# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:22:14 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-(4-methoxyphenyl)-N'-pyridin-4-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)Nc2ccncc2)cc1
#
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
 JHJ  JHJ  N-(4-methoxyphenyl)-N'-pyridin-4-ylurea  ligand  31  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JHJ
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
 JHJ  C10   C  C     0   0.731   0.8591   0.1066   0.0832
 JHJ  N12   N  NH1   0  -0.786   2.0678   0.7543   0.2076
 JHJ  C13   C  CR6   0   0.467   3.3376   0.2234   0.0956
 JHJ  C15   C  CR16  0  -0.064   5.7044   0.6158   0.1643
 JHJ  C17   C  CR16  0  -0.071   4.9775  -1.4796  -0.2481
 JHJ  C01   C  CH3   0  -0.436  -6.1374  -1.4898   0.2045
 JHJ  C03   C  CR6   0   0.373  -4.2635  -0.0814  -0.1583
 JHJ  C04   C  CR16  0  -0.382  -3.3995  -0.9307   0.5270
 JHJ  C05   C  CR16  0  -0.273  -2.0563  -0.6027   0.6691
 JHJ  C06   C  CR6   0   0.325  -1.5475   0.5630   0.1114
 JHJ  C07   C  CR16  0  -0.302  -2.4175   1.4102  -0.5739
 JHJ  C08   C  CR16  0  -0.336  -3.7580   1.1011  -0.7000
 JHJ  C14   C  CR16  0  -0.423   4.4159   1.0995   0.2635
 JHJ  C18   C  CR16  0  -0.379   3.6432  -1.1136  -0.1702
 JHJ  N09   N  NH1   0  -0.783  -0.2017   0.9462   0.2518
 JHJ  N16   N  N     0  -0.422   6.0053  -0.6551  -0.0884
 JHJ  O11   O  O     0  -0.490   0.7508  -1.0843  -0.1394
 JHJ  H121  H  HNH1  0   0.417   2.0423   1.7428   0.4072
 JHJ  H151  H  HCR6  0   0.265   6.5376   1.2968   0.2978
 JHJ  H171  H  HCR6  0   0.263   5.2189  -2.5169  -0.4541
 JHJ  H013  H  HCH3  0   0.259  -7.1933  -1.4806  -0.0544
 JHJ  H012  H  HCH3  0   0.228  -5.6807  -2.3909  -0.2133
 JHJ  H011  H  HCH3  0   0.227  -6.0440  -1.5214   1.2932
 JHJ  H041  H  HCR6  0   0.281  -3.7486  -1.8515   0.9737
 JHJ  H051  H  HCR6  0   0.268  -1.4190  -1.2689   1.2319
 JHJ  H071  H  HCR6  0   0.270  -2.0424   2.3262  -1.0138
 JHJ  H081  H  HCR6  0   0.266  -4.4192   1.7734  -1.2323
 JHJ  H141  H  HCR6  0   0.282   4.2520   2.1500   0.4693
 JHJ  H181  H  HCR6  0   0.289   2.8817  -1.8603  -0.3131
 JHJ  H091  H  HNH1  0   0.411  -0.0298   1.9402   0.2737
 JHJ  O02   O  O2    0  -0.472  -5.5790  -0.3117  -0.3403

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
 JHJ  C18  C17   aromatic  1.386  0.020  1.386
 JHJ  C18  C13   aromatic  1.397  0.020  1.397
 JHJ  C17  N16   aromatic  1.327  0.020  1.327
 JHJ  N16  C15   aromatic  1.330  0.020  1.330
 JHJ  N12  C13   single    1.381  0.020  1.381
 JHJ  N12  C10   single    1.377  0.020  1.377
 JHJ  C13  C14   aromatic  1.399  0.020  1.399
 JHJ  N09  C10   single    1.363  0.020  1.363
 JHJ  N09  C06   single    1.406  0.020  1.406
 JHJ  C05  C06   aromatic  1.389  0.020  1.389
 JHJ  C05  C04   aromatic  1.390  0.020  1.390
