# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:58:29 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-ylsulfanyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(cc1NC(=O)Nc2ccc(Sc3ccncc3)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
 N58  N58  1-(3-tert-butyl-1-methyl-1H-pyrazol-5-yl)-3-[4-(pyridin-4-ylsulfanyl)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_N58
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
 N58  O1   O  O     0  -0.482   1.3249  -0.7539  -0.5703
 N58  C9   C  C     0   0.750   1.3333   0.4462  -0.3825
 N58  N3   N  NH1   0  -0.803   2.4725   1.1458  -0.0815
 N58  C8   C  CR5   0   0.661   3.7241   0.5710   0.0371
 N58  C7   C  CR15  0  -0.545   4.1528  -0.7229   0.2451
 N58  C2   C  CR5   0   0.338   5.5583  -0.6163   0.3033
 N58  C3   C  CT    0  -0.189   6.5417  -1.7394   0.5053
 N58  C6   C  CH3   0  -0.633   6.1971  -2.4860   1.7993
 N58  C5   C  CH3   0  -0.630   6.4410  -2.7130  -0.6756
 N58  C4   C  CH3   0  -0.637   7.9712  -1.2082   0.5987
 N58  N2   N  N     0  -0.320   5.9461   0.6325   0.1463
 N58  N1   N  NR5   0  -0.334   4.8253   1.3469  -0.0289
 N58  C1   C  CH3   0  -0.556   4.8859   2.7778  -0.1965
 N58  N4   N  NH1   0  -0.796   0.2272   1.2512  -0.4418
 N58  C10  C  CR6   0   0.389  -1.0857   0.8923  -0.7210
 N58  C20  C  CR16  0  -0.310  -1.5359  -0.4194  -0.8943
 N58  C19  C  CR16  0  -0.200  -2.8749  -0.6575  -1.1637
 N58  C13  C  CR6   0  -0.213  -3.7852   0.3863  -1.2637
 N58  C12  C  CR16  0  -0.197  -3.3377   1.6937  -1.0954
 N58  C11  C  CR16  0  -0.346  -2.0074   1.9416  -0.8243
 N58  S    S  S2    0   0.102  -5.4781   0.0644  -1.6489
 N58  C14  C  CR6   0  -0.015  -6.2470  -0.0092  -0.0683
 N58  C18  C  CR16  0  -0.317  -5.5697   0.0787   1.1424
 N58  C17  C  CR16  0  -0.058  -6.3048   0.0020   2.3155
 N58  N5   N  N     0  -0.415  -7.6224  -0.1519   2.3616
 N58  C16  C  CR16  0  -0.057  -8.2591  -0.2373   1.1976
 N58  C15  C  CR16  0  -0.342  -7.6309  -0.1734  -0.0335
 N58  H1   H  HNH1  0   0.429   2.4051   2.1391   0.0821
 N58  H2   H  HCR5  0   0.263   3.5473  -1.6056   0.3443
 N58  H3   H  HCH3  0   0.226   5.1918  -2.9090   1.7658
 N58  H4   H  HCH3  0   0.226   6.8972  -3.3086   1.9591
 N58  H5   H  HCH3  0   0.227   6.2509  -1.8245   2.6658
 N58  H6   H  HCH3  0   0.226   6.6771  -2.2176  -1.6191
 N58  H7   H  HCH3  0   0.225   7.1423  -3.5400  -0.5455
 N58  H8   H  HCH3  0   0.226   5.4393  -3.1371  -0.7628
 N58  H9   H  HCH3  0   0.224   8.0893  -0.5086   1.4272
 N58  H10  H  HCH3  0   0.224   8.6628  -2.0374   0.7602
 N58  H11  H  HCH3  0   0.224   8.2735  -0.6949  -0.3149
 N58  H12  H  HCH3  0   0.260   4.5576   3.3037   0.7012
 N58  H13  H  HCH3  0   0.279   5.9170   3.0475  -0.4011
 N58  H14  H  HCH3  0   0.259   4.2740   3.0970  -1.0394
 N58  H15  H  HNH1  0   0.421   0.3689   2.2417  -0.3084
 N58  H16  H  HCR6  0   0.289  -0.8604  -1.2547  -0.8230
 N58  H17  H  HCR6  0   0.276  -3.2081  -1.6787  -1.2948
 N58  H18  H  HCR6  0   0.279  -4.0306   2.5212  -1.1727
 N58  H19  H  HCR6  0   0.279  -1.6752   2.9645  -0.6934
 N58  H20  H  HCR6  0   0.275  -4.4968   0.2019   1.1897
