# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 14:31:21 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 1-{5-bromo-2-[(3R)-3-hydroxypiperidin-1-yl]phenyl}-3-(5-cyanopyrazin-2-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCCN(C1)c2ccc(Br)cc2NC(=O)Nc3cnc(cn3)C#N
#
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
 H3K  H3K  1-{5-bromo-2-[(3R)-3-hydroxypiperidin-1-yl]phenyl}-3-(5-cyanopyrazin-2-yl)urea  ligand  43  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H3K
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
 H3K  N6   N   NS    0  -0.238  -8.2207  -2.2342  -0.0020
 H3K  C17  C   CSP   0   0.064  -7.0849  -2.0509   0.0440
 H3K  C15  C   CR6   0   0.132  -5.6776  -1.8079   0.0952
 H3K  N4   N   N     0  -0.344  -4.8916  -2.8096   0.5062
 H3K  C14  C   CR16  0  -0.157  -3.6089  -2.5782   0.5563
 H3K  C16  C   CR16  0  -0.040  -5.1533  -0.5796  -0.2695
 H3K  N5   N   N     0  -0.379  -3.8516  -0.3413  -0.2261
 H3K  C13  C   CR6   0   0.515  -3.0698  -1.3206   0.1894
 H3K  N3   N   NH1   0  -0.774  -1.7134  -1.1678   0.2498
 H3K  C12  C   C     0   0.744  -0.9942   0.0194   0.1551
 H3K  O2   O   O     0  -0.458  -1.5044   1.1165   0.1793
 H3K  N2   N   NH1   0  -0.783   0.3391  -0.2231   0.0505
 H3K  C11  C   CR6   0   0.340   1.3826   0.6883  -0.0227
 H3K  C10  C   CR16  0  -0.296   1.2560   2.0706   0.1063
 H3K  C9   C   CR6   0  -0.107   2.3965   2.8551   0.0137
 H3K  BR   BR  BR    0  -0.045   2.2146   4.7284   0.1875
 H3K  C8   C   CR16  0  -0.252   3.6534   2.3180  -0.2026
 H3K  C7   C   CR16  0  -0.266   3.7630   0.9394  -0.3246
 H3K  C6   C   CR6   0   0.222   2.6516   0.1188  -0.2374
 H3K  N1   N   NT    0  -0.539   2.7177  -1.2951  -0.3529
 H3K  C4   C   CH2   0  -0.285   3.1814  -1.7667  -1.6556
 H3K  C3   C   CH2   0  -0.455   2.9597  -3.2651  -1.7712
 H3K  C2   C   CH2   0  -0.484   3.6294  -4.0022  -0.6172
 H3K  C5   C   CH2   0  -0.305   3.4028  -1.9375   0.7629
 H3K  C1   C   CH1   0   0.064   3.1609  -3.4394   0.7173
 H3K  O1   O   OH1   0  -0.674   3.8439  -4.0012   1.8164
 H3K  H16  H   HCR6  0   0.302  -2.9625  -3.3822   0.8895
 H3K  H17  H   HCR6  0   0.300  -5.7953   0.2241  -0.6098
 H3K  H15  H   HNH1  0   0.429  -1.1949  -2.0094   0.4552
 H3K  H14  H   HNH1  0   0.406   0.6867  -1.1716  -0.0773
 H3K  H13  H   HCR6  0   0.298   0.2923   2.5227   0.2742
 H3K  H12  H   HCR6  0   0.280   4.5321   2.9435  -0.2751
 H3K  H11  H   HCR6  0   0.270   4.7399   0.5033  -0.4942
 H3K  H7   H   HCH2  0   0.253   2.6240  -1.2399  -2.4315
 H3K  H8   H   HCH2  0   0.212   4.2467  -1.5371  -1.8099
 H3K  H6   H   HCH2  0   0.227   1.8850  -3.4689  -1.7763
 H3K  H5   H   HCH2  0   0.244   3.3554  -3.6160  -2.7256
 H3K  H4   H   HCH2  0   0.243   3.4156  -5.0733  -0.6738
