# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:44:17 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-(benzyloxy)-5-methyl-N-(4-methyl-1,3-thiazol-2-yl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnc(Nc2scc(C)n2)c(OCc3ccccc3)c1
#
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
 VO2  VO2  3-(benzyloxy)-5-methyl-N-(4-methyl-1,3-thiazol-2-yl)pyridin-2-amine  ligand  39  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VO2
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
 VO2  C1   C  CR5   0   0.283   2.2980  -0.8702   0.0172
 VO2  N2   N  N     0  -0.458   2.4182  -2.1632   0.0029
 VO2  C3   C  CR5   0   0.324   3.7361  -2.5401   0.0185
 VO2  C4   C  CR15  0  -0.572   4.6225  -1.5155   0.0456
 VO2  S5   S  S2    0   0.197   3.7971   0.0045   0.0519
 VO2  C6   C  CH3   0  -0.725   4.0790  -3.9914   0.0038
 VO2  N7   N  NH1   0  -0.725   1.0703  -0.2813   0.0056
 VO2  C8   C  CR6   0   0.466   0.8035   1.0682   0.0079
 VO2  N9   N  N     0  -0.458   1.8075   1.9087   0.0303
 VO2  C10  C  CR16  0  -0.114   1.5655   3.2229   0.0315
 VO2  C11  C  CR6   0   0.006   0.2965   3.7589   0.0073
 VO2  C12  C  CR16  0  -0.309  -0.7795   2.8571  -0.0140
 VO2  C13  C  CR6   0   0.267  -0.5431   1.5015  -0.0118
 VO2  O14  O  O2    0  -0.473  -1.4714   0.5293  -0.0249
 VO2  C15  C  CH2   0  -0.271  -2.8452   0.9092  -0.0218
 VO2  C16  C  CR6   0   0.098  -3.6560  -0.3487  -0.0120
 VO2  C17  C  CR16  0  -0.292  -4.0569  -0.9382  -1.2069
 VO2  C18  C  CR16  0  -0.242  -4.7800  -2.1231  -1.1997
 VO2  C19  C  CR16  0  -0.260  -5.1068  -2.7300   0.0062
 VO2  C20  C  CR16  0  -0.243  -4.7092  -2.1477   1.2032
 VO2  C21  C  CR16  0  -0.289  -3.9867  -0.9628   1.1925
 VO2  C28  C  CH3   0  -0.726   0.0588   5.2377  -0.0032
 VO2  H1   H  HCR5  0   0.288   5.6998  -1.5659   0.0599
 VO2  H2   H  HCH3  0   0.245   3.6759  -4.4797  -0.8849
 VO2  H3   H  HCH3  0   0.243   5.1572  -4.1388   0.0124
 VO2  H4   H  HCH3  0   0.245   3.6594  -4.5027   0.8719
 VO2  H5   H  HNH1  0   0.418   0.2920  -0.9235  -0.0129
 VO2  H6   H  HCR6  0   0.254   2.4371   3.8680   0.0528
 VO2  H7   H  HCR6  0   0.293  -1.7912   3.2436  -0.0304
 VO2  H8   H  HCH2  0   0.249  -3.0600   1.5191   0.8616
 VO2  H9   H  HCH2  0   0.249  -3.0678   1.5099  -0.9094
 VO2  H10  H  HCR6  0   0.256  -3.8084  -0.4651  -2.1496
 VO2  H11  H  HCR6  0   0.259  -5.0879  -2.5718  -2.1351
 VO2  H12  H  HCR6  0   0.260  -5.6729  -3.6524   0.0136
 VO2  H13  H  HCR6  0   0.259  -4.9616  -2.6160   2.1456
 VO2  H14  H  HCR6  0   0.256  -3.6838  -0.5089   2.1287
 VO2  H15  H  HCH3  0   0.248  -0.3867   5.5600  -0.9459
 VO2  H16  H  HCH3  0   0.247  -0.6238   5.5362   0.7936
 VO2  H17  H  HCH3  0   0.246   0.9888   5.7889   0.1293

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
 VO2  C6   C3   single    1.491  0.020  1.491
 VO2  C3   N2   aromatic  1.371  0.020  1.371
 VO2  C3   C4   aromatic  1.355  0.020  1.355
 VO2  N2   C1   aromatic  1.299  0.020  1.299
 VO2  C4   S5   aromatic  1.730  0.020  1.730
 VO2  C1   N7   single    1.362  0.020  1.362
 VO2  C1   S5   aromatic  1.736  0.020  1.736
 VO2  C18  C17  aromatic  1.388  0.020  1.388
 VO2  C18  C19  aromatic  1.389  0.020  1.389
 VO2  N7   C8   single    1.376  0.020  1.376
 VO2  C17  C16  aromatic  1.391  0.020  1.391
 VO2  C19  C20  aromatic  1.389  0.020  1.389
 VO2  O14  C15  single    1.425  0.020  1.425
 VO2  O14  C13  single    1.344  0.020  1.344