 N58  H21  H  HCR6  0   0.267  -5.7902   0.0696   3.2679
 N58  H22  H  HCR6  0   0.268  -9.3355  -0.3613   1.2400
 N58  H23  H  HCR6  0   0.281  -8.2154  -0.2487  -0.9414

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
 N58  C17  N5   aromatic  1.327  0.020  1.327
 N58  C17  C18  aromatic  1.387  0.020  1.387
 N58  N5   C16  aromatic  1.329  0.020  1.329
 N58  C18  C14  aromatic  1.390  0.020  1.390
 N58  C16  C15  aromatic  1.384  0.020  1.384
 N58  C14  C15  aromatic  1.394  0.020  1.394
 N58  C14  S    single    1.759  0.020  1.759
 N58  S    C13  single    1.766  0.020  1.766
 N58  C12  C13  aromatic  1.392  0.020  1.392
 N58  C12  C11  aromatic  1.380  0.020  1.380
 N58  C13  C19  aromatic  1.389  0.020  1.389
 N58  C11  C10  aromatic  1.400  0.020  1.400
 N58  C19  C20  aromatic  1.386  0.020  1.386
 N58  C10  C20  aromatic  1.398  0.020  1.398
 N58  C10  N4   single    1.389  0.020  1.389
 N58  N4   C9   single    1.369  0.020  1.369
 N58  C9   O1   double    1.215  0.020  1.215
 N58  C9   N3   single    1.370  0.020  1.370
 N58  N3   C8   single    1.382  0.020  1.382
 N58  C8   C7   aromatic  1.379  0.020  1.379
 N58  C8   N1   aromatic  1.349  0.020  1.349
 N58  C7   C2   aromatic  1.411  0.020  1.411
 N58  N1   C1   single    1.442  0.020  1.442
 N58  N1   N2   aromatic  1.341  0.020  1.341
 N58  C2   C3   single    1.506  0.020  1.506
 N58  C2   N2   aromatic  1.317  0.020  1.317
 N58  C6   C3   single    1.533  0.020  1.533
 N58  C4   C3   single    1.528  0.020  1.528
 N58  C3   C5   single    1.534  0.020  1.534
 N58  N3   H1   single    0.860  0.020  1.020
 N58  C7   H2   single    0.930  0.020  1.080
 N58  C6   H3   single    0.970  0.020  1.090
 N58  C6   H4   single    0.970  0.020  1.090
 N58  C6   H5   single    0.970  0.020  1.090
 N58  C5   H6   single    0.970  0.020  1.090
 N58  C5   H7   single    0.970  0.020  1.090
 N58  C5   H8   single    0.970  0.020  1.090
 N58  C4   H9   single    0.970  0.020  1.090
 N58  C4   H10  single    0.970  0.020  1.090
 N58  C4   H11  single    0.970  0.020  1.090
 N58  C1   H12  single    0.970  0.020  1.090
 N58  C1   H13  single    0.970  0.020  1.090
 N58  C1   H14  single    0.970  0.020  1.090
 N58  N4   H15  single    0.860  0.020  1.020
 N58  C20  H16  single    0.930  0.020  1.080
 N58  C19  H17  single    0.930  0.020  1.080
 N58  C12  H18  single    0.930  0.020  1.080
 N58  C11  H19  single    0.930  0.020  1.080
 N58  C18  H20  single    0.930  0.020  1.080
 N58  C17  H21  single    0.930  0.020  1.080
 N58  C16  H22  single    0.930  0.020  1.080
 N58  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
 N58  N4   C9   N3   112.39  3.000
 N58  N3   C9   O1   122.96  3.000
 N58  N4   C9   O1   124.65  3.000
 N58  H1   N3   C8   117.12  3.000
 N58  H1   N3   C9   118.86  3.000
 N58  C8   N3   C9   124.01  3.000
 N58  N1   C8   C7   107.05  3.000
 N58  N1   C8   N3   119.73  3.000
 N58  C7   C8   N3   133.21  3.000
 N58  H2   C7   C2   128.28  3.000
 N58  H2   C7   C8   127.54  3.000
 N58  C2   C7   C8   104.19  3.000
 N58  N2   C2   C3   122.05  3.000
 N58  N2   C2   C7   111.10  3.000
 N58  C3   C2   C7   126.84  3.000
