# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:27:40 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: N-(2-methoxy-5-methylphenyl)-N'-4H-1,2,4-triazol-4-ylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)cc1NC(=O)Nn2cnnc2
#
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
 VZS  VZS  N-(2-methoxy-5-methylphenyl)-N'-4H-1,2,4-triazol-4-ylurea  ligand  31  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VZS
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
 VZS  N1   N  NC1   0  -0.571   4.5651  25.5348  16.0520
 VZS  N3   N  N     0  -0.317   7.3175  25.1073  18.1427
 VZS  C4   C  CR6   0   0.087   1.1523  30.1826  15.8553
 VZS  C5   C  CH3   0  -0.724   1.5406  31.5992  16.1688
 VZS  C6   C  CR16  0  -0.355   2.1141  29.1711  15.9255
 VZS  C7   C  CR6   0   0.303   1.7926  27.8496  15.6535
 VZS  C8   C  C     0   0.751   3.9591  26.7778  16.1774
 VZS  C10  C  CR15  0   0.108   6.9802  25.4157  16.0422
 VZS  O1   O  O     0  -0.478   4.5551  27.7236  16.6485
 VZS  N2   N  NR5   0  -0.265   5.7700  25.3689  16.6493
 VZS  N4   N  N     0  -0.320   7.9160  25.2556  16.9246
 VZS  C9   C  CR15  0   0.102   6.0359  25.1831  17.9669
 VZS  N    N  NH1   0  -0.777   2.6945  26.7802  15.6927
 VZS  C1   C  CR6   0   0.312   0.4688  27.5274  15.2885
 VZS  O    O  O2    0  -0.487   0.2407  26.2218  15.0291
 VZS  C    C  CH3   0  -0.432  -1.0513  25.8295  14.6104
 VZS  C3   C  CR16  0  -0.313  -0.1418  29.8459  15.4993
 VZS  C2   C  CR16  0  -0.367  -0.4847  28.5264  15.2140
 VZS  H1   H  HNC1  0   0.433   4.0267  24.6886  15.9312
 VZS  H2   H  HCH3  0   0.244   1.8540  31.7047  17.2089
 VZS  H3   H  HCH3  0   0.243   2.3752  31.9316  15.5496
 VZS  H4   H  HCH3  0   0.242   0.7111  32.2854  16.0036
 VZS  H5   H  HCR6  0   0.274   3.1252  29.4333  16.1946
 VZS  H6   H  HCR5  0   0.315   7.1027  25.5598  14.9804
 VZS  H7   H  HCR5  0   0.318   5.2703  25.1061  18.7228
 VZS  H8   H  HNH1  0   0.419   2.3275  25.9048  15.3479
 VZS  H9   H  HCH3  0   0.262  -1.0063  24.7587  14.4308
 VZS  H10  H  HCH3  0   0.231  -1.8031  26.0284  15.3780
 VZS  H11  H  HCH3  0   0.232  -1.3464  26.3325  13.6865
 VZS  H12  H  HCR6  0   0.250  -0.9061  30.6105  15.4382
 VZS  H13  H  HCR6  0   0.281  -1.5051  28.2972  14.9376

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
 VZS  C    O    single    1.414  0.020  1.414
 VZS  O    C1   single    1.351  0.020  1.351
 VZS  C2   C1   aromatic  1.383  0.020  1.383
 VZS  C2   C3   aromatic  1.393  0.020  1.393
 VZS  C1   C7   aromatic  1.410  0.020  1.410
 VZS  C3   C4   aromatic  1.384  0.020  1.384
 VZS  C7   N    single    1.400  0.020  1.400
 VZS  C7   C6   aromatic  1.387  0.020  1.387
 VZS  N    C8   single    1.354  0.020  1.354
