# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:16:36 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: N-phenyl-N'-pyridin-3-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccccc1)Nc2cccnc2
#
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
 K0G  K0G  N-phenyl-N'-pyridin-3-ylurea  ligand  27  16  .  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_K0G
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
 K0G  N1   N  NH1   0  -0.783  -1.1238   0.7509   0.1465
 K0G  C4   C  CR16  0  -0.272   5.1510  -0.4988  -0.1697
 K0G  C5   C  CR16  0  -0.251   4.1599  -1.3026  -0.7152
 K0G  C6   C  CR16  0  -0.301   2.8244  -0.9256  -0.6751
 K0G  C7   C  CR6   0   0.281  -2.4315   0.2742   0.1612
 K0G  C8   C  CR16  0  -0.196  -2.8212  -0.9618   0.6731
 K0G  C10  C  CR16  0  -0.085  -5.0825  -0.3828   0.1350
 K0G  N    N  NH1   0  -0.785   1.1480   0.7480  -0.0056
 K0G  C    C  C     0   0.725   0.0131  -0.0117   0.0539
 K0G  O    O  O     0  -0.492   0.0040  -1.2282   0.0301
 K0G  C1   C  CR6   0   0.366   2.4639   0.2758  -0.0636
 K0G  C11  C  CR16  0  -0.141  -3.4347   1.1141  -0.3311
 K0G  C2   C  CR16  0  -0.338   3.4613   1.0863   0.4818
 K0G  C3   C  CR16  0  -0.246   4.7918   0.7042   0.4232
 K0G  C9   C  CR16  0  -0.319  -4.1679  -1.2879   0.6484
 K0G  N2   N  N     0  -0.390  -4.7191   0.8028  -0.3406
 K0G  H1   H  HNH1  0   0.413  -1.0329   1.7440  -0.0060
 K0G  H3   H  HCR6  0   0.258   4.4247  -2.2379  -1.1909
 K0G  H4   H  HCR6  0   0.270   2.0814  -1.5621  -1.1291
 K0G  H5   H  HCR6  0   0.286  -2.1056  -1.6534   1.0887
 K0G  H6   H  HCR6  0   0.263  -6.1398  -0.6191   0.1084
 K0G  H7   H  HNH1  0   0.413   1.0578   1.7361   0.1781
 K0G  H8   H  HCR6  0   0.271  -3.1662   2.0879  -0.7317
 K0G  H9   H  HCR6  0   0.268   3.1915   2.0228   0.9557
 K0G  H10  H  HCR6  0   0.259   5.5479   1.3504   0.8500
 K0G  H11  H  HCR6  0   0.274  -4.5042  -2.2393   1.0367
 K0G  H2   H  HCR6  0   0.255   6.1883  -0.8028  -0.2115

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
 K0G  C4   C3   aromatic  1.388  0.020  1.388
 K0G  C4   C5   aromatic  1.388  0.020  1.388
 K0G  C3   C2   aromatic  1.385  0.020  1.385
 K0G  C5   C6   aromatic  1.388  0.020  1.388
 K0G  C2   C1   aromatic  1.396  0.020  1.396
 K0G  C6   C1   aromatic  1.395  0.020  1.395
 K0G  C1   N    single    1.399  0.020  1.399
 K0G  N    C    single    1.367  0.020  1.367
 K0G  C    O    double    1.217  0.020  1.217
 K0G  C    N1   single    1.372  0.020  1.372
 K0G  N1   C7   single    1.392  0.020  1.392
 K0G  C7   C8   aromatic  1.393  0.020  1.393
 K0G  C7   C11  aromatic  1.398  0.020  1.398
 K0G  C8   C9   aromatic  1.386  0.020  1.386
 K0G  C11  N2   aromatic  1.322  0.020  1.322
 K0G  C9   C10  aromatic  1.385  0.020  1.385
 K0G  N2   C10  aromatic  1.328  0.020  1.328
 K0G  N1   H1   single    0.860  0.020  1.020
 K0G  C4   H2   single    0.930  0.020  1.080
 K0G  C5   H3   single    0.930  0.020  1.080
 K0G  C6   H4   single    0.930  0.020  1.080
 K0G  C8   H5   single    0.930  0.020  1.080
 K0G  C10  H6   single    0.930  0.020  1.080
 K0G  N    H7   single    0.860  0.020  1.020
 K0G  C11  H8   single    0.930  0.020  1.080
 K0G  C2   H9   single    0.930  0.020  1.080
 K0G  C3   H10  single    0.930  0.020  1.080
 K0G  C9   H11  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
 K0G  H1   N1   C    117.53  3.000
 K0G  H1   N1   C7   115.05  3.000
 K0G  C    N1   C7   126.07  3.000
 K0G  H2   C4   C3   120.54  3.000
 K0G  H2   C4   C5   120.45  3.000
 K0G  C3   C4   C5   119.01  3.000
 K0G  H3   C5   C6   118.87  3.000
