# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:27:31 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: N-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)Nc2sccc2)cn1
#
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
 VZM  VZM  N-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea  ligand  28  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VZM
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
 VZM  N1   N  NH1   0  -0.746   -8.0370  14.7048   4.7536
 VZM  C4   C  CR6   0   0.232   -6.2636  14.5417   1.6088
 VZM  C5   C  C     0   0.733   -7.8872  14.8120   3.4019
 VZM  C6   C  CR5   0   0.117   -9.1842  15.0471   5.4423
 VZM  C7   C  CR15  0  -0.309   -9.3390  14.9716   6.7973
 VZM  C8   C  CR15  0  -0.172  -10.6318  15.3892   7.2159
 VZM  C10  C  CR16  0  -0.112   -5.0256  15.0773   1.3038
 VZM  O1   O  O     0  -0.497   -8.7891  15.2054   2.6807
 VZM  S    S  S2    0   0.219  -10.6156  15.6288   4.6660
 VZM  C9   C  CR15  0  -0.493  -11.4242  15.7701   6.1817
 VZM  N    N  NH1   0  -0.786   -6.6601  14.4272   2.9489
 VZM  C3   C  CR16  0  -0.162   -7.0499  14.0887   0.5442
 VZM  C2   C  CR16  0  -0.393   -6.5761  14.2094  -0.7411
 VZM  N2   N  N     0  -0.458   -4.5512  15.1754   0.0639
 VZM  C1   C  CR6   0   0.527   -5.3043  14.7643  -0.9310
 VZM  O    O  O2    0  -0.475   -4.8612  14.8616  -2.1874
 VZM  C    C  CH3   0  -0.416   -3.5789  15.4312  -2.4011
 VZM  H1   H  HNH1  0   0.423   -7.2720  14.3644   5.3171
 VZM  H2   H  HCR5  0   0.269   -8.5594  14.6328   7.4658
 VZM  H3   H  HCR5  0   0.264  -10.9470  15.4037   8.2495
 VZM  H4   H  HCR6  0   0.273   -4.3778  15.4345   2.0983
 VZM  H5   H  HCR5  0   0.288  -12.4404  16.1312   6.2156
 VZM  H6   H  HNH1  0   0.412   -5.9251  14.2739   3.6230
 VZM  H7   H  HCR6  0   0.283   -8.0146  13.6354   0.7202
 VZM  H8   H  HCR6  0   0.276   -7.1616  13.8710  -1.5853
 VZM  H9   H  HCH3  0   0.246   -3.4147  15.3998  -3.4752
 VZM  H10  H  HCH3  0   0.228   -3.5329  16.4670  -2.0617
 VZM  H11  H  HCH3  0   0.228   -2.7928  14.8649  -1.9000

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
 VZM  C    O    single    1.419  0.020  1.419
 VZM  O    C1   single    1.336  0.020  1.336
 VZM  C1   C2   aromatic  1.400  0.020  1.400
 VZM  C1   N2   aromatic  1.314  0.020  1.314
 VZM  C2   C3   aromatic  1.375  0.020  1.375
 VZM  N2   C10  aromatic  1.331  0.020  1.331
 VZM  C3   C4   aromatic  1.399  0.020  1.399
 VZM  C10  C4   aromatic  1.383  0.020  1.383
 VZM  C4   N    single    1.402  0.020  1.402
 VZM  O1   C5   double    1.220  0.020  1.220
 VZM  N    C5   single    1.363  0.020  1.363
 VZM  C5   N1   single    1.364  0.020  1.364
 VZM  S    C6   aromatic  1.729  0.020  1.729
 VZM  S    C9   aromatic  1.724  0.020  1.724
 VZM  N1   C6   single    1.381  0.020  1.381
 VZM  C6   C7   aromatic  1.366  0.020  1.366
 VZM  C9   C8   aromatic  1.357  0.020  1.357
 VZM  C7   C8   aromatic  1.422  0.020  1.422
 VZM  N1   H1   single    0.860  0.020  1.020
 VZM  C7   H2   single    0.930  0.020  1.080
 VZM  C8   H3   single    0.930  0.020  1.080
 VZM  C10  H4   single    0.930  0.020  1.080
 VZM  C9   H5   single    0.930  0.020  1.080
 VZM  N    H6   single    0.860  0.020  1.020
 VZM  C3   H7   single    0.930  0.020  1.080
 VZM  C2   H8   single    0.930  0.020  1.080
 VZM  C    H9   single    0.970  0.020  1.090
 VZM  C    H10  single    0.970  0.020  1.090
 VZM  C    H11  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
 VZM  H1   N1   C6   115.78  3.000
 VZM  H1   N1   C5   119.76  3.000
 VZM  C6   N1   C5   124.46  3.000
 VZM  C3   C4   N    122.81  3.000
 VZM  N    C4   C10  119.71  3.000
 VZM  C3   C4   C10  117.44  3.000
 VZM  N    C5   O1   124.05  3.000
