# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:40:14 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-{5-chloro-2-[(3R)-pyrrolidin-3-yloxy]phenyl}-3-(5-cyanopyrazin-2-yl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(O[C@@H]2CCNC2)c(NC(=O)Nc3cnc(cn3)C#N)c1
#
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
 H2K  H2K  1-{5-chloro-2-[(3R)-pyrrolidin-3-yloxy]phenyl}-3-(5-cyanopyrazin-2-yl)urea  ligand  40  25  .  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_H2K
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
 H2K  N6   N   NS    0  -0.238  -7.8925  -2.1858  -0.5829
 H2K  C15  C   CSP   0   0.063  -6.7770  -1.9600  -0.4078
 H2K  C13  C   CR6   0   0.132  -5.3947  -1.6638  -0.1984
 H2K  N4   N   N     0  -0.344  -4.6546  -2.5778   0.4391
 H2K  C12  C   CR16  0  -0.160  -3.3954  -2.2975   0.6292
 H2K  C14  C   CR16  0  -0.040  -4.8471  -0.4731  -0.6435
 H2K  N5   N   N     0  -0.379  -3.5682  -0.1847  -0.4569
 H2K  C11  C   CR6   0   0.517  -2.8327  -1.0774   0.1792
 H2K  N3   N   NH1   0  -0.771  -1.5023  -0.8723   0.4139
 H2K  C10  C   C     0   0.731  -0.7689   0.2864   0.1932
 H2K  O2   O   O     0  -0.456  -1.2516   1.3331  -0.1711
 H2K  N2   N   NH1   0  -0.776   0.5569   0.0961   0.4563
 H2K  C9   C   CR6   0   0.261   1.5454   1.0711   0.2854
 H2K  C16  C   CR16  0  -0.244   1.3529   2.3977   0.6419
 H2K  C1   C   CR6   0  -0.064   2.3775   3.3124   0.4507
 H2K  CL   CL  CL    0  -0.135   2.1159   4.9700   0.8925
 H2K  C4   C   CR6   0   0.361   2.7852   0.6595  -0.2368
 H2K  C3   C   CR16  0  -0.377   3.7993   1.5932  -0.4033
 H2K  C2   C   CR16  0  -0.218   3.5965   2.9262  -0.0702
 H2K  O1   O   O2    0  -0.490   2.8735  -0.6462  -0.5458
 H2K  C5   C   CH1   0  -0.021   4.1306  -1.2131  -0.9262
 H2K  C8   C   CH2   0  -0.351   5.0503  -1.3705   0.2864
 H2K  N1   N   NH1   0  -0.584   4.5362  -2.5172   1.0180
 H2K  C7   C   CH2   0  -0.304   4.0837  -3.4641  -0.0046
 H2K  C6   C   CH2   0  -0.500   3.8675  -2.6624  -1.3135
 H2K  H13  H   HCR6  0   0.302  -2.7872  -3.0307   1.1477
 H2K  H14  H   HCR6  0   0.300  -5.4512   0.2598  -1.1646
 H2K  H12  H   HNH1  0   0.431  -1.0211  -1.6519   0.8381
 H2K  H11  H   HNH1  0   0.411   0.8931  -0.8484   0.5727
 H2K  H15  H   HCR6  0   0.290   0.4176   2.7175   1.0751
 H2K  H2   H   HCR6  0   0.292   4.7602   1.3067  -0.8064
 H2K  H1   H   HCR6  0   0.283   4.3919   3.6435  -0.2159
 H2K  H3   H   HCH1  0   0.255   4.5687  -0.6353  -1.7444
 H2K  H9   H   HCH2  0   0.242   6.0618  -1.5789  -0.0765
 H2K  H10  H   HCH2  0   0.258   5.1113  -0.4891   0.9257
 H2K  H8   H   HNH1  0   0.348   3.7387  -2.2168   1.5630
 H2K  H6   H   HCH2  0   0.225   4.8441  -4.2319  -0.1626
 H2K  H7   H   HCH2  0   0.239   3.1799  -3.9731   0.3288
 H2K  H4   H   HCH2  0   0.257   2.8734  -2.7930  -1.7414
 H2K  H5   H   HCH2  0   0.254   4.5874  -2.9622  -2.0757

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
 H2K  CL   C1   single    1.735  0.020  1.735
 H2K  O2   C10  double    1.209  0.020  1.209
 H2K  C16  C1   aromatic  1.387  0.020  1.387
 H2K  C16  C9   aromatic  1.387  0.020  1.387
 H2K  C1   C2   aromatic  1.381  0.020  1.381
 H2K  C10  N2   single    1.365  0.020  1.365
 H2K  C10  N3   single    1.389  0.020  1.389
 H2K  N2   C9   single    1.399  0.020  1.399
 H2K  C2   C3   aromatic  1.389  0.020  1.389
 H2K  C9   C4   aromatic  1.407  0.020  1.407
 H2K  N3   C11  single    1.366  0.020  1.366