 JHJ  C10  O11   double    1.216  0.020  1.216
 JHJ  C15  C14   aromatic  1.380  0.020  1.380
 JHJ  C06  C07   aromatic  1.394  0.020  1.394
 JHJ  C04  C03   aromatic  1.392  0.020  1.392
 JHJ  C07  C08   aromatic  1.381  0.020  1.381
 JHJ  C03  C08   aromatic  1.395  0.020  1.395
 JHJ  C03  O02   single    1.348  0.020  1.348
 JHJ  C01  O02   single    1.413  0.020  1.413
 JHJ  N12  H121  single    0.860  0.020  1.020
 JHJ  C15  H151  single    0.930  0.020  1.080
 JHJ  C17  H171  single    0.930  0.020  1.080
 JHJ  C01  H013  single    0.970  0.020  1.090
 JHJ  C01  H012  single    0.970  0.020  1.090
 JHJ  C01  H011  single    0.970  0.020  1.090
 JHJ  C04  H041  single    0.930  0.020  1.080
 JHJ  C05  H051  single    0.930  0.020  1.080
 JHJ  C07  H071  single    0.930  0.020  1.080
 JHJ  C08  H081  single    0.930  0.020  1.080
 JHJ  C14  H141  single    0.930  0.020  1.080
 JHJ  C18  H181  single    0.930  0.020  1.080
 JHJ  N09  H091  single    0.860  0.020  1.020

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
 JHJ  O11   C10  N09   123.81  3.000
 JHJ  O11   C10  N12   123.73  3.000
 JHJ  N09   C10  N12   112.47  3.000
 JHJ  H121  N12  C13   114.58  3.000
 JHJ  H121  N12  C10   117.17  3.000
 JHJ  C13   N12  C10   128.25  3.000
 JHJ  C18   C13  C14   116.96  3.000
 JHJ  C14   C13  N12   117.27  3.000
 JHJ  C18   C13  N12   125.77  3.000
 JHJ  H151  C15  N16   116.71  3.000
 JHJ  H151  C15  C14   119.24  3.000
 JHJ  N16   C15  C14   124.04  3.000
 JHJ  H171  C17  N16   116.39  3.000
 JHJ  H171  C17  C18   118.53  3.000
 JHJ  N16   C17  C18   125.08  3.000
 JHJ  H011  C01  H012  108.73  3.000
 JHJ  H011  C01  H013  108.69  3.000
 JHJ  H012  C01  H013  108.77  3.000
 JHJ  H011  C01  O02   111.98  3.000
 JHJ  H012  C01  O02   112.01  3.000
 JHJ  H013  C01  O02   106.56  3.000
 JHJ  O02   C03  C08   116.48  3.000
 JHJ  O02   C03  C04   124.62  3.000
 JHJ  C08   C03  C04   118.90  3.000
 JHJ  H041  C04  C05   118.08  3.000
 JHJ  H041  C04  C03   121.50  3.000
 JHJ  C05   C04  C03   120.41  3.000
 JHJ  H051  C05  C06   120.72  3.000
 JHJ  H051  C05  C04   118.55  3.000
 JHJ  C06   C05  C04   120.73  3.000
 JHJ  N09   C06  C07   118.72  3.000
 JHJ  C07   C06  C05   118.61  3.000
 JHJ  N09   C06  C05   122.63  3.000
 JHJ  H071  C07  C08   119.22  3.000
 JHJ  H071  C07  C06   119.82  3.000
 JHJ  C08   C07  C06   120.96  3.000
 JHJ  H081  C08  C07   119.90  3.000
 JHJ  H081  C08  C03   119.72  3.000
 JHJ  C07   C08  C03   120.38  3.000
 JHJ  H141  C14  C15   119.67  3.000
 JHJ  H141  C14  C13   120.90  3.000
 JHJ  C15   C14  C13   119.43  3.000
 JHJ  H181  C18  C17   119.38  3.000
 JHJ  H181  C18  C13   122.32  3.000
 JHJ  C17   C18  C13   118.30  3.000
 JHJ  H091  N09  C06   115.70  3.000
 JHJ  H091  N09  C10   118.48  3.000
 JHJ  C06   N09  C10   124.36  3.000
 JHJ  C17   N16  C15   116.18  3.000