 K0G  H3   C5   C4   119.91  3.000
 K0G  C6   C5   C4   121.22  3.000
 K0G  H4   C6   C1   120.97  3.000
 K0G  H4   C6   C5   119.35  3.000
 K0G  C1   C6   C5   119.67  3.000
 K0G  C11  C7   C8   117.49  3.000
 K0G  C11  C7   N1   117.69  3.000
 K0G  C8   C7   N1   124.78  3.000
 K0G  H5   C8   C9   120.05  3.000
 K0G  H5   C8   C7   121.66  3.000
 K0G  C9   C8   C7   118.29  3.000
 K0G  H6   C10  N2   116.93  3.000
 K0G  H6   C10  C9   120.71  3.000
 K0G  N2   C10  C9   122.36  3.000
 K0G  H7   N    C1   114.97  3.000
 K0G  H7   N    C    117.52  3.000
 K0G  C1   N    C    126.51  3.000
 K0G  O    C    N    124.12  3.000
 K0G  O    C    N1   123.42  3.000
 K0G  N    C    N1   112.45  3.000
 K0G  C2   C1   N    117.37  3.000
 K0G  N    C1   C6   123.48  3.000
 K0G  C2   C1   C6   119.10  3.000
 K0G  H8   C11  N2   116.66  3.000
 K0G  H8   C11  C7   119.40  3.000
 K0G  N2   C11  C7   123.94  3.000
 K0G  H9   C2   C3   119.73  3.000
 K0G  H9   C2   C1   119.64  3.000
 K0G  C3   C2   C1   120.62  3.000
 K0G  H10  C3   C2   119.31  3.000
 K0G  H10  C3   C4   120.33  3.000
 K0G  C2   C3   C4   120.36  3.000
 K0G  H11  C9   C10  120.17  3.000
 K0G  H11  C9   C8   120.19  3.000
 K0G  C10  C9   C8   119.63  3.000
 K0G  C11  N2   C10  118.27  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
 K0G  CONST_01  C1   C2   C3   C4     0.00  0.0  0
 K0G  CONST_02  C1   C6   C5   C4     0.00  0.0  0
 K0G  CONST_03  C2   C3   C4   C5     0.00  0.0  0
 K0G  CONST_04  C2   C1   C6   C5     0.00  0.0  0
 K0G  CONST_05  C3   C4   C5   C6     0.00  0.0  0
 K0G  CONST_06  C3   C2   C1   C6     0.00  0.0  0
 K0G  CONST_07  C10  C9   C8   C7     0.00  0.0  0
 K0G  CONST_08  C10  N2   C11  C7     0.00  0.0  0
 K0G  CONST_09  N2   C11  C7   C8     0.00  0.0  0
 K0G  CONST_10  N2   C10  C9   C8     0.00  0.0  0
 K0G  CONST_11  C9   C8   C7   C11    0.00  0.0  0
 K0G  CONST_12  C9   C10  N2   C11    0.00  0.0  0
 K0G  CONST_13  C9   C8   C7   N1   180.00  0.0  0
 K0G  CONST_14  N2   C11  C7   N1   180.00  0.0  0
 K0G  CONST_15  N    C1   C6   C5   180.00  0.0  0
 K0G  CONST_16  C3   C2   C1   N    180.00  0.0  0
 K0G  CONST_17  H9   C2   C3   C4   180.00  0.0  0
 K0G  CONST_18  H4   C6   C5   C4   180.00  0.0  0
 K0G  CONST_19  H10  C3   C4   C5   180.00  0.0  0
 K0G  CONST_20  H2   C4   C5   C6   180.00  0.0  0
 K0G  CONST_21  H11  C9   C8   C7   180.00  0.0  0
 K0G  CONST_22  H8   C11  C7   C8   180.00  0.0  0
 K0G  CONST_23  H6   C10  C9   C8   180.00  0.0  0
 K0G  CONST_24  H5   C8   C9   C10  180.00  0.0  0
 K0G  CONST_25  H3   C5   C6   C1   180.00  0.0  0
 K0G  CONST_32  O    C    N1   C7     0.00  0.0  0
 K0G  CONST_33  C1   N    C    O      0.00  0.0  0
 K0G  CONST_34  C1   N    C    N1   180.00  0.0  0
 K0G  CONST_35  N    C    N1   C7   180.00  0.0  0

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
 K0G  plan-1  C4   0.020
 K0G  plan-1  C5   0.020
 K0G  plan-1  C6   0.020
 K0G  plan-1  N    0.020
 K0G  plan-1  C1   0.020
 K0G  plan-1  C2   0.020
 K0G  plan-1  C3   0.020
 K0G  plan-1  H3   0.020
 K0G  plan-1  H4   0.020
 K0G  plan-1  H9   0.020
 K0G  plan-1  H10  0.020
 K0G  plan-1  H2   0.020
 K0G  plan-2  N1   0.020
 K0G  plan-2  C7   0.020
 K0G  plan-2  C8   0.020
 K0G  plan-2  C10  0.020
 K0G  plan-2  C11  0.020
 K0G  plan-2  C9   0.020
 K0G  plan-2  N2   0.020
 K0G  plan-2  H5   0.020
 K0G  plan-2  H6   0.020
 K0G  plan-2  H8   0.020
 K0G  plan-2  H11  0.020
 K0G  plan-3  N1   0.020
 K0G  plan-3  C7   0.020
 K0G  plan-3  N    0.020
 K0G  plan-3  C    0.020
 K0G  plan-3  O    0.020
 K0G  plan-3  C1   0.020
 K0G  plan-3  H1   0.020
 K0G  plan-3  H7   0.020

