# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:32:04 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-(benzyloxy)-N-(4-methyl-1,3-thiazol-2-yl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1csc(Nc2ncccc2OCc3ccccc3)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
 VO1  VO1  3-(benzyloxy)-N-(4-methyl-1,3-thiazol-2-yl)pyridin-2-amine  ligand  36  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VO1
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
 VO1  C1   C  CR5   0   0.283   2.2814  -0.6081   0.0056
 VO1  N2   N  N     0  -0.456   2.4008  -1.9008   0.0044
 VO1  C3   C  CR5   0   0.324   3.7188  -2.2783   0.0196
 VO1  C4   C  CR15  0  -0.571   4.6051  -1.2533   0.0329
 VO1  S5   S  S2    0   0.200   3.7804   0.2665   0.0257
 VO1  C6   C  CH3   0  -0.725   4.0614  -3.7296   0.0200
 VO1  N7   N  NH1   0  -0.724   1.0519  -0.0202  -0.0073
 VO1  C8   C  CR6   0   0.472   0.7828   1.3269  -0.0091
 VO1  N9   N  N     0  -0.463   1.7915   2.1663  -0.0014
 VO1  C10  C  CR16  0  -0.069   1.5489   3.4797  -0.0023
 VO1  C11  C  CR16  0  -0.343   0.2748   3.9953  -0.0116
 VO1  C12  C  CR16  0  -0.280  -0.8083   3.1101  -0.0198
 VO1  C13  C  CR6   0   0.257  -0.5666   1.7539  -0.0186
 VO1  O14  O  O2    0  -0.473  -1.4891   0.7764  -0.0253
 VO1  C15  C  CH2   0  -0.269  -2.8650   1.1490  -0.0239
 VO1  C16  C  CR6   0   0.096  -3.6686  -0.1136  -0.0303
 VO1  C17  C  CR16  0  -0.291  -4.0523  -0.6983  -1.2333
 VO1  C18  C  CR16  0  -0.242  -4.7677  -1.8878  -1.2413
 VO1  C19  C  CR16  0  -0.260  -5.1037  -2.5042  -0.0428
 VO1  C20  C  CR16  0  -0.243  -4.7230  -1.9270   1.1620
 VO1  C21  C  CR16  0  -0.289  -4.0081  -0.7374   1.1666
 VO1  H1   H  HCR5  0   0.288   5.6825  -1.3045   0.0449
 VO1  H2   H  HCH3  0   0.245   3.6575  -4.2281  -0.8628
 VO1  H3   H  HCH3  0   0.244   5.1396  -3.8769   0.0292
 VO1  H4   H  HCH3  0   0.245   3.6423  -4.2309   0.8941
 VO1  H5   H  HNH1  0   0.419   0.2747  -0.6641  -0.0160
 VO1  H6   H  HCR6  0   0.263   2.4164   4.1279   0.0050
 VO1  H7   H  HCR6  0   0.270   0.1105   5.0633  -0.0120
 VO1  H8   H  HCR6  0   0.300  -1.8174   3.5001  -0.0265
 VO1  H9   H  HCH2  0   0.249  -3.0869   1.7488   0.8647
 VO1  H10  H  HCH2  0   0.250  -3.0871   1.7570  -0.9066
 VO1  H11  H  HCR6  0   0.256  -3.7969  -0.2174  -2.1702
 VO1  H12  H  HCR6  0   0.259  -5.0626  -2.3327  -2.1827
 VO1  H13  H  HCR6  0   0.260  -5.6643  -3.4301  -0.0475
 VO1  H14  H  HCR6  0   0.259  -4.9826  -2.4028   2.0987
 VO1  H15  H  HCR6  0   0.256  -3.7178  -0.2877   2.1088

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
 VO1  C6   C3   single    1.491  0.020  1.491
 VO1  C3   N2   aromatic  1.371  0.020  1.371
 VO1  C3   C4   aromatic  1.355  0.020  1.355
 VO1  N2   C1   aromatic  1.298  0.020  1.298
 VO1  C4   S5   aromatic  1.729  0.020  1.729
 VO1  C1   N7   single    1.363  0.020  1.363
 VO1  C1   S5   aromatic  1.736  0.020  1.736
 VO1  N7   C8   single    1.374  0.020  1.374
 VO1  O14  C15  single    1.425  0.020  1.425
 VO1  O14  C13  single    1.344  0.020  1.344
 VO1  C17  C18  aromatic  1.388  0.020  1.388
 VO1  C17  C16  aromatic  1.392  0.020  1.392
 VO1  C18  C19  aromatic  1.389  0.020  1.389