 H3K  H3   H   HCH2  0   0.221   4.7167  -3.8867  -0.6869
 H3K  H10  H   HCH2  0   0.214   4.4875  -1.7434   0.7453
 H3K  H9   H   HCH2  0   0.257   3.0119  -1.5252   1.6955
 H3K  H1   H   HCH1  0   0.194   2.0763  -3.6047   0.8069
 H3K  H2   H   HOH1  0   0.451   3.7045  -4.9532   1.8008

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
 H3K  BR   C9   single    1.890  0.020  1.890
 H3K  O2   C12  double    1.210  0.020  1.210
 H3K  C9   C10  aromatic  1.387  0.020  1.387
 H3K  C9   C8   aromatic  1.384  0.020  1.384
 H3K  C10  C11  aromatic  1.394  0.020  1.394
 H3K  C12  N3   single    1.391  0.020  1.391
 H3K  C12  N2   single    1.359  0.020  1.359
 H3K  C8   C7   aromatic  1.388  0.020  1.388
 H3K  N3   C13  single    1.366  0.020  1.366
 H3K  C11  N2   single    1.387  0.020  1.387
 H3K  C11  C6   aromatic  1.407  0.020  1.407
 H3K  C7   C6   aromatic  1.384  0.020  1.384
 H3K  C6   N1   single    1.420  0.020  1.420
 H3K  C13  C14  aromatic  1.417  0.020  1.417
 H3K  C13  N5   aromatic  1.320  0.020  1.320
 H3K  C4   N1   single    1.461  0.020  1.461
 H3K  C4   C3   single    1.519  0.020  1.519
 H3K  C14  N4   aromatic  1.304  0.020  1.304
 H3K  N5   C16  aromatic  1.324  0.020  1.324
 H3K  N1   C5   single    1.458  0.020  1.458
 H3K  C3   C2   single    1.524  0.020  1.524
 H3K  N4   C15  aromatic  1.338  0.020  1.338
 H3K  C16  C15  aromatic  1.384  0.020  1.384
 H3K  C15  C17  single    1.429  0.020  1.429
 H3K  C5   C1   single    1.522  0.020  1.522
 H3K  C17  N6   triple    1.151  0.020  1.151
 H3K  C2   C1   single    1.522  0.020  1.522
 H3K  C1   O1   single    1.411  0.020  1.411
 H3K  C14  H16  single    0.930  0.020  1.080
 H3K  C16  H17  single    0.930  0.020  1.080
 H3K  N3   H15  single    0.860  0.020  1.020
 H3K  N2   H14  single    0.860  0.020  1.020
 H3K  C10  H13  single    0.930  0.020  1.080
 H3K  C8   H12  single    0.930  0.020  1.080
 H3K  C7   H11  single    0.930  0.020  1.080
 H3K  C4   H7   single    0.970  0.020  1.090
 H3K  C4   H8   single    0.970  0.020  1.090
 H3K  C3   H6   single    0.970  0.020  1.090
 H3K  C3   H5   single    0.970  0.020  1.090
 H3K  C2   H4   single    0.970  0.020  1.090
 H3K  C2   H3   single    0.970  0.020  1.090
 H3K  C5   H10  single    0.970  0.020  1.090
 H3K  C5   H9   single    0.970  0.020  1.090
 H3K  C1   H1   single    0.970  0.020  1.090
 H3K  O1   H2   single    0.850  0.020  0.980

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
 H3K  C15  C17  N6   180.00  3.000
 H3K  C16  C15  N4   121.52  3.000
 H3K  C16  C15  C17  120.96  3.000
 H3K  N4   C15  C17  117.53  3.000
 H3K  C14  N4   C15  117.17  3.000
 H3K  H16  C14  C13  120.74  3.000
 H3K  H16  C14  N4   117.81  3.000
 H3K  C13  C14  N4   121.46  3.000
 H3K  H17  C16  N5   117.35  3.000
 H3K  H17  C16  C15  121.09  3.000
