# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 17:16:00 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 4-amino-5-(2-methylphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1C2=NNC(=S)N2N
#
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
 L13  L13  4-amino-5-(2-methylphenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione  ligand  24  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L13
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
 L13  N14   N  NC2   0  -0.619  -1.0038  -1.5776  -1.0079
 L13  N5    N  NR5   0  -0.364  -1.1639  -0.4332  -0.2657
 L13  C1    C  CR5   0   0.351  -2.3500   0.1844   0.0125
 L13  S6    S  S1    0  -0.401  -3.8750  -0.3199  -0.4262
 L13  N2    N  NR15  0  -0.458  -1.9618   1.2660   0.6938
 L13  N3    N  N     0  -0.238  -0.6272   1.3587   0.8563
 L13  C4    C  CR5   0   0.389  -0.1438   0.3170   0.2607
 L13  C7    C  CR6   0   0.019   1.2759  -0.0340   0.1786
 L13  C12   C  CR16  0  -0.248   1.6729  -1.3129   0.5672
 L13  C11   C  CR16  0  -0.267   3.0088  -1.6756   0.5360
 L13  C10   C  CR16  0  -0.234   3.9542  -0.7561   0.1047
 L13  C9    C  CR16  0  -0.300   3.5582   0.5131  -0.2900
 L13  C8    C  CR6   0   0.100   2.2209   0.9029  -0.2623
 L13  C13   C  CH3   0  -0.737   1.8407   2.2846  -0.7108
 L13  H141  H  HNC2  0   0.390  -1.4899  -2.3357  -0.5432
 L13  H142  H  HNC2  0   0.391  -1.4490  -1.4390  -1.9083
 L13  HN2   H  HNR5  0   0.439  -2.5709   1.9717   1.0779
 L13  H12   H  HCR6  0   0.257   0.9343  -2.0253   0.9096
 L13  H11   H  HCR6  0   0.262   3.3074  -2.6671   0.8485
 L13  H10   H  HCR6  0   0.262   5.0018  -1.0262   0.0729
 L13  H9    H  HCR6  0   0.256   4.3029   1.2206  -0.6339
 L13  H131  H  HCH3  0   0.247   1.0023   2.2685  -1.4076
 L13  H132  H  HCH3  0   0.255   1.5437   2.9121   0.1294
 L13  H133  H  HCH3  0   0.250   2.6792   2.7693  -1.2081

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
 L13  N14  N5    single    1.373  0.020  1.373
 L13  N14  H141  single    0.890  0.020  1.040
 L13  N14  H142  single    0.890  0.020  1.040
 L13  N5   C1    aromatic  1.366  0.020  1.366
 L13  N5   C4    aromatic  1.371  0.020  1.371
 L13  C1   S6    double    1.665  0.020  1.665
 L13  C1   N2    aromatic  1.336  0.020  1.336
 L13  N2   N3    aromatic  1.348  0.020  1.348
 L13  N2   HN2   single    0.860  0.020  1.020
 L13  N3   C4    aromatic  1.294  0.020  1.294
 L13  C4   C7    single    1.465  0.020  1.465
 L13  C7   C12   aromatic  1.394  0.020  1.394
 L13  C7   C8    aromatic  1.402  0.020  1.402
 L13  C12  C11   aromatic  1.385  0.020  1.385
 L13  C12  H12   single    0.930  0.020  1.080
 L13  C11  C10   aromatic  1.388  0.020  1.388
 L13  C11  H11   single    0.930  0.020  1.080
 L13  C10  C9    aromatic  1.387  0.020  1.387
 L13  C10  H10   single    0.930  0.020  1.080
 L13  C9   C8    aromatic  1.393  0.020  1.393
 L13  C9   H9    single    0.930  0.020  1.080
 L13  C8   C13   single    1.502  0.020  1.502
 L13  C13  H131  single    0.970  0.020  1.090
 L13  C13  H132  single    0.970  0.020  1.090
 L13  C13  H133  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
 L13  H142  N14  H141  107.39  3.000
 L13  H142  N14  N5    108.35  3.000
 L13  H141  N14  N5    108.64  3.000
 L13  C4    N5   C1    108.69  3.000
 L13  C4    N5   N14   125.21  3.000
 L13  C1    N5   N14   126.02  3.000
 L13  N2    C1   S6    130.22  3.000
 L13  N2    C1   N5    102.57  3.000
 L13  S6    C1   N5    127.21  3.000
