# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 00:36:25 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 1-(5-chloro-2,4-dimethoxyphenyl)-3-pyrazin-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(NC(=O)Nc2cnccn2)cc1Cl
#
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
 H1K  H1K  1-(5-chloro-2,4-dimethoxyphenyl)-3-pyrazin-2-ylurea  ligand  34  21  .  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_H1K
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
 H1K  O1   O   O     0  -0.476   1.1821  -0.8118  -0.5683
 H1K  C4   C   C     0   0.710   1.3097   0.0815   0.2411
 H1K  N2   N   NH1   0  -0.770   2.5220   0.6286   0.6142
 H1K  C5   C   CR6   0   0.473   3.7706   0.3350   0.1066
 H1K  C8   C   CR16  0  -0.156   4.8956   0.7379   0.8490
 H1K  N4   N   N     0  -0.342   6.1175   0.5218   0.4175
 H1K  C7   C   CR16  0  -0.124   6.2566  -0.1042  -0.7502
 H1K  C6   C   CR16  0  -0.107   5.1488  -0.4989  -1.4746
 H1K  N3   N   N     0  -0.378   3.9077  -0.2745  -1.0554
 H1K  N1   N   NH1   0  -0.772   0.2653   0.6433   0.9178
 H1K  C3   C   CR6   0   0.208  -1.0676   0.2790   0.6552
 H1K  C2   C   CR16  0  -0.224  -1.5307  -0.9913   0.9560
 H1K  C9   C   CR6   0   0.405  -1.9481   1.2094   0.0907
 H1K  O2   O   O2    0  -0.460  -1.4346   2.4169  -0.1811
 H1K  C10  C   CH3   0  -0.442  -2.2781   3.4148  -0.7259
 H1K  C11  C   CR16  0  -0.553  -3.2748   0.8588  -0.1481
 H1K  C12  C   CR6   0   0.491  -3.7304  -0.4250   0.1425
 H1K  C1   C   CR6   0  -0.197  -2.8394  -1.3472   0.6937
 H1K  CL   CL  CL    0  -0.118  -3.3957  -2.9427   1.0664
 H1K  O3   O   O2    0  -0.455  -4.9822  -0.8433  -0.0700
 H1K  C13  C   CH3   0  -0.442  -5.9261   0.0670  -0.6058
 H1K  H3   H   HNH1  0   0.420   2.5223   1.2384   1.4178
 H1K  H6   H   HCR6  0   0.282   4.7778   1.2444   1.8018
 H1K  H5   H   HCR6  0   0.275   7.2603  -0.2892  -1.1104
 H1K  H4   H   HCR6  0   0.274   5.2612  -1.0047  -2.4261
 H1K  H2   H   HNH1  0   0.406   0.4173   1.5018   1.4262
 H1K  H1   H   HCR6  0   0.285  -0.8612  -1.7090   1.4104
 H1K  H9   H   HCH3  0   0.234  -2.6851   3.1169  -1.6949
 H1K  H7   H   HCH3  0   0.235  -3.1026   3.6620  -0.0532
 H1K  H8   H   HCH3  0   0.267  -1.6595   4.2980  -0.8614
 H1K  H10  H   HCR6  0   0.314  -3.9537   1.5821  -0.5773
 H1K  H12  H   HCH3  0   0.235  -6.0711   0.9309   0.0467
 H1K  H11  H   HCH3  0   0.235  -5.6360   0.4144  -1.5999
 H1K  H13  H   HCH3  0   0.267  -6.8635  -0.4770  -0.6838

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
 H1K  CL   C1   single    1.730  0.020  1.730
 H1K  C2   C1   aromatic  1.381  0.020  1.381
 H1K  C2   C3   aromatic  1.385  0.020  1.385
 H1K  C1   C12  aromatic  1.396  0.020  1.396
 H1K  O1   C4   double    1.212  0.020  1.212
 H1K  C4   N2   single    1.381  0.020  1.381
 H1K  C4   N1   single    1.365  0.020  1.365
 H1K  N2   C5   single    1.379  0.020  1.379
 H1K  N1   C3   single    1.406  0.020  1.406
