# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:44:43 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-propan-2-yl-3-pyridin-4-yl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)NC(=O)Nc1ccncc1
#
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
 NXH  NXH  1-propan-2-yl-3-pyridin-4-yl-urea  ligand  26  13  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXH
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
 NXH  C1   C  CH3   0  -0.647  -3.7816  -0.6050   1.3437
 NXH  C2   C  CH1   0  -0.084  -3.4105  -0.2106  -0.0815
 NXH  C3   C  CH3   0  -0.671  -4.4638   0.6918  -0.7072
 NXH  N4   N  NH1   0  -0.676  -2.1218   0.4617  -0.1368
 NXH  C5   C  C     0   0.753  -0.9509  -0.2077  -0.1208
 NXH  C8   C  CR6   0   0.465   1.4872   0.2700  -0.0695
 NXH  C10  C  CR16  0  -0.072   3.3602  -1.2148  -0.0192
 NXH  C12  C  CR16  0  -0.066   3.7747   1.0015  -0.0605
 NXH  C13  C  CR16  0  -0.423   2.4293   1.3063  -0.0806
 NXH  O6   O  O     0  -0.514  -0.8693  -1.4257  -0.1537
 NXH  N7   N  NH1   0  -0.787   0.1547   0.6229  -0.0843
 NXH  C9   C  CR16  0  -0.382   1.9866  -1.0353  -0.0376
 NXH  N11  N  N     0  -0.424   4.2587  -0.2375  -0.0303
 NXH  H1   H  HCH3  0   0.220  -3.8557   0.2764   1.9832
 NXH  H2   H  HCH3  0   0.227  -4.7456  -1.1155   1.3605
 NXH  H3   H  HCH3  0   0.235  -3.0399  -1.2778   1.7739
 NXH  H4   H  HCH1  0   0.243  -3.3319  -1.1147  -0.6877
 NXH  H5   H  HCH3  0   0.225  -4.5950   1.6101  -0.1303
 NXH  H6   H  HCH3  0   0.240  -4.1955   0.9647  -1.7280
 NXH  H7   H  HCH3  0   0.239  -5.4259   0.1811  -0.7359
 NXH  H8   H  HNH1  0   0.395  -2.1243   1.4604  -0.0004
 NXH  H9   H  HCR6  0   0.261   3.7495  -2.2272   0.0066
 NXH  H10  H  HCR6  0   0.263   4.5003   1.8072  -0.0698
 NXH  H11  H  HCR6  0   0.278   2.1142   2.3422  -0.1045
 NXH  H12  H  HNH1  0   0.413  -0.0165   1.6178  -0.0921
 NXH  H13  H  HCR6  0   0.288   1.3390  -1.8949  -0.0265

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
 NXH  C1   C2   single    1.525  0.020  1.525
 NXH  C3   C2   single    1.522  0.020  1.522
 NXH  C2   N4   single    1.455  0.020  1.455
 NXH  N4   C5   single    1.349  0.020  1.349
 NXH  O6   C5   double    1.221  0.020  1.221
 NXH  C5   N7   single    1.383  0.020  1.383
 NXH  N7   C8   single    1.379  0.020  1.379
 NXH  C9   C8   aromatic  1.398  0.020  1.398
 NXH  C9   C10  aromatic  1.385  0.020  1.385
 NXH  C8   C13  aromatic  1.401  0.020  1.401
 NXH  C10  N11  aromatic  1.328  0.020  1.328
 NXH  C13  C12  aromatic  1.380  0.020  1.380
 NXH  N11  C12  aromatic  1.331  0.020  1.331
 NXH  C1   H1   single    0.970  0.020  1.090
 NXH  C1   H2   single    0.970  0.020  1.090
 NXH  C1   H3   single    0.970  0.020  1.090
 NXH  C2   H4   single    0.970  0.020  1.090
 NXH  C3   H5   single    0.970  0.020  1.090
 NXH  C3   H6   single    0.970  0.020  1.090
 NXH  C3   H7   single    0.970  0.020  1.090
 NXH  N4   H8   single    0.860  0.020  1.020
 NXH  C10  H9   single    0.930  0.020  1.080
 NXH  C12  H10  single    0.930  0.020  1.080
 NXH  C13  H11  single    0.930  0.020  1.080
 NXH  N7   H12  single    0.860  0.020  1.020
 NXH  C9   H13  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
 NXH  H3   C1   H2   107.84  3.000
