# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:12:15 2021
#   Inital geometry file: a 65 line input string
#   Ligand name: [(4S)-1-(4-chlorophenyl)-1,2,3-triazolidin-4-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN(NN1)c2ccc(Cl)cc2
#
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
 S3Y  S3Y  '[(4S)-1-(4-chlorophenyl)-1,2,3-triazolidin-4-yl]methanol'  ligand  26  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S3Y
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
 S3Y  C02   C   CH2   0  -0.146  -26.7827  102.4114  140.4443
 S3Y  C03   C   CH1   0  -0.149  -27.7775  101.6081  139.6418
 S3Y  C04   C   CH2   0  -0.301  -27.8852  102.0800  138.1895
 S3Y  C06   C   CR6   0   0.372  -27.4553  100.5972  136.2603
 S3Y  C07   C   CR16  0  -0.344  -27.1129   99.3074  135.8383
 S3Y  C08   C   CR16  0  -0.201  -26.4967   99.1025  134.6152
 S3Y  C09   C   CR6   0  -0.072  -26.2163  100.1792  133.7889
 S3Y  C11   C   CR16  0  -0.200  -26.5583  101.4628  134.1797
 S3Y  C12   C   CR16  0  -0.345  -27.1759  101.6685  135.4025
 S3Y  N05   N   NT    0  -0.403  -28.1126  100.8291  137.4568
 S3Y  N13   N   NH1   0  -0.324  -28.1663   99.7681  138.3661
 S3Y  N14   N   NH1   0  -0.487  -27.3474  100.2265  139.4373
 S3Y  O01   O   OH1   0  -0.672  -26.7599  101.9026  141.7580
 S3Y  CL10  CL  CL    0  -0.149  -25.4416   99.9169  132.2556
 S3Y  H021  H   HCH2  0   0.206  -27.0785  103.4682  140.4224
 S3Y  H022  H   HCH2  0   0.198  -25.8007  102.3372  139.9593
 S3Y  H031  H   HCH1  0   0.241  -28.7665  101.6620  140.1224
 S3Y  H041  H   HCH2  0   0.253  -28.6963  102.7957  138.0516
 S3Y  H042  H   HCH2  0   0.243  -26.9529  102.5521  137.8629
 S3Y  H071  H   HCR6  0   0.268  -27.3262   98.4589  136.4716
 S3Y  H081  H   HCR6  0   0.274  -26.2363   98.0970  134.3126
 S3Y  H111  H   HCR6  0   0.275  -26.3529  102.3084  133.5370
 S3Y  H121  H   HCR6  0   0.277  -27.4524  102.6780  135.6755
 S3Y  H131  H   HNH1  0   0.364  -29.1348   99.7285  138.6865
 S3Y  H141  H   HNH1  0   0.368  -27.5339   99.6418  140.2434
 S3Y  H011  H   HOH1  0   0.458  -26.0931  102.3826  142.2571

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
 S3Y  C02   O01   single    1.409  0.020  1.409
 S3Y  C03   C02   single    1.510  0.020  1.510
 S3Y  C04   C03   single    1.531  0.020  1.531
 S3Y  N05   C04   single    1.467  0.020  1.467
 S3Y  C07   C06   aromatic  1.400  0.020  1.400
 S3Y  C08   C07   aromatic  1.385  0.020  1.385
 S3Y  C09   C08   aromatic  1.386  0.020  1.386
 S3Y  CL10  C09   single    1.738  0.020  1.738
 S3Y  C11   C09   aromatic  1.385  0.020  1.385
 S3Y  C12   C11   aromatic  1.385  0.020  1.385
 S3Y  C06   N05   single    1.385  0.020  1.385
 S3Y  N13   N05   single    1.398  0.020  1.398
 S3Y  N14   N13   single    1.424  0.020  1.424
 S3Y  C03   N14   single    1.461  0.020  1.461
 S3Y  C06   C12   aromatic  1.401  0.020  1.401
 S3Y  C02   H021  single    0.970  0.020  1.090
 S3Y  C02   H022  single    0.970  0.020  1.090
 S3Y  C03   H031  single    0.970  0.020  1.090
 S3Y  C04   H041  single    0.970  0.020  1.090
 S3Y  C04   H042  single    0.970  0.020  1.090
 S3Y  C07   H071  single    0.930  0.020  1.080
 S3Y  C08   H081  single    0.930  0.020  1.080
 S3Y  C11   H111  single    0.930  0.020  1.080
 S3Y  C12   H121  single    0.930  0.020  1.080
 S3Y  N13   H131  single    0.890  0.020  1.040
 S3Y  N14   H141  single    0.890  0.020  1.040
 S3Y  O01   H011  single    0.850  0.020  0.980