 H2K  C3   C4   aromatic  1.389  0.020  1.389
 H2K  C4   O1   single    1.345  0.020  1.345
 H2K  C11  N5   aromatic  1.320  0.020  1.320
 H2K  C11  C12  aromatic  1.417  0.020  1.417
 H2K  N5   C14  aromatic  1.324  0.020  1.324
 H2K  C12  N4   aromatic  1.304  0.020  1.304
 H2K  O1   C5   single    1.431  0.020  1.431
 H2K  C14  C13  aromatic  1.384  0.020  1.384
 H2K  N4   C13  aromatic  1.338  0.020  1.338
 H2K  C13  C15  single    1.429  0.020  1.429
 H2K  C6   C5   single    1.523  0.020  1.523
 H2K  C6   C7   single    1.550  0.020  1.550
 H2K  C5   C8   single    1.530  0.020  1.530
 H2K  C15  N6   triple    1.152  0.020  1.152
 H2K  C7   N1   single    1.465  0.020  1.465
 H2K  C8   N1   single    1.454  0.020  1.454
 H2K  C12  H13  single    0.930  0.020  1.080
 H2K  C14  H14  single    0.930  0.020  1.080
 H2K  N3   H12  single    0.860  0.020  1.020
 H2K  N2   H11  single    0.860  0.020  1.020
 H2K  C16  H15  single    0.930  0.020  1.080
 H2K  C3   H2   single    0.930  0.020  1.080
 H2K  C2   H1   single    0.930  0.020  1.080
 H2K  C5   H3   single    0.970  0.020  1.090
 H2K  C8   H9   single    0.970  0.020  1.090
 H2K  C8   H10  single    0.970  0.020  1.090
 H2K  N1   H8   single    0.890  0.020  1.040
 H2K  C7   H6   single    0.970  0.020  1.090
 H2K  C7   H7   single    0.970  0.020  1.090
 H2K  C6   H4   single    0.970  0.020  1.090
 H2K  C6   H5   single    0.970  0.020  1.090

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
 H2K  C13  C15  N6   180.00  3.000
 H2K  C14  C13  N4   121.48  3.000
 H2K  N4   C13  C15  117.60  3.000
 H2K  C14  C13  C15  120.92  3.000
 H2K  C12  N4   C13  117.18  3.000
 H2K  H13  C12  C11  120.75  3.000
 H2K  H13  C12  N4   117.76  3.000
 H2K  C11  C12  N4   121.49  3.000
 H2K  H14  C14  N5   117.32  3.000
 H2K  H14  C14  C13  121.07  3.000
 H2K  N5   C14  C13  121.61  3.000
 H2K  C11  N5   C14  117.31  3.000
 H2K  N3   C11  N5   121.59  3.000
 H2K  N5   C11  C12  120.93  3.000
 H2K  N3   C11  C12  117.47  3.000
 H2K  H12  N3   C10  117.34  3.000
 H2K  H12  N3   C11  114.85  3.000
 H2K  C10  N3   C11  127.74  3.000
 H2K  N2   C10  O2   124.52  3.000
 H2K  N2   C10  N3   111.46  3.000
 H2K  O2   C10  N3   124.01  3.000
 H2K  H11  N2   C9   115.52  3.000
 H2K  H11  N2   C10  118.44  3.000
 H2K  C9   N2   C10  124.44  3.000
 H2K  C4   C9   C16  119.83  3.000
 H2K  C4   C9   N2   117.65  3.000
 H2K  C16  C9   N2   122.49  3.000
 H2K  H15  C16  C1   120.02  3.000
 H2K  H15  C16  C9   120.45  3.000
 H2K  C1   C16  C9   119.53  3.000
 H2K  C2   C1   CL   119.76  3.000
 H2K  C2   C1   C16  121.32  3.000
 H2K  CL   C1   C16  118.92  3.000
 H2K  O1   C4   C3   125.27  3.000
 H2K  O1   C4   C9   115.29  3.000
 H2K  C3   C4   C9   119.43  3.000
 H2K  H2   C3   C2   118.28  3.000
 H2K  H2   C3   C4   121.05  3.000
 H2K  C2   C3   C4   120.66  3.000
 H2K  H1   C2   C3   119.81  3.000
 H2K  H1   C2   C1   120.99  3.000
 H2K  C3   C2   C1   119.20  3.000
 H2K  C5   O1   C4   120.24  3.000
 H2K  H3   C5   C6   112.45  3.000
 H2K  H3   C5   C8   113.99  3.000
 H2K  C6   C5   C8   101.97  3.000
 H2K  H3   C5   O1   109.98  3.000
 H2K  C8   C5   O1   110.99  3.000
 H2K  C6   C5   O1   107.03  3.000
 H2K  H10  C8   H9   107.25  3.000
 H2K  H10  C8   N1   111.23  3.000
 H2K  H9   C8   N1   110.08  3.000
 H2K  H10  C8   C5   114.52  3.000
 H2K  H9   C8   C5   108.20  3.000
 H2K  N1   C8   C5   105.51  3.000