 NXH  H3   C1   H1   108.27  3.000
 NXH  H2   C1   H1   107.99  3.000
 NXH  H3   C1   C2   111.28  3.000
 NXH  H2   C1   C2   110.52  3.000
 NXH  H1   C1   C2   110.81  3.000
 NXH  H4   C2   N4   107.33  3.000
 NXH  H4   C2   C3   108.23  3.000
 NXH  N4   C2   C3   108.88  3.000
 NXH  H4   C2   C1   108.81  3.000
 NXH  N4   C2   C1   111.76  3.000
 NXH  C3   C2   C1   111.67  3.000
 NXH  H7   C3   H6   108.06  3.000
 NXH  H7   C3   H5   107.57  3.000
 NXH  H6   C3   H5   108.28  3.000
 NXH  H7   C3   C2   110.12  3.000
 NXH  H6   C3   C2   111.29  3.000
 NXH  H5   C3   C2   111.38  3.000
 NXH  H8   N4   C5   119.49  3.000
 NXH  H8   N4   C2   116.78  3.000
 NXH  C5   N4   C2   122.63  3.000
 NXH  N7   C5   O6   123.11  3.000
 NXH  N7   C5   N4   113.34  3.000
 NXH  O6   C5   N4   123.55  3.000
 NXH  C9   C8   N7   125.77  3.000
 NXH  C9   C8   C13  116.79  3.000
 NXH  N7   C8   C13  117.43  3.000
 NXH  H9   C10  N11  116.37  3.000
 NXH  H9   C10  C9   118.49  3.000
 NXH  N11  C10  C9   125.14  3.000
 NXH  H10  C12  N11  116.66  3.000
 NXH  H10  C12  C13  119.23  3.000
 NXH  N11  C12  C13  124.11  3.000
 NXH  H11  C13  C12  119.69  3.000
 NXH  H11  C13  C8   120.81  3.000
 NXH  C12  C13  C8   119.50  3.000
 NXH  H12  N7   C8   114.59  3.000
 NXH  H12  N7   C5   117.13  3.000
 NXH  C8   N7   C5   128.25  3.000
 NXH  H13  C9   C10  119.54  3.000
 NXH  H13  C9   C8   122.08  3.000
 NXH  C10  C9   C8   118.39  3.000
 NXH  C12  N11  C10  116.07  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
 NXH  CONST_01  N11  C10  C9   C8     0.00   0.0  0
 NXH  CONST_02  N11  C12  C13  C8     0.00   0.0  0
 NXH  CONST_03  C13  C8   C9   C10    0.00   0.0  0
 NXH  CONST_04  C13  C12  N11  C10    0.00   0.0  0
 NXH  CONST_05  C9   C8   C13  C12    0.00   0.0  0
 NXH  CONST_06  C9   C10  N11  C12    0.00   0.0  0
 NXH  CONST_07  N7   C8   C9   C10  180.00   0.0  0
 NXH  CONST_08  N7   C8   C13  C12  180.00   0.0  0
 NXH  CONST_09  H9   C10  C9   C8   180.00   0.0  0
 NXH  CONST_10  H10  C12  C13  C8   180.00   0.0  0
 NXH  CONST_11  H13  C9   C8   C13  180.00   0.0  0
 NXH  CONST_12  H11  C13  C8   C9   180.00   0.0  0
 NXH  CONST_13  C9   C8   N7   C5     0.00   0.0  0
 NXH  CONST_14  C13  C8   N7   C5   180.00   0.0  0
 NXH  CONST_15  H12  N7   C8   C13    0.00   0.0  0
 NXH  CONST_16  O6   C5   N7   C8     0.00   0.0  0
 NXH  CONST_17  C8   N7   C5   N4   180.00   0.0  0
 NXH  CONST_18  O6   C5   N4   C2     0.00   0.0  0
 NXH  CONST_19  N7   C5   N4   C2   180.00   0.0  0
 NXH  CONST_20  H8   N4   C5   O6   180.00   0.0  0
 NXH  Var_01    C5   N4   C2   C1    80.57  30.0  3
 NXH  Var_02    H5   C3   C2   C1    59.43  30.0  3
 NXH  Var_03    H1   C1   C2   C3   -61.37  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
 NXH  plan-1  C8   0.020
 NXH  plan-1  C10  0.020
 NXH  plan-1  C12  0.020
 NXH  plan-1  C13  0.020
 NXH  plan-1  N7   0.020
 NXH  plan-1  C9   0.020
 NXH  plan-1  N11  0.020
 NXH  plan-1  H9   0.020
 NXH  plan-1  H10  0.020
 NXH  plan-1  H11  0.020
 NXH  plan-1  H13  0.020
 NXH  plan-2  C2   0.020
 NXH  plan-2  N4   0.020
 NXH  plan-2  C5   0.020
 NXH  plan-2  C8   0.020
 NXH  plan-2  O6   0.020
 NXH  plan-2  N7   0.020
 NXH  plan-2  H8   0.020
 NXH  plan-2  H12  0.020