 H1K  O3   C12  single    1.337  0.020  1.337
 H1K  O3   C13  single    1.417  0.020  1.417
 H1K  C3   C9   aromatic  1.400  0.020  1.400
 H1K  C12  C11  aromatic  1.393  0.020  1.393
 H1K  C9   C11  aromatic  1.393  0.020  1.393
 H1K  C9   O2   single    1.340  0.020  1.340
 H1K  C5   N3   aromatic  1.319  0.020  1.319
 H1K  C5   C8   aromatic  1.407  0.020  1.407
 H1K  N3   C6   aromatic  1.329  0.020  1.329
 H1K  O2   C10  single    1.416  0.020  1.416
 H1K  C8   N4   aromatic  1.314  0.020  1.314
 H1K  C6   C7   aromatic  1.381  0.020  1.381
 H1K  N4   C7   aromatic  1.332  0.020  1.332
 H1K  N2   H3   single    0.860  0.020  1.020
 H1K  C8   H6   single    0.930  0.020  1.080
 H1K  C7   H5   single    0.930  0.020  1.080
 H1K  C6   H4   single    0.930  0.020  1.080
 H1K  N1   H2   single    0.860  0.020  1.020
 H1K  C2   H1   single    0.930  0.020  1.080
 H1K  C10  H9   single    0.970  0.020  1.090
 H1K  C10  H7   single    0.970  0.020  1.090
 H1K  C10  H8   single    0.970  0.020  1.090
 H1K  C11  H10  single    0.930  0.020  1.080
 H1K  C13  H12  single    0.970  0.020  1.090
 H1K  C13  H11  single    0.970  0.020  1.090
 H1K  C13  H13  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
 H1K  N1   C4   N2   111.99  3.000
 H1K  N1   C4   O1   123.62  3.000
 H1K  N2   C4   O1   124.37  3.000
 H1K  H3   N2   C5   114.93  3.000
 H1K  H3   N2   C4   117.05  3.000
 H1K  C5   N2   C4   127.64  3.000
 H1K  N3   C5   C8   120.93  3.000
 H1K  C8   C5   N2   117.95  3.000
 H1K  N3   C5   N2   121.10  3.000
 H1K  H6   C8   N4   117.77  3.000
 H1K  H6   C8   C5   120.67  3.000
 H1K  N4   C8   C5   121.56  3.000
 H1K  C7   N4   C8   117.54  3.000
 H1K  H5   C7   C6   121.36  3.000
 H1K  H5   C7   N4   117.96  3.000
 H1K  C6   C7   N4   120.68  3.000
 H1K  H4   C6   N3   116.91  3.000
 H1K  H4   C6   C7   120.72  3.000
 H1K  N3   C6   C7   122.37  3.000
 H1K  C6   N3   C5   116.93  3.000
 H1K  H2   N1   C3   117.20  3.000
 H1K  H2   N1   C4   118.98  3.000
 H1K  C3   N1   C4   121.72  3.000
 H1K  C9   C3   C2   119.13  3.000
 H1K  C9   C3   N1   119.95  3.000
 H1K  C2   C3   N1   120.92  3.000
 H1K  H1   C2   C1   119.69  3.000
 H1K  H1   C2   C3   119.52  3.000
 H1K  C1   C2   C3   120.79  3.000
 H1K  C11  C9   O2   123.85  3.000
 H1K  O2   C9   C3   116.08  3.000
 H1K  C11  C9   C3   120.06  3.000
 H1K  C10  O2   C9   119.01  3.000
 H1K  H8   C10  H7   108.81  3.000
 H1K  H8   C10  H9   108.85  3.000
 H1K  H7   C10  H9   109.06  3.000
 H1K  H8   C10  O2   106.36  3.000
 H1K  H7   C10  O2   111.86  3.000
 H1K  H9   C10  O2   111.79  3.000
 H1K  H10  C11  C12  119.62  3.000
 H1K  H10  C11  C9   119.86  3.000
 H1K  C12  C11  C9   120.51  3.000
 H1K  O3   C12  C1   116.98  3.000
 H1K  O3   C12  C11  124.16  3.000
 H1K  C1   C12  C11  118.86  3.000
 H1K  CL   C1   C12  119.28  3.000
 H1K  C12  C1   C2   120.63  3.000
 H1K  CL   C1   C2   120.08  3.000