 VO1  C15  C16  single    1.497  0.020  1.497
 VO1  C16  C21  aromatic  1.392  0.020  1.392
 VO1  C19  C20  aromatic  1.389  0.020  1.389
 VO1  C21  C20  aromatic  1.388  0.020  1.388
 VO1  C8   C13  aromatic  1.415  0.020  1.415
 VO1  C8   N9   aromatic  1.312  0.020  1.312
 VO1  C13  C12  aromatic  1.378  0.020  1.378
 VO1  N9   C10  aromatic  1.336  0.020  1.336
 VO1  C12  C11  aromatic  1.399  0.020  1.399
 VO1  C10  C11  aromatic  1.374  0.020  1.374
 VO1  C4   H1   single    0.930  0.020  1.080
 VO1  C6   H2   single    0.970  0.020  1.090
 VO1  C6   H3   single    0.970  0.020  1.090
 VO1  C6   H4   single    0.970  0.020  1.090
 VO1  N7   H5   single    0.860  0.020  1.020
 VO1  C10  H6   single    0.930  0.020  1.080
 VO1  C11  H7   single    0.930  0.020  1.080
 VO1  C12  H8   single    0.930  0.020  1.080
 VO1  C15  H9   single    0.970  0.020  1.090
 VO1  C15  H10  single    0.970  0.020  1.090
 VO1  C17  H11  single    0.930  0.020  1.080
 VO1  C18  H12  single    0.930  0.020  1.080
 VO1  C19  H13  single    0.930  0.020  1.080
 VO1  C20  H14  single    0.930  0.020  1.080
 VO1  C21  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
 VO1  N7   C1   S5   124.19  3.000
 VO1  S5   C1   N2   114.98  3.000
 VO1  N7   C1   N2   120.83  3.000
 VO1  C3   N2   C1   111.26  3.000
 VO1  C6   C3   C4   125.86  3.000
 VO1  C4   C3   N2   114.87  3.000
 VO1  C6   C3   N2   119.27  3.000
 VO1  H1   C4   S5   121.21  3.000
 VO1  H1   C4   C3   128.13  3.000
 VO1  S5   C4   C3   110.66  3.000
 VO1  C4   S5   C1    88.23  3.000
 VO1  H4   C6   H3   108.15  3.000
 VO1  H4   C6   H2   107.22  3.000
 VO1  H3   C6   H2   108.16  3.000
 VO1  H4   C6   C3   111.04  3.000
 VO1  H3   C6   C3   111.06  3.000
 VO1  H2   C6   C3   111.06  3.000
 VO1  H5   N7   C8   118.34  3.000
 VO1  H5   N7   C1   114.81  3.000
 VO1  C8   N7   C1   126.85  3.000
 VO1  C13  C8   N9   122.68  3.000
 VO1  N9   C8   N7   118.47  3.000
 VO1  C13  C8   N7   118.85  3.000
 VO1  C10  N9   C8   119.30  3.000
 VO1  H6   C10  C11  121.20  3.000
 VO1  H6   C10  N9   116.30  3.000
 VO1  C11  C10  N9   122.50  3.000
 VO1  H7   C11  C12  120.51  3.000
 VO1  H7   C11  C10  120.78  3.000
 VO1  C12  C11  C10  118.71  3.000
 VO1  H8   C12  C13  121.24  3.000
 VO1  H8   C12  C11  119.62  3.000
 VO1  C13  C12  C11  119.15  3.000
 VO1  O14  C13  C12  126.55  3.000
 VO1  C12  C13  C8   117.66  3.000
 VO1  O14  C13  C8   115.79  3.000
 VO1  C15  O14  C13  118.19  3.000
 VO1  H10  C15  H9   108.01  3.000
 VO1  H10  C15  C16  110.86  3.000
 VO1  H9   C15  C16  110.91  3.000
 VO1  H10  C15  O14  109.89  3.000
 VO1  H9   C15  O14  109.85  3.000
 VO1  C16  C15  O14  107.32  3.000
 VO1  C21  C16  C17  119.20  3.000
 VO1  C21  C16  C15  120.36  3.000
 VO1  C17  C16  C15  120.42  3.000
 VO1  H11  C17  C18  119.79  3.000
 VO1  H11  C17  C16  119.73  3.000
 VO1  C18  C17  C16  120.48  3.000
 VO1  H12  C18  C19  120.15  3.000
 VO1  H12  C18  C17  119.85  3.000
 VO1  C19  C18  C17  120.00  3.000
 VO1  H13  C19  C20  120.08  3.000
 VO1  H13  C19  C18  120.08  3.000
 VO1  C20  C19  C18  119.85  3.000
 VO1  H14  C20  C21  119.84  3.000
 VO1  H14  C20  C19  120.15  3.000
 VO1  C21  C20  C19  120.01  3.000