 JHJ  C03   O02  C01   118.43  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
 JHJ  CONST_01  N16   C17  C18  C13     0.00   0.0  0
 JHJ  CONST_02  N16   C15  C14  C13     0.00   0.0  0
 JHJ  CONST_03  C18   C17  N16  C15     0.00   0.0  0
 JHJ  CONST_04  C18   C13  C14  C15     0.00   0.0  0
 JHJ  CONST_05  C14   C13  C18  C17     0.00   0.0  0
 JHJ  CONST_06  C14   C15  N16  C17     0.00   0.0  0
 JHJ  CONST_07  C06   C05  C04  C03     0.00   0.0  0
 JHJ  CONST_08  C06   C07  C08  C03     0.00   0.0  0
 JHJ  CONST_09  C07   C06  C05  C04     0.00   0.0  0
 JHJ  CONST_10  C07   C08  C03  C04     0.00   0.0  0
 JHJ  CONST_11  C08   C07  C06  C05     0.00   0.0  0
 JHJ  CONST_12  C08   C03  C04  C05     0.00   0.0  0
 JHJ  CONST_13  C17   C18  C13  N12   180.00   0.0  0
 JHJ  CONST_14  C15   C14  C13  N12   180.00   0.0  0
 JHJ  CONST_15  N09   C06  C05  C04   180.00   0.0  0
 JHJ  CONST_16  O02   C03  C04  C05   180.00   0.0  0
 JHJ  CONST_17  O02   C03  C08  C07   180.00   0.0  0
 JHJ  CONST_18  N09   C06  C07  C08   180.00   0.0  0
 JHJ  CONST_19  H171  C17  C18  C13   180.00   0.0  0
 JHJ  CONST_20  H151  C15  C14  C13   180.00   0.0  0
 JHJ  CONST_21  H051  C05  C04  C03   180.00   0.0  0
 JHJ  CONST_22  H071  C07  C08  C03   180.00   0.0  0
 JHJ  CONST_23  H081  C08  C03  C04   180.00   0.0  0
 JHJ  CONST_24  H041  C04  C05  C06   180.00   0.0  0
 JHJ  CONST_25  H181  C18  C13  C14   180.00   0.0  0
 JHJ  CONST_26  H141  C14  C13  C18   180.00   0.0  0
 JHJ  CONST_27  C18   C13  N12  C10     0.00   0.0  0
 JHJ  CONST_28  C14   C13  N12  C10   180.00   0.0  0
 JHJ  CONST_32  H121  N12  C13  C14     0.00   0.0  0
 JHJ  CONST_33  O11   C10  N12  C13     0.00   0.0  0
 JHJ  CONST_34  O11   C10  N09  C06     0.00   0.0  0
 JHJ  CONST_35  C06   N09  C10  N12   180.00   0.0  0
 JHJ  CONST_36  N09   C10  N12  C13   180.00   0.0  0
 JHJ  Var_01    C04   C03  O02  C01     0.44  30.0  2
 JHJ  Var_02    H013  C01  O02  C03  -179.95  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
 JHJ  plan-1  C03   0.020
 JHJ  plan-1  C04   0.020
 JHJ  plan-1  C05   0.020
 JHJ  plan-1  C06   0.020
 JHJ  plan-1  C07   0.020
 JHJ  plan-1  C08   0.020
 JHJ  plan-1  N09   0.020
 JHJ  plan-1  H041  0.020
 JHJ  plan-1  H051  0.020
 JHJ  plan-1  H071  0.020
 JHJ  plan-1  H081  0.020
 JHJ  plan-1  O02   0.020
 JHJ  plan-2  N12   0.020
 JHJ  plan-2  C13   0.020
 JHJ  plan-2  C15   0.020
 JHJ  plan-2  C17   0.020
 JHJ  plan-2  C14   0.020
 JHJ  plan-2  C18   0.020
 JHJ  plan-2  N16   0.020
 JHJ  plan-2  H151  0.020
 JHJ  plan-2  H171  0.020
 JHJ  plan-2  H141  0.020
 JHJ  plan-2  H181  0.020
 JHJ  plan-3  C10   0.020
 JHJ  plan-3  N12   0.020
 JHJ  plan-3  C13   0.020
 JHJ  plan-3  C06   0.020
 JHJ  plan-3  N09   0.020
 JHJ  plan-3  O11   0.020
 JHJ  plan-3  H121  0.020
 JHJ  plan-3  H091  0.020