 H1K  C13  O3   C12  118.88  3.000
 H1K  H13  C13  H11  108.84  3.000
 H1K  H13  C13  H12  108.93  3.000
 H1K  H11  C13  H12  109.11  3.000
 H1K  H13  C13  O3   106.27  3.000
 H1K  H11  C13  O3   111.82  3.000
 H1K  H12  C13  O3   111.76  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
 H1K  CONST_01  C7   C6   N3   C5     0.00   0.0  0
 H1K  CONST_02  C7   N4   C8   C5     0.00   0.0  0
 H1K  CONST_03  C6   N3   C5   C8     0.00   0.0  0
 H1K  CONST_04  C6   C7   N4   C8     0.00   0.0  0
 H1K  CONST_05  N3   C5   C8   N4     0.00   0.0  0
 H1K  CONST_06  N3   C6   C7   N4     0.00   0.0  0
 H1K  CONST_07  C12  C1   C2   C3     0.00   0.0  0
 H1K  CONST_08  C12  C11  C9   C3     0.00   0.0  0
 H1K  CONST_09  C11  C12  C1   C2     0.00   0.0  0
 H1K  CONST_10  C11  C9   C3   C2     0.00   0.0  0
 H1K  CONST_11  C1   C2   C3   C9     0.00   0.0  0
 H1K  CONST_12  C1   C12  C11  C9     0.00   0.0  0
 H1K  CONST_13  C6   N3   C5   N2   180.00   0.0  0
 H1K  CONST_14  N4   C8   C5   N2   180.00   0.0  0
 H1K  CONST_15  C1   C2   C3   N1   180.00   0.0  0
 H1K  CONST_16  C11  C9   C3   N1   180.00   0.0  0
 H1K  CONST_17  CL   C1   C2   C3   180.00   0.0  0
 H1K  CONST_18  O3   C12  C1   C2   180.00   0.0  0
 H1K  CONST_19  O2   C9   C3   C2   180.00   0.0  0
 H1K  CONST_20  O3   C12  C11  C9   180.00   0.0  0
 H1K  CONST_21  C12  C11  C9   O2   180.00   0.0  0
 H1K  CONST_22  CL   C1   C12  C11  180.00   0.0  0
 H1K  CONST_23  H4   C6   N3   C5   180.00   0.0  0
 H1K  CONST_24  H5   C7   N4   C8   180.00   0.0  0
 H1K  CONST_25  H6   C8   N4   C7   180.00   0.0  0
 H1K  CONST_26  H10  C11  C9   C3   180.00   0.0  0
 H1K  CONST_27  H1   C2   C3   C9   180.00   0.0  0
 H1K  CONST_32  H3   N2   C5   C8     0.00   0.0  0
 H1K  CONST_34  C5   N2   C4   O1     0.00   0.0  0
 H1K  CONST_35  C3   N1   C4   O1     0.00   0.0  0
 H1K  CONST_36  C3   N1   C4   N2   180.00   0.0  0
 H1K  CONST_37  N1   C4   N2   C5   180.00   0.0  0
 H1K  Var_01    C11  C9   O2   C10    0.93  30.0  2
 H1K  Var_02    H9   C10  O2   C9   -61.41  30.0  3
 H1K  Var_03    H12  C13  O3   C12  -60.76  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
 H1K  plan-1  N2   0.020
 H1K  plan-1  C5   0.020
 H1K  plan-1  C8   0.020
 H1K  plan-1  N4   0.020
 H1K  plan-1  C7   0.020
 H1K  plan-1  C6   0.020
 H1K  plan-1  N3   0.020
 H1K  plan-1  H6   0.020
 H1K  plan-1  H5   0.020
 H1K  plan-1  H4   0.020
 H1K  plan-2  N1   0.020
 H1K  plan-2  C3   0.020
 H1K  plan-2  C2   0.020
 H1K  plan-2  C9   0.020
 H1K  plan-2  O2   0.020
 H1K  plan-2  C11  0.020
 H1K  plan-2  C12  0.020
 H1K  plan-2  C1   0.020
 H1K  plan-2  CL   0.020
 H1K  plan-2  O3   0.020
 H1K  plan-2  H1   0.020
 H1K  plan-2  H10  0.020
 H1K  plan-3  O1   0.020
 H1K  plan-3  C4   0.020
 H1K  plan-3  N2   0.020
 H1K  plan-3  C5   0.020
 H1K  plan-3  N1   0.020
 H1K  plan-3  C3   0.020
 H1K  plan-3  H3   0.020
 H1K  plan-3  H2   0.020

