# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 20:40:37 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: 4-[[(2~{S})-oxolan-2-yl]methyl]-3-pyridin-3-yl-1~{H}-1,2,4-triazole-5-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=C1NN=C(N1C[C@@H]2CCCO2)c3cccnc3
#
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
 N8Q  N8Q  4-[[(2~{S})-oxolan-2-yl]methyl]-3-pyridin-3-yl-1~{H}-1,2,4-triazole-5-thione  ligand  32  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N8Q
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
 N8Q  S01  S  S1    0  -0.394  -9.0970  33.8875  -18.3937
 N8Q  O02  O  O2    0  -0.508  -4.8683  36.3924  -18.1044
 N8Q  N03  N  NR5   0  -0.490  -7.1601  34.9411  -16.7549
 N8Q  N04  N  NR15  0  -0.456  -7.6643  32.9267  -16.3188
 N8Q  N05  N  N     0  -0.242  -6.7973  33.2837  -15.3620
 N8Q  N06  N  N     0  -0.400  -5.3067  35.7182  -12.3450
 N8Q  C07  C  CH1   0   0.085  -6.2181  36.4546  -18.5389
 N8Q  C08  C  CH2   0  -0.489  -6.3083  35.4802  -19.7072
 N8Q  C09  C  CH2   0  -0.501  -4.9181  35.6099  -20.3164
 N8Q  C10  C  CH2   0  -0.348  -7.1713  36.2580  -17.3653
 N8Q  C11  C  CH2   0  -0.145  -4.0563  35.7301  -19.0701
 N8Q  C12  C  CR5   0   0.416  -6.5044  34.5191  -15.6205
 N8Q  C13  C  CR5   0   0.365  -7.9570  33.9110  -17.1747
 N8Q  C14  C  CR6   0  -0.089  -5.7161  35.3136  -14.6739
 N8Q  C15  C  CR16  0  -0.181  -4.7220  36.2235  -15.0166
 N8Q  C16  C  CR16  0  -0.056  -5.9669  35.1069  -13.3139
 N8Q  C17  C  CR16  0  -0.321  -4.0355  36.8705  -14.0022
 N8Q  C18  C  CR16  0  -0.053  -4.3570  36.5831  -12.6859
 N8Q  H1   H  HNR5  0   0.440  -8.0698  32.0034  -16.3240
 N8Q  H2   H  HCH1  0   0.229  -6.4360  37.4685  -18.9032
 N8Q  H3   H  HCH2  0   0.252  -7.1148  35.7335  -20.3932
 N8Q  H4   H  HCH2  0   0.243  -6.4752  34.4572  -19.3673
 N8Q  H5   H  HCH2  0   0.253  -4.6383  34.7586  -20.9360
 N8Q  H6   H  HCH2  0   0.240  -4.8476  36.5104  -20.9303
 N8Q  H7   H  HCH2  0   0.287  -6.9623  36.9930  -16.5880
 N8Q  H8   H  HCH2  0   0.282  -8.1876  36.4408  -17.7155
 N8Q  H9   H  HCH2  0   0.210  -3.7713  34.7426  -18.6927
 N8Q  H10  H  HCH2  0   0.227  -3.1439  36.3077  -19.2310
 N8Q  H11  H  HCR6  0   0.317  -4.4789  36.4141  -16.0514
 N8Q  H12  H  HCR6  0   0.271  -6.7466  34.4178  -13.0084
 N8Q  H13  H  HCR6  0   0.279  -3.2520  37.5796  -14.2300
 N8Q  H14  H  HCR6  0   0.274  -3.8280  37.0684  -11.8737

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
 N8Q  C09  C08  single    1.523  0.020  1.523
 N8Q  C09  C11  single    1.520  0.020  1.520
 N8Q  C08  C07  single    1.524  0.020  1.524
 N8Q  C11  O02  single    1.425  0.020  1.425
 N8Q  C07  O02  single    1.419  0.020  1.419
 N8Q  C07  C10  single    1.525  0.020  1.525
 N8Q  S01  C13  double    1.669  0.020  1.669
 N8Q  C10  N03  single    1.452  0.020  1.452