 N58  C4   C3   C5   109.22  3.000
 N58  C5   C3   C6   109.02  3.000
 N58  C4   C3   C6   109.15  3.000
 N58  C5   C3   C2   109.09  3.000
 N58  C4   C3   C2   111.09  3.000
 N58  C6   C3   C2   109.24  3.000
 N58  H5   C6   H4   107.98  3.000
 N58  H5   C6   H3   107.74  3.000
 N58  H4   C6   H3   107.64  3.000
 N58  H5   C6   C3   111.34  3.000
 N58  H4   C6   C3   110.26  3.000
 N58  H3   C6   C3   111.71  3.000
 N58  H8   C5   H7   107.74  3.000
 N58  H8   C5   H6   107.82  3.000
 N58  H7   C5   H6   107.92  3.000
 N58  H8   C5   C3   111.62  3.000
 N58  H7   C5   C3   110.29  3.000
 N58  H6   C5   C3   111.30  3.000
 N58  H11  C4   H10  107.81  3.000
 N58  H11  C4   H9   107.73  3.000
 N58  H10  C4   H9   107.83  3.000
 N58  H11  C4   C3   111.82  3.000
 N58  H10  C4   C3   109.73  3.000
 N58  H9   C4   C3   111.76  3.000
 N58  N1   N2   C2   105.94  3.000
 N58  C1   N1   N2   120.58  3.000
 N58  N2   N1   C8   111.70  3.000
 N58  C1   N1   C8   127.65  3.000
 N58  H14  C1   H13  108.36  3.000
 N58  H14  C1   H12  109.05  3.000
 N58  H13  C1   H12  108.74  3.000
 N58  H14  C1   N1   110.92  3.000
 N58  H13  C1   N1   107.97  3.000
 N58  H12  C1   N1   111.72  3.000
 N58  H15  N4   C10  114.37  3.000
 N58  H15  N4   C9   117.24  3.000
 N58  C10  N4   C9   128.33  3.000
 N58  C11  C10  C20  118.82  3.000
 N58  C20  C10  N4   124.87  3.000
 N58  C11  C10  N4   116.31  3.000
 N58  H16  C20  C19  119.05  3.000
 N58  H16  C20  C10  121.19  3.000
 N58  C19  C20  C10  119.76  3.000
 N58  H17  C19  C13  119.92  3.000
 N58  H17  C19  C20  118.88  3.000
 N58  C13  C19  C20  121.20  3.000
 N58  S    C13  C12  120.39  3.000
 N58  C12  C13  C19  119.11  3.000
 N58  S    C13  C19  120.47  3.000
 N58  H18  C12  C11  119.60  3.000
 N58  H18  C12  C13  120.24  3.000
 N58  C11  C12  C13  120.15  3.000
 N58  H19  C11  C12  119.27  3.000
 N58  H19  C11  C10  119.78  3.000
 N58  C12  C11  C10  120.95  3.000
 N58  C14  S    C13  103.33  3.000
 N58  C15  C14  C18  117.99  3.000
 N58  C15  C14  S    117.47  3.000
 N58  C18  C14  S    124.54  3.000
 N58  H20  C18  C17  119.70  3.000
 N58  H20  C18  C14  121.93  3.000
 N58  C17  C18  C14  118.37  3.000
 N58  H21  C17  N5   116.60  3.000
 N58  H21  C17  C18  119.20  3.000
 N58  N5   C17  C18  124.20  3.000
 N58  C16  N5   C17  116.90  3.000
 N58  H22  C16  C15  119.39  3.000
 N58  H22  C16  N5   116.65  3.000
 N58  C15  C16  N5   123.96  3.000
 N58  H23  C15  C16  119.86  3.000
 N58  H23  C15  C14  121.55  3.000
 N58  C16  C15  C14  118.58  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
 N58  CONST_01  N2   C2   C7   C8     0.00   0.0  0
 N58  CONST_02  C2   N2   N1   C8     0.00   0.0  0
 N58  CONST_03  N2   N1   C8   C7     0.00   0.0  0
 N58  CONST_04  N1   N2   C2   C7     0.00   0.0  0
 N58  CONST_05  N1   C8   C7   C2     0.00   0.0  0
 N58  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 N58  CONST_07  C13  C19  C20  C10    0.00   0.0  0
 N58  CONST_08  C12  C13  C19  C20    0.00   0.0  0
 N58  CONST_09  C12  C11  C10  C20    0.00   0.0  0
 N58  CONST_10  C11  C12  C13  C19    0.00   0.0  0
 N58  CONST_11  C11  C10  C20  C19    0.00   0.0  0