 H3K  N5   C16  C15  121.56  3.000
 H3K  C13  N5   C16  117.32  3.000
 H3K  N3   C13  N5   121.25  3.000
 H3K  N5   C13  C14  120.98  3.000
 H3K  N3   C13  C14  117.75  3.000
 H3K  H15  N3   C12  117.37  3.000
 H3K  H15  N3   C13  115.19  3.000
 H3K  C12  N3   C13  127.28  3.000
 H3K  N2   C12  O2   125.23  3.000
 H3K  N2   C12  N3   111.11  3.000
 H3K  O2   C12  N3   123.66  3.000
 H3K  H14  N2   C11  110.40  3.000
 H3K  H14  N2   C12  120.70  3.000
 H3K  C11  N2   C12  128.66  3.000
 H3K  C6   C11  C10  119.81  3.000
 H3K  C6   C11  N2   114.86  3.000
 H3K  C10  C11  N2   125.32  3.000
 H3K  H13  C10  C9   120.55  3.000
 H3K  H13  C10  C11  120.77  3.000
 H3K  C9   C10  C11  118.68  3.000
 H3K  C8   C9   BR   119.11  3.000
 H3K  C8   C9   C10  122.52  3.000
 H3K  BR   C9   C10  118.37  3.000
 H3K  H12  C8   C7   120.30  3.000
 H3K  H12  C8   C9   121.61  3.000
 H3K  C7   C8   C9   118.09  3.000
 H3K  H11  C7   C6   119.69  3.000
 H3K  H11  C7   C8   118.99  3.000
 H3K  C6   C7   C8   121.31  3.000
 H3K  N1   C6   C7   123.21  3.000
 H3K  N1   C6   C11  117.20  3.000
 H3K  C7   C6   C11  119.59  3.000
 H3K  C5   N1   C4   113.01  3.000
 H3K  C5   N1   C6   113.47  3.000
 H3K  C4   N1   C6   114.12  3.000
 H3K  H8   C4   H7   107.10  3.000
 H3K  H8   C4   C3   109.65  3.000
 H3K  H7   C4   C3   110.34  3.000
 H3K  H8   C4   N1   111.40  3.000
 H3K  H7   C4   N1   108.43  3.000
 H3K  C3   C4   N1   109.87  3.000
 H3K  H5   C3   H6   106.99  3.000
 H3K  H5   C3   C2   110.32  3.000
 H3K  H6   C3   C2   110.19  3.000
 H3K  H5   C3   C4   109.32  3.000
 H3K  H6   C3   C4   109.12  3.000
 H3K  C2   C3   C4   110.81  3.000
 H3K  H3   C2   H4   107.09  3.000
 H3K  H3   C2   C1   108.80  3.000
 H3K  H4   C2   C1   110.32  3.000
 H3K  H3   C2   C3   109.69  3.000
 H3K  H4   C2   C3   110.39  3.000
 H3K  C1   C2   C3   110.47  3.000
 H3K  H9   C5   H10  107.43  3.000
 H3K  H9   C5   C1   109.95  3.000
 H3K  H10  C5   C1   109.26  3.000
 H3K  H9   C5   N1   108.59  3.000
 H3K  H10  C5   N1   111.87  3.000
 H3K  C1   C5   N1   109.70  3.000
 H3K  H1   C1   O1   110.72  3.000
 H3K  H1   C1   C5   107.60  3.000
 H3K  O1   C1   C5   107.02  3.000
 H3K  H1   C1   C2   108.61  3.000
 H3K  O1   C1   C2   112.75  3.000
 H3K  C5   C1   C2   110.01  3.000
 H3K  H2   O1   C1   108.14  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
 H3K  CONST_01  C13  C14  N4   C15     0.00   0.0  0
 H3K  CONST_02  C13  N5   C16  C15     0.00   0.0  0
 H3K  CONST_03  N5   C13  C14  N4      0.00   0.0  0
 H3K  CONST_04  N5   C16  C15  N4      0.00   0.0  0
 H3K  CONST_05  C16  N5   C13  C14     0.00   0.0  0
 H3K  CONST_06  C16  C15  N4   C14     0.00   0.0  0
 H3K  CONST_07  C8   C9   C10  C11     0.00   0.0  0
 H3K  CONST_08  C8   C7   C6   C11     0.00   0.0  0
