0  0
 N61  CONST_31  H18  C12  C11  C10   180.00   0.0  0
 N61  CONST_32  H17  C19  C20  C10   180.00   0.0  0
 N61  CONST_33  H19  C11  C10  C20   180.00   0.0  0
 N61  CONST_34  H16  C20  C19  C13   180.00   0.0  0
 N61  CONST_35  H21  C17  C18  C14   180.00   0.0  0
 N61  CONST_36  H22  C16  C15  C14   180.00   0.0  0
 N61  CONST_37  H23  C15  C14  C18   180.00   0.0  0
 N61  CONST_38  H20  C18  C17  N5    180.00   0.0  0
 N61  CONST_42  N1   C8   N3   C9    180.00   0.0  0
 N61  CONST_45  C10  N4   C9   O1      0.00   0.0  0
 N61  CONST_46  C8   N3   C9   O1      0.00   0.0  0
 N61  CONST_47  C10  N4   C9   N3    180.00   0.0  0
 N61  CONST_48  N4   C9   N3   C8    180.00   0.0  0
 N61  Var_01    C18  C14  O2   C13    -3.63  30.0  2
 N61  Var_02    C4   C3   C2   C7   -162.60  30.0  2
 N61  Var_03    H12  C1   N1   C8     70.28  30.0  2
 N61  Var_04    H9   C4   C3   C2     59.66  30.0  3
 N61  Var_05    H3   C6   C3   C2     61.45  30.0  3
 N61  Var_06    H6   C5   C3   C2     60.98  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
 N61  plan-1  N3   0.020
 N61  plan-1  C8   0.020
 N61  plan-1  C7   0.020
 N61  plan-1  C2   0.020
 N61  plan-1  C3   0.020
 N61  plan-1  N2   0.020
 N61  plan-1  N1   0.020
 N61  plan-1  C1   0.020
 N61  plan-1  H2   0.020
 N61  plan-2  N4   0.020
 N61  plan-2  C10  0.020
 N61  plan-2  C20  0.020
 N61  plan-2  C19  0.020
 N61  plan-2  C13  0.020
 N61  plan-2  C12  0.020
 N61  plan-2  C11  0.020
 N61  plan-2  O2   0.020
 N61  plan-2  H16  0.020
 N61  plan-2  H17  0.020
 N61  plan-2  H18  0.020
 N61  plan-2  H19  0.020
 N61  plan-3  O2   0.020
 N61  plan-3  C14  0.020
 N61  plan-3  C18  0.020
 N61  plan-3  C17  0.020
 N61  plan-3  N5   0.020
 N61  plan-3  C16  0.020
 N61  plan-3  C15  0.020
 N61  plan-3  H20  0.020
 N61  plan-3  H21  0.020
 N61  plan-3  H22  0.020
 N61  plan-3  H23  0.020
 N61  plan-4  O1   0.020
 N61  plan-4  C9   0.020
 N61  plan-4  N3   0.020
 N61  plan-4  C8   0.020
 N61  plan-4  N4   0.020
 N61  plan-4  C10  0.020
 N61  plan-4  H1   0.020
 N61  plan-4  H15  0.020