 N8Q  C13  N03  single    1.368  0.020  1.368
 N8Q  C13  N04  single    1.337  0.020  1.337
 N8Q  N03  C12  single    1.377  0.020  1.377
 N8Q  N04  N05  single    1.340  0.020  1.340
 N8Q  C12  N05  double    1.296  0.020  1.296
 N8Q  C12  C14  single    1.466  0.020  1.466
 N8Q  C15  C14  aromatic  1.391  0.020  1.391
 N8Q  C15  C17  aromatic  1.385  0.020  1.385
 N8Q  C14  C16  aromatic  1.398  0.020  1.398
 N8Q  C17  C18  aromatic  1.385  0.020  1.385
 N8Q  C16  N06  aromatic  1.322  0.020  1.322
 N8Q  C18  N06  aromatic  1.329  0.020  1.329
 N8Q  N04  H1   single    0.860  0.020  1.020
 N8Q  C07  H2   single    0.970  0.020  1.090
 N8Q  C08  H3   single    0.970  0.020  1.090
 N8Q  C08  H4   single    0.970  0.020  1.090
 N8Q  C09  H5   single    0.970  0.020  1.090
 N8Q  C09  H6   single    0.970  0.020  1.090
 N8Q  C10  H7   single    0.970  0.020  1.090
 N8Q  C10  H8   single    0.970  0.020  1.090
 N8Q  C11  H9   single    0.970  0.020  1.090
 N8Q  C11  H10  single    0.970  0.020  1.090
 N8Q  C15  H11  single    0.930  0.020  1.080
 N8Q  C16  H12  single    0.930  0.020  1.080
 N8Q  C17  H13  single    0.930  0.020  1.080
 N8Q  C18  H14  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
 N8Q  C11  O02  C07  110.78  3.000
 N8Q  C13  N03  C12  107.43  3.000
 N8Q  C12  N03  C10  128.93  3.000
 N8Q  C13  N03  C10  123.33  3.000
 N8Q  H1   N04  C13  125.65  3.000
 N8Q  H1   N04  N05  120.53  3.000
 N8Q  C13  N04  N05  113.75  3.000
 N8Q  C12  N05  N04  104.95  3.000
 N8Q  C18  N06  C16  118.02  3.000
 N8Q  H2   C07  C10  104.48  3.000
 N8Q  H2   C07  C08  108.90  3.000
 N8Q  C10  C07  C08  118.08  3.000
 N8Q  H2   C07  O02  109.29  3.000
 N8Q  C10  C07  O02  110.68  3.000
 N8Q  C08  C07  O02  105.24  3.000
 N8Q  H4   C08  H3   107.53  3.000
 N8Q  H4   C08  C09  110.13  3.000
 N8Q  H3   C08  C09  113.85  3.000
 N8Q  H4   C08  C07  111.70  3.000
 N8Q  H3   C08  C07  112.21  3.000
 N8Q  C09  C08  C07  101.43  3.000
 N8Q  H6   C09  H5   107.94  3.000
 N8Q  H6   C09  C11  111.04  3.000
 N8Q  H5   C09  C11  112.49  3.000
 N8Q  H6   C09  C08  110.73  3.000
 N8Q  H5   C09  C08  113.29  3.000
 N8Q  C11  C09  C08  101.32  3.000
 N8Q  H8   C10  H7   107.14  3.000
 N8Q  H8   C10  C07  108.29  3.000
 N8Q  H7   C10  C07  110.01  3.000
 N8Q  H8   C10  N03  107.12  3.000
 N8Q  H7   C10  N03  108.08  3.000
 N8Q  C07  C10  N03  115.84  3.000
 N8Q  H10  C11  H9   108.08  3.000
 N8Q  H10  C11  C09  113.25  3.000
 N8Q  H9   C11  C09  111.03  3.000
 N8Q  H10  C11  O02  109.28  3.000
 N8Q  H9   C11  O02  109.50  3.000
 N8Q  C09  C11  O02  105.63  3.000
 N8Q  C14  C12  N05  120.63  3.000
 N8Q  C14  C12  N03  128.47  3.000
 N8Q  N05  C12  N03  110.43  3.000
 N8Q  N04  C13  N03  103.32  3.000
 N8Q  N04  C13  S01  127.35  3.000
 N8Q  N03  C13  S01  129.23  3.000
 N8Q  C16  C14  C15  117.69  3.000