 VO2  C16  C15  single    1.497  0.020  1.497
 VO2  C16  C21  aromatic  1.392  0.020  1.392
 VO2  C8   C13  aromatic  1.415  0.020  1.415
 VO2  C8   N9   aromatic  1.310  0.020  1.310
 VO2  C20  C21  aromatic  1.388  0.020  1.388
 VO2  C13  C12  aromatic  1.376  0.020  1.376
 VO2  N9   C10  aromatic  1.336  0.020  1.336
 VO2  C12  C11  aromatic  1.404  0.020  1.404
 VO2  C10  C11  aromatic  1.378  0.020  1.378
 VO2  C11  C28  single    1.498  0.020  1.498
 VO2  C4   H1   single    0.930  0.020  1.080
 VO2  C6   H2   single    0.970  0.020  1.090
 VO2  C6   H3   single    0.970  0.020  1.090
 VO2  C6   H4   single    0.970  0.020  1.090
 VO2  N7   H5   single    0.860  0.020  1.020
 VO2  C10  H6   single    0.930  0.020  1.080
 VO2  C12  H7   single    0.930  0.020  1.080
 VO2  C15  H8   single    0.970  0.020  1.090
 VO2  C15  H9   single    0.970  0.020  1.090
 VO2  C17  H10  single    0.930  0.020  1.080
 VO2  C18  H11  single    0.930  0.020  1.080
 VO2  C19  H12  single    0.930  0.020  1.080
 VO2  C20  H13  single    0.930  0.020  1.080
 VO2  C21  H14  single    0.930  0.020  1.080
 VO2  C28  H15  single    0.970  0.020  1.090
 VO2  C28  H16  single    0.970  0.020  1.090
 VO2  C28  H17  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
 VO2  N7   C1   S5   124.11  3.000
 VO2  S5   C1   N2   114.96  3.000
 VO2  N7   C1   N2   120.93  3.000
 VO2  C3   N2   C1   111.26  3.000
 VO2  C6   C3   C4   125.85  3.000
 VO2  C4   C3   N2   114.91  3.000
 VO2  C6   C3   N2   119.24  3.000
 VO2  H1   C4   S5   121.17  3.000
 VO2  H1   C4   C3   128.19  3.000
 VO2  S5   C4   C3   110.64  3.000
 VO2  C4   S5   C1    88.23  3.000
 VO2  H4   C6   H3   108.13  3.000
 VO2  H4   C6   H2   107.23  3.000
 VO2  H3   C6   H2   108.17  3.000
 VO2  H4   C6   C3   111.08  3.000
 VO2  H3   C6   C3   111.07  3.000
 VO2  H2   C6   C3   111.01  3.000
 VO2  H5   N7   C8   118.34  3.000
 VO2  H5   N7   C1   114.85  3.000
 VO2  C8   N7   C1   126.81  3.000
 VO2  C13  C8   N9   122.24  3.000
 VO2  N9   C8   N7   118.75  3.000
 VO2  C13  C8   N7   119.02  3.000
 VO2  C10  N9   C8   119.49  3.000
 VO2  H6   C10  C11  120.61  3.000
 VO2  H6   C10  N9   116.06  3.000
 VO2  C11  C10  N9   123.32  3.000
 VO2  C28  C11  C12  120.82  3.000
 VO2  C28  C11  C10  122.03  3.000
 VO2  C12  C11  C10  117.15  3.000
 VO2  H7   C12  C13  120.80  3.000
 VO2  H7   C12  C11  119.13  3.000
 VO2  C13  C12  C11  120.07  3.000
 VO2  O14  C13  C12  126.43  3.000
 VO2  C12  C13  C8   117.73  3.000
 VO2  O14  C13  C8   115.84  3.000
 VO2  C15  O14  C13  118.22  3.000
 VO2  H9   C15  H8   107.98  3.000
 VO2  H9   C15  C16  110.88  3.000
 VO2  H8   C15  C16  110.90  3.000
 VO2  H9   C15  O14  109.91  3.000
 VO2  H8   C15  O14  109.84  3.000
 VO2  C16  C15  O14  107.35  3.000
 VO2  C21  C16  C17  119.19  3.000
 VO2  C21  C16  C15  120.35  3.000
 VO2  C17  C16  C15  120.44  3.000
 VO2  H10  C17  C18  119.78  3.000
 VO2  H10  C17  C16  119.74  3.000
 VO2  C18  C17  C16  120.48  3.000
 VO2  H11  C18  C19  120.15  3.000
 VO2  H11  C18  C17  119.85  3.000
 VO2  C19  C18  C17  120.00  3.000
 VO2  H12  C19  C20  120.07  3.000
 VO2  H12  C19  C18  120.09  3.000
 VO2  C20  C19  C18  119.84  3.000
 VO2  H13  C20  C21  119.85  3.000
 VO2  H13  C20  C19  120.15  3.000
 VO2  C21  C20  C19  120.01  3.000
 VO2  H14  C21  C20  119.76  3.000
 VO2  H14  C21  C16  119.76  3.000
 VO2  C20  C21  C16  120.47  3.000