 VZS  C4   C6   aromatic  1.398  0.020  1.398
 VZS  C4   C5   single    1.502  0.020  1.502
 VZS  C10  N2   aromatic  1.355  0.020  1.355
 VZS  C10  N4   aromatic  1.296  0.020  1.296
 VZS  C8   N1   single    1.389  0.020  1.389
 VZS  C8   O1   double    1.213  0.020  1.213
 VZS  N1   N2   single    1.355  0.020  1.355
 VZS  N2   C9   aromatic  1.357  0.020  1.357
 VZS  N4   N3   aromatic  1.365  0.020  1.365
 VZS  C9   N3   aromatic  1.296  0.020  1.296
 VZS  N1   H1   single    0.890  0.020  1.040
 VZS  C5   H2   single    0.970  0.020  1.090
 VZS  C5   H3   single    0.970  0.020  1.090
 VZS  C5   H4   single    0.970  0.020  1.090
 VZS  C6   H5   single    0.930  0.020  1.080
 VZS  C10  H6   single    0.930  0.020  1.080
 VZS  C9   H7   single    0.930  0.020  1.080
 VZS  N    H8   single    0.860  0.020  1.020
 VZS  C    H9   single    0.970  0.020  1.090
 VZS  C    H10  single    0.970  0.020  1.090
 VZS  C    H11  single    0.970  0.020  1.090
 VZS  C3   H12  single    0.930  0.020  1.080
 VZS  C2   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
 VZS  H1   N1   N2   115.10  3.000
 VZS  H1   N1   C8   121.87  3.000
 VZS  N2   N1   C8   117.25  3.000
 VZS  C9   N3   N4   107.83  3.000
 VZS  C3   C4   C6   118.71  3.000
 VZS  C6   C4   C5   119.62  3.000
 VZS  C3   C4   C5   121.67  3.000
 VZS  H4   C5   H3   107.73  3.000
 VZS  H4   C5   H2   107.60  3.000
 VZS  H3   C5   H2   106.96  3.000
 VZS  H4   C5   C4   111.45  3.000
 VZS  H3   C5   C4   111.51  3.000
 VZS  H2   C5   C4   111.37  3.000
 VZS  H5   C6   C7   119.86  3.000
 VZS  H5   C6   C4   118.80  3.000
 VZS  C7   C6   C4   121.35  3.000
 VZS  C1   C7   N    115.95  3.000
 VZS  N    C7   C6   124.97  3.000
 VZS  C1   C7   C6   119.08  3.000
 VZS  N    C8   O1   126.61  3.000
 VZS  O1   C8   N1   121.23  3.000
 VZS  N    C8   N1   112.14  3.000
 VZS  H6   C10  N4   127.22  3.000
 VZS  H6   C10  N2   123.18  3.000
 VZS  N4   C10  N2   109.60  3.000
 VZS  C9   N2   C10  105.36  3.000
 VZS  C9   N2   N1   128.25  3.000
 VZS  C10  N2   N1   126.34  3.000
 VZS  C10  N4   N3   107.73  3.000
 VZS  H7   C9   N2   123.44  3.000
 VZS  H7   C9   N3   127.07  3.000
 VZS  N2   C9   N3   109.49  3.000
 VZS  H8   N    C8   117.39  3.000
 VZS  H8   N    C7   114.75  3.000
 VZS  C8   N    C7   127.82  3.000
 VZS  C2   C1   O    124.85  3.000
 VZS  C2   C1   C7   119.74  3.000
 VZS  O    C1   C7   115.41  3.000
 VZS  C    O    C1   118.65  3.000
 VZS  H11  C    H10  108.93  3.000
 VZS  H11  C    H9   108.98  3.000
 VZS  H10  C    H9   108.90  3.000
 VZS  H11  C    O    111.69  3.000
 VZS  H10  C    O    111.73  3.000
 VZS  H9   C    O    106.53  3.000
 VZS  H12  C3   C2   118.92  3.000
 VZS  H12  C3   C4   120.18  3.000