 N8Q  C16  C14  C12  116.84  3.000
 N8Q  C15  C14  C12  125.45  3.000
 N8Q  H11  C15  C17  120.51  3.000
 N8Q  H11  C15  C14  120.83  3.000
 N8Q  C17  C15  C14  118.65  3.000
 N8Q  H12  C16  C14  119.79  3.000
 N8Q  H12  C16  N06  116.51  3.000
 N8Q  C14  C16  N06  123.69  3.000
 N8Q  H13  C17  C18  120.31  3.000
 N8Q  H13  C17  C15  120.74  3.000
 N8Q  C18  C17  C15  118.94  3.000
 N8Q  H14  C18  C17  120.39  3.000
 N8Q  H14  C18  N06  116.61  3.000
 N8Q  C17  C18  N06  123.00  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
 N8Q  CONST_01  C15  C14  C16  N06    0.00   0.0  0
 N8Q  CONST_02  C15  C17  C18  N06    0.00   0.0  0
 N8Q  CONST_03  C18  C17  C15  C14    0.00   0.0  0
 N8Q  CONST_04  C18  N06  C16  C14    0.00   0.0  0
 N8Q  CONST_05  C17  C15  C14  C16    0.00   0.0  0
 N8Q  CONST_06  C17  C18  N06  C16    0.00   0.0  0
 N8Q  CONST_07  C12  C14  C16  N06  180.00   0.0  0
 N8Q  CONST_08  C17  C15  C14  C12  180.00   0.0  0
 N8Q  CONST_09  N05  N04  C13  N03    0.00   0.0  0
 N8Q  CONST_10  N04  N05  C12  N03    0.00   0.0  0
 N8Q  CONST_11  C12  N03  C13  N04    0.00   0.0  0
 N8Q  CONST_12  C14  C12  N05  N04  180.00   0.0  0
 N8Q  CONST_13  C13  N03  C12  N05    0.00   0.0  0
 N8Q  CONST_14  C13  N04  N05  C12    0.00   0.0  0
 N8Q  CONST_15  C14  C12  N03  C13  180.00   0.0  0
 N8Q  CONST_16  C12  N03  C13  S01  180.00   0.0  0
 N8Q  CONST_17  N05  N04  C13  S01  180.00   0.0  0
 N8Q  CONST_18  C10  N03  C13  N04  180.00   0.0  0
 N8Q  CONST_19  C10  N03  C12  N05  180.00   0.0  0
 N8Q  CONST_20  C14  C12  N03  C10    0.00   0.0  0
 N8Q  CONST_21  H13  C17  C18  N06  180.00   0.0  0
 N8Q  CONST_22  H11  C15  C14  C12    0.00   0.0  0
 N8Q  CONST_23  H12  C16  C14  C12    0.00   0.0  0
 N8Q  CONST_24  H14  C18  C17  C15  180.00   0.0  0
 N8Q  CONST_25  H1   N04  C13  N03  180.00   0.0  0
 N8Q  CONST_26  C10  N03  C13  S01    0.00   0.0  0
 N8Q  Var_01    C08  C09  C11  O02  -31.60  30.0  1
 N8Q  Var_02    C15  C14  C12  N03  -48.32  30.0  2
 N8Q  Var_03    C11  C09  C08  C07   38.56  30.0  1
 N8Q  Var_04    C09  C11  O02  C07   11.51  30.0  1
 N8Q  Var_05    C13  N03  C10  C07  -88.89  30.0  3

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
 N8Q  chir_01  C07  C08  O02  C10  positiv

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
 N8Q  plan-1  S01  0.020
 N8Q  plan-1  N03  0.020
 N8Q  plan-1  N04  0.020
 N8Q  plan-1  N05  0.020
 N8Q  plan-1  C10  0.020
 N8Q  plan-1  C12  0.020
 N8Q  plan-1  C13  0.020
 N8Q  plan-1  C14  0.020
 N8Q  plan-1  H1   0.020
 N8Q  plan-2  N06  0.020
 N8Q  plan-2  C12  0.020
 N8Q  plan-2  C14  0.020
 N8Q  plan-2  C15  0.020
 N8Q  plan-2  C16  0.020
 N8Q  plan-2  C17  0.020
 N8Q  plan-2  C18  0.020
 N8Q  plan-2  H11  0.020
 N8Q  plan-2  H12  0.020
 N8Q  plan-2  H13  0.020
 N8Q  plan-2  H14  0.020