 H2K  H8   N1   C7   108.93  3.000
 H2K  H8   N1   C8   108.40  3.000
 H2K  C7   N1   C8   105.52  3.000
 H2K  H7   C7   H6   107.07  3.000
 H2K  H7   C7   C6   112.60  3.000
 H2K  H6   C7   C6   109.79  3.000
 H2K  H7   C7   N1   110.15  3.000
 H2K  H6   C7   N1   109.89  3.000
 H2K  C6   C7   N1   107.35  3.000
 H2K  H5   C6   H4   107.15  3.000
 H2K  H5   C6   C7   110.85  3.000
 H2K  H4   C6   C7   113.37  3.000
 H2K  H5   C6   C5   108.98  3.000
 H2K  H4   C6   C5   111.80  3.000
 H2K  C7   C6   C5   104.68  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
 H2K  CONST_01  C11  N5   C14  C13    0.00   0.0  0
 H2K  CONST_02  C11  C12  N4   C13    0.00   0.0  0
 H2K  CONST_03  N5   C11  C12  N4     0.00   0.0  0
 H2K  CONST_04  N5   C14  C13  N4     0.00   0.0  0
 H2K  CONST_05  C14  N5   C11  C12    0.00   0.0  0
 H2K  CONST_06  C14  C13  N4   C12    0.00   0.0  0
 H2K  CONST_07  C2   C1   C16  C9     0.00   0.0  0
 H2K  CONST_08  C2   C3   C4   C9     0.00   0.0  0
 H2K  CONST_09  C3   C2   C1   C16    0.00   0.0  0
 H2K  CONST_10  C3   C4   C9   C16    0.00   0.0  0
 H2K  CONST_11  C4   C9   C16  C1     0.00   0.0  0
 H2K  CONST_12  C4   C3   C2   C1     0.00   0.0  0
 H2K  CONST_13  N5   C14  C13  C15  180.00   0.0  0
 H2K  CONST_14  C12  N4   C13  C15  180.00   0.0  0
 H2K  CONST_15  N3   C11  C12  N4   180.00   0.0  0
 H2K  CONST_16  N3   C11  N5   C14  180.00   0.0  0
 H2K  CONST_17  C1   C16  C9   N2   180.00   0.0  0
 H2K  CONST_18  C3   C4   C9   N2   180.00   0.0  0
 H2K  CONST_19  CL   C1   C16  C9   180.00   0.0  0
 H2K  CONST_20  O1   C4   C9   C16  180.00   0.0  0
 H2K  CONST_21  C3   C2   C1   CL   180.00   0.0  0
 H2K  CONST_22  O1   C4   C3   C2   180.00   0.0  0
 H2K  CONST_23  H13  C12  N4   C13  180.00   0.0  0
 H2K  CONST_24  H14  C14  C13  N4   180.00   0.0  0
 H2K  CONST_25  H2   C3   C4   C9   180.00   0.0  0
 H2K  CONST_26  H1   C2   C1   C16  180.00   0.0  0
 H2K  CONST_27  H15  C16  C9   C4   180.00   0.0  0
 H2K  CONST_28  C10  N3   C11  C12  180.00   0.0  0
 H2K  CONST_29  C10  N3   C11  N5     0.00   0.0  0
 H2K  CONST_32  H12  N3   C11  C12    0.00   0.0  0
 H2K  CONST_34  O2   C10  N3   C11    0.00   0.0  0
 H2K  CONST_35  C9   N2   C10  O2     0.00   0.0  0
 H2K  CONST_36  N2   C10  N3   C11  180.00   0.0  0
 H2K  CONST_37  C9   N2   C10  N3   180.00   0.0  0
 H2K  Var_01    N1   C7   C6   C5    -3.88  30.0  1
 H2K  Var_02    C7   N1   C8   C5    36.76  30.0  1
 H2K  Var_03    C6   C7   N1   C8   -20.19  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
 H2K  chir_01  C5  O1  C6  C8  positiv

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
 H2K  plan-1  N6   0.020
 H2K  plan-1  C15  0.020
 H2K  plan-1  C13  0.020
 H2K  plan-1  N4   0.020
 H2K  plan-1  C12  0.020
 H2K  plan-1  C14  0.020
 H2K  plan-1  N5   0.020
 H2K  plan-1  C11  0.020
 H2K  plan-1  N3   0.020
 H2K  plan-1  H13  0.020
 H2K  plan-1  H14  0.020
 H2K  plan-2  N2   0.020
 H2K  plan-2  C9   0.020
 H2K  plan-2  C16  0.020
 H2K  plan-2  C1   0.020
 H2K  plan-2  CL   0.020
 H2K  plan-2  C4   0.020
 H2K  plan-2  C3   0.020
 H2K  plan-2  C2   0.020
 H2K  plan-2  O1   0.020
 H2K  plan-2  H15  0.020
 H2K  plan-2  H2   0.020
 H2K  plan-2  H1   0.020
 H2K  plan-3  C11  0.020
 H2K  plan-3  N3   0.020
 H2K  plan-3  C10  0.020
 H2K  plan-3  O2   0.020
 H2K  plan-3  N2   0.020
 H2K  plan-3  C9   0.020
 H2K  plan-3  H12  0.020
 H2K  plan-3  H11  0.020