 VO2  H17  C28  H16  107.88  3.000
 VO2  H17  C28  H15  107.70  3.000
 VO2  H16  C28  H15  107.14  3.000
 VO2  H17  C28  C11  111.31  3.000
 VO2  H16  C28  C11  111.37  3.000
 VO2  H15  C28  C11  111.25  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
 VO2  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 VO2  CONST_02  C3   C4   S5   C1      0.00   0.0  0
 VO2  CONST_03  S5   C4   C3   N2      0.00   0.0  0
 VO2  CONST_04  C4   S5   C1   N2      0.00   0.0  0
 VO2  CONST_05  S5   C1   N2   C3      0.00   0.0  0
 VO2  CONST_06  C11  C12  C13  C8      0.00   0.0  0
 VO2  CONST_07  C11  C10  N9   C8      0.00   0.0  0
 VO2  CONST_08  C12  C13  C8   N9      0.00   0.0  0
 VO2  CONST_09  C12  C11  C10  N9      0.00   0.0  0
 VO2  CONST_10  C13  C8   N9   C10     0.00   0.0  0
 VO2  CONST_11  C13  C12  C11  C10     0.00   0.0  0
 VO2  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 VO2  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 VO2  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 VO2  CONST_15  C20  C21  C16  C17     0.00   0.0  0
 VO2  CONST_16  C21  C16  C17  C18     0.00   0.0  0
 VO2  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 VO2  CONST_18  C6   C3   N2   C1    180.00   0.0  0
 VO2  CONST_19  N7   C1   N2   C3    180.00   0.0  0
 VO2  CONST_20  N7   C1   S5   C4    180.00   0.0  0
 VO2  CONST_21  C6   C3   C4   S5    180.00   0.0  0
 VO2  CONST_22  C12  C13  C8   N7    180.00   0.0  0
 VO2  CONST_23  C10  N9   C8   N7    180.00   0.0  0
 VO2  CONST_24  O14  C13  C8   N9    180.00   0.0  0
 VO2  CONST_25  C28  C11  C10  N9    180.00   0.0  0
 VO2  CONST_26  O14  C13  C12  C11   180.00   0.0  0
 VO2  CONST_27  C28  C11  C12  C13   180.00   0.0  0
 VO2  CONST_28  C18  C17  C16  C15   180.00   0.0  0
 VO2  CONST_29  C20  C21  C16  C15   180.00   0.0  0
 VO2  CONST_30  H1   C4   S5   C1    180.00   0.0  0
 VO2  CONST_31  H7   C12  C13  C8    180.00   0.0  0
 VO2  CONST_32  H6   C10  N9   C8    180.00   0.0  0
 VO2  CONST_33  H11  C18  C17  C16   180.00   0.0  0
 VO2  CONST_34  H13  C20  C21  C16   180.00   0.0  0
 VO2  CONST_35  H12  C19  C18  C17   180.00   0.0  0
 VO2  CONST_36  H14  C21  C16  C17   180.00   0.0  0
 VO2  CONST_37  H10  C17  C18  C19   180.00   0.0  0
 VO2  Var_01    C13  C8   N7   C1    179.72  30.0  2
 VO2  Var_02    C8   N7   C1   N2   -179.46  30.0  2
 VO2  Var_03    C16  C15  O14  C13  -178.95  30.0  3
 VO2  Var_04    C17  C16  C15  O14   -90.82  30.0  2
 VO2  Var_05    H2   C6   C3   N2     59.25  30.0  2
 VO2  Var_06    H15  C28  C11  C10   113.40  30.0  2

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
 VO2  plan-1  C1   0.020
 VO2  plan-1  N2   0.020
 VO2  plan-1  C3   0.020
 VO2  plan-1  C4   0.020
 VO2  plan-1  S5   0.020
 VO2  plan-1  C6   0.020
 VO2  plan-1  N7   0.020
 VO2  plan-1  H1   0.020
 VO2  plan-2  N7   0.020
 VO2  plan-2  C8   0.020
 VO2  plan-2  N9   0.020
 VO2  plan-2  C10  0.020
 VO2  plan-2  C11  0.020
 VO2  plan-2  C12  0.020
 VO2  plan-2  C13  0.020
 VO2  plan-2  O14  0.020
 VO2  plan-2  C28  0.020
 VO2  plan-2  H6   0.020
 VO2  plan-2  H7   0.020
 VO2  plan-3  C15  0.020
 VO2  plan-3  C16  0.020
 VO2  plan-3  C17  0.020
 VO2  plan-3  C18  0.020
 VO2  plan-3  C19  0.020
 VO2  plan-3  C20  0.020
 VO2  plan-3  C21  0.020
 VO2  plan-3  H10  0.020
 VO2  plan-3  H11  0.020
 VO2  plan-3  H12  0.020
 VO2  plan-3  H13  0.020
 VO2  plan-3  H14  0.020