 L13  HN2   N2   N3    120.28  3.000
 L13  HN2   N2   C1    125.83  3.000
 L13  N3    N2   C1    113.89  3.000
 L13  C4    N3   N2    105.02  3.000
 L13  C7    C4   N3    125.52  3.000
 L13  C7    C4   N5    124.63  3.000
 L13  N3    C4   N5    109.83  3.000
 L13  C8    C7   C12   120.58  3.000
 L13  C8    C7   C4    120.72  3.000
 L13  C12   C7   C4    118.70  3.000
 L13  H12   C12  C11   119.56  3.000
 L13  H12   C12  C7    119.86  3.000
 L13  C11   C12  C7    120.57  3.000
 L13  H11   C11  C10   120.61  3.000
 L13  H11   C11  C12   119.99  3.000
 L13  C10   C11  C12   119.40  3.000
 L13  H10   C10  C9    119.76  3.000
 L13  H10   C10  C11   120.22  3.000
 L13  C9    C10  C11   120.02  3.000
 L13  H9    C9   C8    118.91  3.000
 L13  H9    C9   C10   119.46  3.000
 L13  C8    C9   C10   121.63  3.000
 L13  C13   C8   C9    119.64  3.000
 L13  C13   C8   C7    122.56  3.000
 L13  C9    C8   C7    117.80  3.000
 L13  H133  C13  H132  107.81  3.000
 L13  H133  C13  H131  107.87  3.000
 L13  H132  C13  H131  106.95  3.000
 L13  H133  C13  C8    110.55  3.000
 L13  H132  C13  C8    111.62  3.000
 L13  H131  C13  C8    111.84  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
 L13  CONST_01  N3    N2   C1   N5     0.00   0.0  0
 L13  CONST_02  N2    N3   C4   N5     0.00   0.0  0
 L13  CONST_05  N3    C4   N5   C1     0.00   0.0  0
 L13  CONST_06  C7    C4   N5   C1   180.00   0.0  0
 L13  CONST_07  C4    N3   N2   C1     0.00   0.0  0
 L13  CONST_08  C4    N5   C1   N2     0.00   0.0  0
 L13  CONST_09  C7    C4   N3   N2   180.00   0.0  0
 L13  CONST_12  C11   C12  C7   C4   180.00   0.0  0
 L13  CONST_13  C9    C8   C7   C4   180.00   0.0  0
 L13  CONST_14  C10   C11  C12  C7     0.00   0.0  0
 L13  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 L13  CONST_16  C9    C8   C7   C12    0.00   0.0  0
 L13  CONST_17  C9    C10  C11  C12    0.00   0.0  0
 L13  CONST_18  C8    C7   C12  C11    0.00   0.0  0
 L13  CONST_19  C8    C9   C10  C11    0.00   0.0  0
 L13  CONST_20  N2    C1   N5   N14  180.00   0.0  0
 L13  CONST_21  N3    C4   N5   N14  180.00   0.0  0
 L13  CONST_22  C7    C4   N5   N14    0.00   0.0  0
 L13  CONST_23  C4    N5   C1   S6   180.00   0.0  0
 L13  CONST_24  N3    N2   C1   S6   180.00   0.0  0
 L13  CONST_25  C13   C8   C7   C4     0.00   0.0  0
 L13  CONST_26  C13   C8   C7   C12  180.00   0.0  0
 L13  CONST_27  C13   C8   C9   C10  180.00   0.0  0
 L13  CONST_28  HN2   N2   C1   N5   180.00   0.0  0
 L13  CONST_29  H12   C12  C7   C4     0.00   0.0  0
 L13  CONST_30  H11   C11  C12  C7   180.00   0.0  0
 L13  CONST_31  H9    C9   C8   C7   180.00   0.0  0
 L13  CONST_32  H10   C10  C11  C12  180.00   0.0  0
 L13  Var_01    H131  C13  C8   C7   -47.60  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
 L13  plan-1  N14   0.020
 L13  plan-1  N5    0.020
 L13  plan-1  C1    0.020
 L13  plan-1  S6    0.020
 L13  plan-1  N2    0.020
 L13  plan-1  N3    0.020
 L13  plan-1  C4    0.020
 L13  plan-1  C7    0.020
 L13  plan-1  HN2   0.020
 L13  plan-2  C4    0.020
 L13  plan-2  C7    0.020
 L13  plan-2  C12   0.020
 L13  plan-2  C11   0.020
 L13  plan-2  C10   0.020
 L13  plan-2  C9    0.020
 L13  plan-2  C8    0.020
 L13  plan-2  C13   0.020
 L13  plan-2  H12   0.020
 L13  plan-2  H11   0.020
 L13  plan-2  H10   0.020
 L13  plan-2  H9    0.020
 L13  plan-3  N14   0.020
 L13  plan-3  N5    0.020
 L13  plan-3  H141  0.020
 L13  plan-3  H142  0.020