 H3K  CONST_09  C7   C8   C9   C10     0.00   0.0  0
 H3K  CONST_10  C7   C6   C11  C10     0.00   0.0  0
 H3K  CONST_11  C6   C11  C10  C9      0.00   0.0  0
 H3K  CONST_12  C6   C7   C8   C9      0.00   0.0  0
 H3K  CONST_13  N1   C6   C11  C10   180.00   0.0  0
 H3K  CONST_14  N1   C6   C7   C8    180.00   0.0  0
 H3K  CONST_15  C14  N4   C15  C17   180.00   0.0  0
 H3K  CONST_16  N5   C16  C15  C17   180.00   0.0  0
 H3K  CONST_17  N3   C13  C14  N4    180.00   0.0  0
 H3K  CONST_18  N3   C13  N5   C16   180.00   0.0  0
 H3K  CONST_19  C9   C10  C11  N2    180.00   0.0  0
 H3K  CONST_20  C7   C6   C11  N2    180.00   0.0  0
 H3K  CONST_21  N1   C6   C11  N2      0.00   0.0  0
 H3K  CONST_22  BR   C9   C10  C11   180.00   0.0  0
 H3K  CONST_23  C7   C8   C9   BR    180.00   0.0  0
 H3K  CONST_24  H16  C14  N4   C15   180.00   0.0  0
 H3K  CONST_25  H17  C16  C15  N4    180.00   0.0  0
 H3K  CONST_26  H11  C7   C6   C11   180.00   0.0  0
 H3K  CONST_27  H12  C8   C9   C10   180.00   0.0  0
 H3K  CONST_28  H13  C10  C9   C8    180.00   0.0  0
 H3K  CONST_29  C12  N3   C13  C14   180.00   0.0  0
 H3K  CONST_30  C12  N3   C13  N5      0.00   0.0  0
 H3K  CONST_31  C10  C11  N2   C12     0.00   0.0  0
 H3K  CONST_32  C6   C11  N2   C12   180.00   0.0  0
 H3K  CONST_33  H15  N3   C13  C14     0.00   0.0  0
 H3K  CONST_34  H14  N2   C11  C10   180.00   0.0  0
 H3K  CONST_35  O2   C12  N3   C13     0.00   0.0  0
 H3K  CONST_36  C11  N2   C12  O2      0.00   0.0  0
 H3K  CONST_37  N2   C12  N3   C13   180.00   0.0  0
 H3K  CONST_38  C11  N2   C12  N3    180.00   0.0  0
 H3K  Var_01    C4   N1   C6   C11   116.80  30.0  2
 H3K  Var_02    C3   C4   N1   C6   -168.98  30.0  1
 H3K  Var_03    C1   C5   N1   C6    167.55  30.0  1
 H3K  Var_04    C2   C3   C4   N1    -55.32  30.0  1
 H3K  Var_05    C1   C2   C3   C4     54.33  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 H3K  chir_01  C1  C5  C2  O1  negativ

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
 H3K  plan-1  N6   0.020
 H3K  plan-1  C17  0.020
 H3K  plan-1  C15  0.020
 H3K  plan-1  N4   0.020
 H3K  plan-1  C14  0.020
 H3K  plan-1  C16  0.020
 H3K  plan-1  N5   0.020
 H3K  plan-1  C13  0.020
 H3K  plan-1  N3   0.020
 H3K  plan-1  H16  0.020
 H3K  plan-1  H17  0.020
 H3K  plan-2  N2   0.020
 H3K  plan-2  C11  0.020
 H3K  plan-2  C10  0.020
 H3K  plan-2  C9   0.020
 H3K  plan-2  BR   0.020
 H3K  plan-2  C8   0.020
 H3K  plan-2  C7   0.020
 H3K  plan-2  C6   0.020
 H3K  plan-2  N1   0.020
 H3K  plan-2  H13  0.020
 H3K  plan-2  H12  0.020
 H3K  plan-2  H11  0.020
 H3K  plan-3  C13  0.020
 H3K  plan-3  N3   0.020
 H3K  plan-3  C12  0.020
 H3K  plan-3  O2   0.020
 H3K  plan-3  N2   0.020
 H3K  plan-3  C11  0.020
 H3K  plan-3  H15  0.020
 H3K  plan-3  H14  0.020

