# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:36:47 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(6-methylpyridin-2-yl)-3-propyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)Nc1cccc(C)n1
#
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
 GOE  GOE  1-(6-methylpyridin-2-yl)-3-propyl-urea  ligand  29  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GOE
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
 GOE  C4   C  CR16  0  -0.368   4.0601  -0.0799  -0.1724
 GOE  C5   C  CR6   0   0.239   3.1507   0.9479   0.0356
 GOE  C6   C  CH3   0  -0.714   3.5965   2.3730   0.1599
 GOE  C7   C  C     0   0.715  -1.0032   0.1337  -0.1404
 GOE  C8   C  CH2   0  -0.237  -3.4363   0.4126  -0.0076
 GOE  C9   C  CH2   0  -0.460  -4.6519  -0.5021  -0.0045
 GOE  C10  C  CH3   0  -0.666  -5.9415   0.2820  -0.1967
 GOE  N1   N  NH1   0  -0.770   0.0234  -0.7377   0.1840
 GOE  N2   N  N     0  -0.440   1.8403   0.7258   0.1511
 GOE  C3   C  CR16  0  -0.138   3.5776  -1.3795  -0.2712
 GOE  N3   N  NH1   0  -0.682  -2.2219  -0.3456   0.2014
 GOE  C1   C  CR6   0   0.494   1.3844  -0.5084   0.0369
 GOE  C2   C  CR16  0  -0.406   2.2215  -1.6102  -0.1752
 GOE  O1   O  O     0  -0.505  -0.8348   1.2008  -0.7031
 GOE  H1   H  HCR6  0   0.259   5.1184   0.1280  -0.2512
 GOE  H2   H  HCH3  0   0.250   3.1218   2.9931  -0.6019
 GOE  H3   H  HCH3  0   0.250   3.3140   2.7830   1.1307
 GOE  H4   H  HCH3  0   0.242   4.6754   2.4682   0.0514
 GOE  H5   H  HCH2  0   0.235  -3.3705   0.9293  -0.9658
 GOE  H6   H  HCH2  0   0.222  -3.5553   1.1838   0.7623
 GOE  H7   H  HCH2  0   0.229  -4.5439  -1.2469  -0.7969
 GOE  H8   H  HCH2  0   0.226  -4.6943  -1.0526   0.9402
 GOE  H9   H  HCH3  0   0.235  -6.8089  -0.3776  -0.1906
 GOE  H10  H  HCH3  0   0.222  -6.0805   1.0181   0.5970
 GOE  H11  H  HCH3  0   0.222  -5.9402   0.8173  -1.1478
 GOE  H12  H  HNH1  0   0.410  -0.2337  -1.6953   0.3671
 GOE  H13  H  HCR6  0   0.270   4.2576  -2.2057  -0.4328
 GOE  H14  H  HNH1  0   0.394  -2.2774  -1.1245   0.8388
 GOE  H15  H  HCR6  0   0.272   1.8132  -2.6084  -0.2665

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
 GOE  C10  C9   single    1.522  0.020  1.522
 GOE  C9   C8   single    1.521  0.020  1.521
 GOE  O1   C7   double    1.218  0.020  1.218
 GOE  C8   N3   single    1.447  0.020  1.447
 GOE  C7   N3   single    1.353  0.020  1.353
 GOE  C7   N1   single    1.385  0.020  1.385
 GOE  C2   C3   aromatic  1.379  0.020  1.379
 GOE  C2   C1   aromatic  1.400  0.020  1.400
 GOE  C3   C4   aromatic  1.390  0.020  1.390
 GOE  N1   C1   single    1.388  0.020  1.388
 GOE  C1   N2   aromatic  1.321  0.020  1.321
 GOE  C4   C5   aromatic  1.388  0.020  1.388
 GOE  N2   C5   aromatic  1.334  0.020  1.334
 GOE  C5   C6   single    1.498  0.020  1.498
 GOE  C4   H1   single    0.930  0.020  1.080
 GOE  C6   H2   single    0.970  0.020  1.090
 GOE  C6   H3   single    0.970  0.020  1.090
 GOE  C6   H4   single    0.970  0.020  1.090
 GOE  C8   H5   single    0.970  0.020  1.090
 GOE  C8   H6   single    0.970  0.020  1.090
 GOE  C9   H7   single    0.970  0.020  1.090
 GOE  C9   H8   single    0.970  0.020  1.090
 GOE  C10  H9   single    0.970  0.020  1.090
 GOE  C10  H10  single    0.970  0.020  1.090
 GOE  C10  H11  single    0.970  0.020  1.090
 GOE  N1   H12  single    0.860  0.020  1.020
 GOE  C3   H13  single    0.930  0.020  1.080
 GOE  N3   H14  single    0.860  0.020  1.020