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
 S3Y  H022  C02  H021  107.29  3.000
 S3Y  H022  C02  O01   111.91  3.000
 S3Y  H021  C02  O01   111.76  3.000
 S3Y  H022  C02  C03   108.58  3.000
 S3Y  H021  C02  C03   108.91  3.000
 S3Y  O01   C02  C03   108.31  3.000
 S3Y  H031  C03  N14   111.83  3.000
 S3Y  H031  C03  C04   109.63  3.000
 S3Y  N14   C03  C04   100.33  3.000
 S3Y  H031  C03  C02   109.50  3.000
 S3Y  N14   C03  C02   112.55  3.000
 S3Y  C04   C03  C02   112.75  3.000
 S3Y  H042  C04  H041  108.22  3.000
 S3Y  H042  C04  N05   110.52  3.000
 S3Y  H041  C04  N05   112.40  3.000
 S3Y  H042  C04  C03   110.85  3.000
 S3Y  H041  C04  C03   112.00  3.000
 S3Y  N05   C04  C03   102.81  3.000
 S3Y  N05   C06  C12   119.73  3.000
 S3Y  C12   C06  C07   118.12  3.000
 S3Y  N05   C06  C07   122.07  3.000
 S3Y  H071  C07  C08   119.31  3.000
 S3Y  H071  C07  C06   119.92  3.000
 S3Y  C08   C07  C06   120.77  3.000
 S3Y  H081  C08  C09   120.43  3.000
 S3Y  H081  C08  C07   119.45  3.000
 S3Y  C09   C08  C07   120.11  3.000
 S3Y  CL10  C09  C11   119.94  3.000
 S3Y  C11   C09  C08   120.13  3.000
 S3Y  CL10  C09  C08   119.93  3.000
 S3Y  H111  C11  C12   119.54  3.000
 S3Y  H111  C11  C09   120.67  3.000
 S3Y  C12   C11  C09   119.80  3.000
 S3Y  H121  C12  C11   118.38  3.000
 S3Y  H121  C12  C06   120.54  3.000
 S3Y  C11   C12  C06   121.07  3.000
 S3Y  N13   N05  C06   116.94  3.000
 S3Y  N13   N05  C04   109.15  3.000
 S3Y  C06   N05  C04   120.04  3.000
 S3Y  H131  N13  N14   108.78  3.000
 S3Y  H131  N13  N05   105.66  3.000
 S3Y  N14   N13  N05   102.87  3.000
 S3Y  H141  N14  N13   107.87  3.000
 S3Y  H141  N14  C03   112.34  3.000
 S3Y  N13   N14  C03   103.90  3.000
 S3Y  H011  O01  C02   108.36  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
 S3Y  CONST_01  C09   C08  C07  C06     0.00   0.0  0
 S3Y  CONST_02  C09   C11  C12  C06     0.00   0.0  0
 S3Y  CONST_03  C11   C12  C06  C07     0.00   0.0  0
 S3Y  CONST_04  C11   C09  C08  C07     0.00   0.0  0
 S3Y  CONST_05  C12   C06  C07  C08     0.00   0.0  0
 S3Y  CONST_06  C12   C11  C09  C08     0.00   0.0  0
 S3Y  CONST_07  N05   C06  C07  C08   180.00   0.0  0
 S3Y  CONST_08  N05   C06  C12  C11   180.00   0.0  0
 S3Y  CONST_09  CL10  C09  C08  C07   180.00   0.0  0
 S3Y  CONST_10  CL10  C09  C11  C12   180.00   0.0  0
 S3Y  CONST_11  H081  C08  C07  C06   180.00   0.0  0
 S3Y  CONST_12  H111  C11  C12  C06   180.00   0.0  0
 S3Y  CONST_13  H121  C12  C06  C07   180.00   0.0  0
 S3Y  CONST_14  H071  C07  C08  C09   180.00   0.0  0
 S3Y  Var_01    C06   N05  C04  C03  -137.64  30.0  1
 S3Y  Var_02    N05   N13  N14  C03    45.05  30.0  1
 S3Y  Var_03    C07   C06  N05  C04   149.56  30.0  3
 S3Y  Var_04    N14   N13  N05  C04   -28.13  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 S3Y  chir_01  C03  C02  C04  N14  negativ

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
 S3Y  plan-1  C06   0.020
 S3Y  plan-1  C07   0.020
 S3Y  plan-1  C08   0.020
 S3Y  plan-1  C09   0.020
 S3Y  plan-1  C11   0.020
 S3Y  plan-1  C12   0.020
 S3Y  plan-1  N05   0.020
 S3Y  plan-1  CL10  0.020
 S3Y  plan-1  H071  0.020
 S3Y  plan-1  H081  0.020
 S3Y  plan-1  H111  0.020
 S3Y  plan-1  H121  0.020