 VZS  C2   C3   C4   120.89  3.000
 VZS  H13  C2   C3   119.03  3.000
 VZS  H13  C2   C1   120.74  3.000
 VZS  C3   C2   C1   120.23  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
 VZS  CONST_01  N2   C10  N4   N3     0.00   0.0  0
 VZS  CONST_02  C10  N2   C9   N3     0.00   0.0  0
 VZS  CONST_03  C1   C2   C3   C4     0.00   0.0  0
 VZS  CONST_04  C1   C7   C6   C4     0.00   0.0  0
 VZS  CONST_05  C2   C1   C7   C6     0.00   0.0  0
 VZS  CONST_06  C2   C3   C4   C6     0.00   0.0  0
 VZS  CONST_07  C3   C2   C1   C7     0.00   0.0  0
 VZS  CONST_08  C3   C4   C6   C7     0.00   0.0  0
 VZS  CONST_09  C9   N3   N4   C10    0.00   0.0  0
 VZS  CONST_10  N4   N3   C9   N2     0.00   0.0  0
 VZS  CONST_11  C9   N2   C10  N4     0.00   0.0  0
 VZS  CONST_12  N4   C10  N2   N1   180.00   0.0  0
 VZS  CONST_13  N3   C9   N2   N1   180.00   0.0  0
 VZS  CONST_14  N    C7   C6   C4   180.00   0.0  0
 VZS  CONST_15  C2   C3   C4   C5   180.00   0.0  0
 VZS  CONST_16  C7   C6   C4   C5   180.00   0.0  0
 VZS  CONST_17  O    C1   C7   C6   180.00   0.0  0
 VZS  CONST_18  C2   C1   C7   N    180.00   0.0  0
 VZS  CONST_19  C3   C2   C1   O    180.00   0.0  0
 VZS  CONST_20  H6   C10  N4   N3   180.00   0.0  0
 VZS  CONST_21  H13  C2   C3   C4   180.00   0.0  0
 VZS  CONST_22  H12  C3   C4   C6   180.00   0.0  0
 VZS  CONST_23  H7   C9   N2   C10  180.00   0.0  0
 VZS  CONST_24  H5   C6   C7   C1   180.00   0.0  0
 VZS  CONST_25  C8   N    C7   C6     0.00   0.0  0
 VZS  CONST_26  C1   C7   N    C8   180.00   0.0  0
 VZS  CONST_29  H8   N    C7   C6   180.00   0.0  0
 VZS  CONST_31  O1   C8   N    C7     0.00   0.0  0
 VZS  CONST_32  N2   N1   C8   O1     0.00   0.0  0
 VZS  CONST_33  C7   N    C8   N1   180.00   0.0  0
 VZS  CONST_34  N    C8   N1   N2   180.00   0.0  0
 VZS  Var_01    C2   C1   O    C      1.98  30.0  2
 VZS  Var_02    H2   C5   C4   C6   -63.94  30.0  2
 VZS  Var_03    H9   C    O    C1   178.35  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
 VZS  plan-1  N1   0.020
 VZS  plan-1  N3   0.020
 VZS  plan-1  C10  0.020
 VZS  plan-1  N2   0.020
 VZS  plan-1  N4   0.020
 VZS  plan-1  C9   0.020
 VZS  plan-1  H6   0.020
 VZS  plan-1  H7   0.020
 VZS  plan-2  C4   0.020
 VZS  plan-2  C5   0.020
 VZS  plan-2  C6   0.020
 VZS  plan-2  C7   0.020
 VZS  plan-2  N    0.020
 VZS  plan-2  C1   0.020
 VZS  plan-2  O    0.020
 VZS  plan-2  C3   0.020
 VZS  plan-2  C2   0.020
 VZS  plan-2  H5   0.020
 VZS  plan-2  H12  0.020
 VZS  plan-2  H13  0.020
 VZS  plan-3  N1   0.020
 VZS  plan-3  C7   0.020
 VZS  plan-3  C8   0.020
 VZS  plan-3  O1   0.020
 VZS  plan-3  N2   0.020
 VZS  plan-3  N    0.020
 VZS  plan-3  H1   0.020
 VZS  plan-3  H8   0.020