 GOE  C2   H15  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
 GOE  H1   C4   C3   120.95  3.000
 GOE  H1   C4   C5   120.65  3.000
 GOE  C3   C4   C5   118.40  3.000
 GOE  N2   C5   C6   116.32  3.000
 GOE  C6   C5   C4   121.45  3.000
 GOE  N2   C5   C4   122.23  3.000
 GOE  H4   C6   H3   108.20  3.000
 GOE  H4   C6   H2   108.18  3.000
 GOE  H3   C6   H2   107.16  3.000
 GOE  H4   C6   C5   111.70  3.000
 GOE  H3   C6   C5   110.75  3.000
 GOE  H2   C6   C5   110.69  3.000
 GOE  O1   C7   N3   123.46  3.000
 GOE  N3   C7   N1   112.67  3.000
 GOE  O1   C7   N1   123.84  3.000
 GOE  H6   C8   H5   106.87  3.000
 GOE  H6   C8   N3   111.00  3.000
 GOE  H5   C8   N3   108.94  3.000
 GOE  H6   C8   C9   109.57  3.000
 GOE  H5   C8   C9   109.56  3.000
 GOE  N3   C8   C9   110.81  3.000
 GOE  H8   C9   H7   106.68  3.000
 GOE  H8   C9   C10  109.60  3.000
 GOE  H7   C9   C10  110.08  3.000
 GOE  H8   C9   C8   109.58  3.000
 GOE  H7   C9   C8   109.23  3.000
 GOE  C10  C9   C8   111.54  3.000
 GOE  H11  C10  H10  107.65  3.000
 GOE  H11  C10  H9   107.62  3.000
 GOE  H10  C10  H9   107.63  3.000
 GOE  H11  C10  C9   111.21  3.000
 GOE  H10  C10  C9   111.32  3.000
 GOE  H9   C10  C9   111.23  3.000
 GOE  H12  N1   C1   115.23  3.000
 GOE  H12  N1   C7   116.81  3.000
 GOE  C1   N1   C7   126.73  3.000
 GOE  C1   N2   C5   119.15  3.000
 GOE  H13  C3   C2   120.04  3.000
 GOE  H13  C3   C4   120.43  3.000
 GOE  C2   C3   C4   119.53  3.000
 GOE  H14  N3   C8   116.75  3.000
 GOE  H14  N3   C7   118.87  3.000
 GOE  C8   N3   C7   122.26  3.000
 GOE  C2   C1   N2   122.83  3.000
 GOE  N2   C1   N1   118.93  3.000
 GOE  C2   C1   N1   118.19  3.000
 GOE  H15  C2   C1   120.87  3.000
 GOE  H15  C2   C3   121.29  3.000
 GOE  C1   C2   C3   117.84  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
 GOE  CONST_01  C1   C2   C3  C4      0.00   0.0  0
 GOE  CONST_02  C1   N2   C5  C4      0.00   0.0  0
 GOE  CONST_03  C2   C3   C4  C5      0.00   0.0  0
 GOE  CONST_04  C2   C1   N2  C5      0.00   0.0  0
 GOE  CONST_05  C3   C2   C1  N2      0.00   0.0  0
 GOE  CONST_06  C3   C4   C5  N2      0.00   0.0  0
 GOE  CONST_07  N1   C1   N2  C5    180.00   0.0  0
 GOE  CONST_08  C3   C4   C5  C6    180.00   0.0  0
 GOE  CONST_09  C1   N2   C5  C6    180.00   0.0  0
 GOE  CONST_10  C3   C2   C1  N1    180.00   0.0  0
 GOE  CONST_11  H15  C2   C3  C4    180.00   0.0  0
 GOE  CONST_12  H13  C3   C4  C5    180.00   0.0  0
 GOE  CONST_13  H1   C4   C5  N2    180.00   0.0  0
 GOE  CONST_17  O1   C7   N1  C1      0.00   0.0  0
 GOE  CONST_18  C1   N1   C7  N3    180.00   0.0  0
 GOE  CONST_19  O1   C7   N3  C8      0.00   0.0  0
 GOE  CONST_20  N1   C7   N3  C8    180.00   0.0  0
 GOE  CONST_21  H14  N3   C7  O1    180.00   0.0  0
 GOE  Var_01    H2   C6   C5  C4    121.50  30.0  2
 GOE  Var_02    C9   C8   N3  C7    160.11  30.0  2
 GOE  Var_03    N3   C8   C9  C10   178.92  30.0  3
 GOE  Var_04    H9   C10  C9  C8   -179.82  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
 GOE  plan-1  C4   0.020
 GOE  plan-1  C5   0.020
 GOE  plan-1  C6   0.020
 GOE  plan-1  N1   0.020
 GOE  plan-1  N2   0.020
 GOE  plan-1  C3   0.020
 GOE  plan-1  C1   0.020
 GOE  plan-1  C2   0.020
 GOE  plan-1  H1   0.020
 GOE  plan-1  H13  0.020
 GOE  plan-1  H15  0.020
 GOE  plan-2  C7   0.020
 GOE  plan-2  C8   0.020
 GOE  plan-2  N1   0.020
 GOE  plan-2  N3   0.020
 GOE  plan-2  C1   0.020
 GOE  plan-2  O1   0.020
 GOE  plan-2  H12  0.020
 GOE  plan-2  H14  0.020