 N58  CONST_12  N5   C17  C18  C14    0.00   0.0  0
 N58  CONST_13  N5   C16  C15  C14    0.00   0.0  0
 N58  CONST_14  C16  N5   C17  C18    0.00   0.0  0
 N58  CONST_15  C16  C15  C14  C18    0.00   0.0  0
 N58  CONST_16  C15  C16  N5   C17    0.00   0.0  0
 N58  CONST_17  C15  C14  C18  C17    0.00   0.0  0
 N58  CONST_18  C2   C7   C8   N3   180.00   0.0  0
 N58  CONST_19  N2   N1   C8   N3   180.00   0.0  0
 N58  CONST_20  C3   C2   C7   C8   180.00   0.0  0
 N58  CONST_21  C1   N1   C8   C7   180.00   0.0  0
 N58  CONST_22  C1   N1   N2   C2   180.00   0.0  0
 N58  CONST_23  N1   N2   C2   C3   180.00   0.0  0
 N58  CONST_24  C12  C11  C10  N4   180.00   0.0  0
 N58  CONST_25  C19  C20  C10  N4   180.00   0.0  0
 N58  CONST_26  S    C13  C19  C20  180.00   0.0  0
 N58  CONST_27  S    C13  C12  C11  180.00   0.0  0
 N58  CONST_28  C17  C18  C14  S    180.00   0.0  0
 N58  CONST_29  C16  C15  C14  S    180.00   0.0  0
 N58  CONST_30  H2   C7   C2   N2   180.00   0.0  0
 N58  CONST_31  H18  C12  C11  C10  180.00   0.0  0
 N58  CONST_32  H17  C19  C20  C10  180.00   0.0  0
 N58  CONST_33  H19  C11  C10  C20  180.00   0.0  0
 N58  CONST_34  H16  C20  C19  C13  180.00   0.0  0
 N58  CONST_35  H21  C17  C18  C14  180.00   0.0  0
 N58  CONST_36  H22  C16  C15  C14  180.00   0.0  0
 N58  CONST_37  H23  C15  C14  C18  180.00   0.0  0
 N58  CONST_38  H20  C18  C17  N5   180.00   0.0  0
 N58  CONST_39  C11  C10  N4   C9   180.00   0.0  0
 N58  CONST_40  C20  C10  N4   C9     0.00   0.0  0
 N58  CONST_44  H15  N4   C10  C20  180.00   0.0  0
 N58  CONST_45  C10  N4   C9   O1     0.00   0.0  0
 N58  CONST_46  C8   N3   C9   O1     0.00   0.0  0
 N58  CONST_47  C10  N4   C9   N3   180.00   0.0  0
 N58  CONST_48  N4   C9   N3   C8   180.00   0.0  0
 N58  Var_01    C18  C14  S    C13   -4.17  30.0  2
 N58  Var_02    C6   C3   C2   C7   -55.91  30.0  2
 N58  Var_03    H12  C1   N1   C8    71.39  30.0  2
 N58  Var_04    H3   C6   C3   C2    60.01  30.0  3
 N58  Var_05    H9   C4   C3   C2    59.56  30.0  3
 N58  Var_06    H6   C5   C3   C2    60.63  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
 N58  plan-1  N3   0.020
 N58  plan-1  C8   0.020
 N58  plan-1  C7   0.020
 N58  plan-1  C2   0.020
 N58  plan-1  C3   0.020
 N58  plan-1  N2   0.020
 N58  plan-1  N1   0.020
 N58  plan-1  C1   0.020
 N58  plan-1  H2   0.020
 N58  plan-2  N4   0.020
 N58  plan-2  C10  0.020
 N58  plan-2  C20  0.020
 N58  plan-2  C19  0.020
 N58  plan-2  C13  0.020
 N58  plan-2  C12  0.020
 N58  plan-2  C11  0.020
 N58  plan-2  S    0.020
 N58  plan-2  H16  0.020
 N58  plan-2  H17  0.020
 N58  plan-2  H18  0.020
 N58  plan-2  H19  0.020
 N58  plan-3  S    0.020
 N58  plan-3  C14  0.020
 N58  plan-3  C18  0.020
 N58  plan-3  C17  0.020
 N58  plan-3  N5   0.020
 N58  plan-3  C16  0.020
 N58  plan-3  C15  0.020
 N58  plan-3  H20  0.020
 N58  plan-3  H21  0.020
 N58  plan-3  H22  0.020
 N58  plan-3  H23  0.020
 N58  plan-4  O1   0.020
 N58  plan-4  C9   0.020
 N58  plan-4  N3   0.020
 N58  plan-4  C8   0.020
 N58  plan-4  N4   0.020
 N58  plan-4  C10  0.020
 N58  plan-4  H1   0.020
 N58  plan-4  H15  0.020