 VZM  N    C5   N1   113.94  3.000
 VZM  O1   C5   N1   122.00  3.000
 VZM  S    C6   C7   111.72  3.000
 VZM  C7   C6   N1   125.11  3.000
 VZM  S    C6   N1   123.17  3.000
 VZM  H2   C7   C8   124.45  3.000
 VZM  H2   C7   C6   123.28  3.000
 VZM  C8   C7   C6   112.27  3.000
 VZM  H3   C8   C9   123.69  3.000
 VZM  H3   C8   C7   123.42  3.000
 VZM  C9   C8   C7   112.89  3.000
 VZM  H4   C10  N2   116.41  3.000
 VZM  H4   C10  C4   120.01  3.000
 VZM  N2   C10  C4   123.57  3.000
 VZM  C9   S    C6    91.21  3.000
 VZM  H5   C9   S    119.80  3.000
 VZM  H5   C9   C8   128.29  3.000
 VZM  S    C9   C8   111.91  3.000
 VZM  H6   N    C5   118.46  3.000
 VZM  H6   N    C4   116.41  3.000
 VZM  C5   N    C4   123.30  3.000
 VZM  H7   C3   C2   119.79  3.000
 VZM  H7   C3   C4   120.92  3.000
 VZM  C2   C3   C4   119.29  3.000
 VZM  H8   C2   C1   120.65  3.000
 VZM  H8   C2   C3   121.03  3.000
 VZM  C1   C2   C3   118.32  3.000
 VZM  C1   N2   C10  118.56  3.000
 VZM  O    C1   N2   119.95  3.000
 VZM  N2   C1   C2   122.81  3.000
 VZM  O    C1   C2   117.24  3.000
 VZM  C    O    C1   118.07  3.000
 VZM  H11  C    H10  108.64  3.000
 VZM  H11  C    H9   109.28  3.000
 VZM  H10  C    H9   109.18  3.000
 VZM  H11  C    O    111.94  3.000
 VZM  H10  C    O    111.85  3.000
 VZM  H9   C    O    105.88  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
 VZM  CONST_01  C1  C2   C3   C4     0.00   0.0  0
 VZM  CONST_02  C1  N2   C10  C4     0.00   0.0  0
 VZM  CONST_03  C8  C9   S    C6     0.00   0.0  0
 VZM  CONST_04  C9  C8   C7   C6     0.00   0.0  0
 VZM  CONST_05  C9  S    C6   C7     0.00   0.0  0
 VZM  CONST_06  S   C9   C8   C7     0.00   0.0  0
 VZM  CONST_07  S   C6   C7   C8     0.00   0.0  0
 VZM  CONST_08  C2  C1   N2   C10    0.00   0.0  0
 VZM  CONST_09  C2  C3   C4   C10    0.00   0.0  0
 VZM  CONST_10  N2  C1   C2   C3     0.00   0.0  0
 VZM  CONST_11  N2  C10  C4   C3     0.00   0.0  0
 VZM  CONST_12  C9  S    C6   N1   180.00   0.0  0
 VZM  CONST_13  C8  C7   C6   N1   180.00   0.0  0
 VZM  CONST_14  O   C1   N2   C10  180.00   0.0  0
 VZM  CONST_15  C2  C3   C4   N    180.00   0.0  0
 VZM  CONST_16  N2  C10  C4   N    180.00   0.0  0
 VZM  CONST_17  O   C1   C2   C3   180.00   0.0  0
 VZM  CONST_18  H8  C2   C3   C4   180.00   0.0  0
 VZM  CONST_19  H5  C9   S    C6   180.00   0.0  0
 VZM  CONST_20  H3  C8   C7   C6   180.00   0.0  0
 VZM  CONST_21  H7  C3   C4   C10  180.00   0.0  0
 VZM  CONST_22  H2  C7   C6   S    180.00   0.0  0
 VZM  CONST_23  H4  C10  C4   C3   180.00   0.0  0
 VZM  CONST_26  S   C6   N1   C5     0.00   0.0  0
 VZM  CONST_27  C7  C6   N1   C5   180.00   0.0  0
 VZM  CONST_28  H1  N1   C6   C7     0.00   0.0  0
 VZM  CONST_30  O1  C5   N    C4     0.00   0.0  0
 VZM  CONST_31  O1  C5   N1   C6     0.00   0.0  0
 VZM  CONST_32  C4  N    C5   N1   180.00   0.0  0
 VZM  CONST_33  N   C5   N1   C6   180.00   0.0  0
 VZM  Var_01    H9  C    O    C1   179.19  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
 VZM  plan-1  N1   0.020
 VZM  plan-1  C6   0.020
 VZM  plan-1  C7   0.020
 VZM  plan-1  C8   0.020
 VZM  plan-1  S    0.020
 VZM  plan-1  C9   0.020
 VZM  plan-1  H2   0.020
 VZM  plan-1  H3   0.020
 VZM  plan-1  H5   0.020
 VZM  plan-2  C4   0.020
 VZM  plan-2  C10  0.020
 VZM  plan-2  N    0.020
 VZM  plan-2  C3   0.020
 VZM  plan-2  C2   0.020
 VZM  plan-2  N2   0.020
 VZM  plan-2  C1   0.020
 VZM  plan-2  O    0.020
 VZM  plan-2  H4   0.020
 VZM  plan-2  H7   0.020
 VZM  plan-2  H8   0.020
 VZM  plan-3  N1   0.020
 VZM  plan-3  C4   0.020
 VZM  plan-3  C5   0.020
 VZM  plan-3  C6   0.020
 VZM  plan-3  O1   0.020
 VZM  plan-3  N    0.020
 VZM  plan-3  H1   0.020
 VZM  plan-3  H6   0.020