 VO1  H15  C21  C20  119.77  3.000
 VO1  H15  C21  C16  119.76  3.000
 VO1  C20  C21  C16  120.47  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
 VO1  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 VO1  CONST_02  C3   C4   S5   C1      0.00   0.0  0
 VO1  CONST_03  S5   C4   C3   N2      0.00   0.0  0
 VO1  CONST_04  C4   S5   C1   N2      0.00   0.0  0
 VO1  CONST_05  S5   C1   N2   C3      0.00   0.0  0
 VO1  CONST_06  C11  C12  C13  C8      0.00   0.0  0
 VO1  CONST_07  C11  C10  N9   C8      0.00   0.0  0
 VO1  CONST_08  C12  C13  C8   N9      0.00   0.0  0
 VO1  CONST_09  C12  C11  C10  N9      0.00   0.0  0
 VO1  CONST_10  C13  C8   N9   C10     0.00   0.0  0
 VO1  CONST_11  C13  C12  C11  C10     0.00   0.0  0
 VO1  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 VO1  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 VO1  CONST_14  C20  C19  C18  C17     0.00   0.0  0
 VO1  CONST_15  C20  C21  C16  C17     0.00   0.0  0
 VO1  CONST_16  C21  C16  C17  C18     0.00   0.0  0
 VO1  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 VO1  CONST_18  C6   C3   N2   C1    180.00   0.0  0
 VO1  CONST_19  N7   C1   N2   C3    180.00   0.0  0
 VO1  CONST_20  N7   C1   S5   C4    180.00   0.0  0
 VO1  CONST_21  C6   C3   C4   S5    180.00   0.0  0
 VO1  CONST_22  C12  C13  C8   N7    180.00   0.0  0
 VO1  CONST_23  C10  N9   C8   N7    180.00   0.0  0
 VO1  CONST_24  O14  C13  C8   N9    180.00   0.0  0
 VO1  CONST_25  O14  C13  C12  C11   180.00   0.0  0
 VO1  CONST_26  C18  C17  C16  C15   180.00   0.0  0
 VO1  CONST_27  C20  C21  C16  C15   180.00   0.0  0
 VO1  CONST_28  H1   C4   S5   C1    180.00   0.0  0
 VO1  CONST_29  H8   C12  C13  C8    180.00   0.0  0
 VO1  CONST_30  H6   C10  N9   C8    180.00   0.0  0
 VO1  CONST_31  H7   C11  C10  N9    180.00   0.0  0
 VO1  CONST_32  H12  C18  C17  C16   180.00   0.0  0
 VO1  CONST_33  H14  C20  C21  C16   180.00   0.0  0
 VO1  CONST_34  H13  C19  C18  C17   180.00   0.0  0
 VO1  CONST_35  H15  C21  C16  C17   180.00   0.0  0
 VO1  CONST_36  H11  C17  C18  C19   180.00   0.0  0
 VO1  Var_01    C13  C8   N7   C1   -179.78  30.0  2
 VO1  Var_02    C8   N7   C1   N2   -179.93  30.0  2
 VO1  Var_03    C16  C15  O14  C13  -179.92  30.0  3
 VO1  Var_04    C17  C16  C15  O14   -90.33  30.0  2
 VO1  Var_05    H2   C6   C3   N2     59.38  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
 VO1  plan-1  C1   0.020
 VO1  plan-1  N2   0.020
 VO1  plan-1  C3   0.020
 VO1  plan-1  C4   0.020
 VO1  plan-1  S5   0.020
 VO1  plan-1  C6   0.020
 VO1  plan-1  N7   0.020
 VO1  plan-1  H1   0.020
 VO1  plan-2  N7   0.020
 VO1  plan-2  C8   0.020
 VO1  plan-2  N9   0.020
 VO1  plan-2  C10  0.020
 VO1  plan-2  C11  0.020
 VO1  plan-2  C12  0.020
 VO1  plan-2  C13  0.020
 VO1  plan-2  O14  0.020
 VO1  plan-2  H6   0.020
 VO1  plan-2  H7   0.020
 VO1  plan-2  H8   0.020
 VO1  plan-3  C15  0.020
 VO1  plan-3  C16  0.020
 VO1  plan-3  C17  0.020
 VO1  plan-3  C18  0.020
 VO1  plan-3  C19  0.020
 VO1  plan-3  C20  0.020
 VO1  plan-3  C21  0.020
 VO1  plan-3  H11  0.020
 VO1  plan-3  H12  0.020
 VO1  plan-3  H13  0.020
 VO1  plan-3  H14  0.020
 VO1  plan-3  H15  0.020

