# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:26:49 2021
#   Inital geometry file: a 98 line input string
#   Ligand name: 3-[5-methylsulfanyl-4-(3,4,5-trimethylphenyl)-1,2,4-triazol-3-yl]propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nnc(CCCO)n1c2cc(C)c(C)c(C)c2
#
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
 DY3  DY3  3-[5-methylsulfanyl-4-(3,4,5-trimethylphenyl)-1,2,4-triazol-3-yl]propan-1-ol  ligand  41  20  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DY3
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
 DY3  N1   N  NR5   0  -0.555  -64.3021  -0.8828  -28.5751
 DY3  C2   C  CR16  0  -0.314  -63.1153  -2.5983  -29.8041
 DY3  C4   C  CR6   0   0.283  -63.5296  -1.2832  -29.6969
 DY3  C5   C  CR6   0   0.015  -62.0724  -2.0929  -31.9211
 DY3  C    C  CR5   0   0.435  -63.9627  -0.0185  -27.5816
 DY3  C6   C  CR16  0  -0.325  -63.2139  -0.3622  -30.6810
 DY3  O    O  OH1   0  -0.665  -62.9735   2.9295  -29.3473
 DY3  C11  C  CH2   0  -0.161  -63.6199   2.9880  -28.0929
 DY3  C10  C  CH2   0  -0.463  -62.8345   2.1710  -27.0871
 DY3  C9   C  CH2   0  -0.535  -62.6640   0.6995  -27.4667
 DY3  C1   C  CR5   0   0.191  -65.5636  -1.3043  -28.2601
 DY3  S    S  S2    0   0.038  -66.4889  -2.4747  -29.1578
 DY3  C8   C  CH3   0  -0.766  -66.7979  -1.5727  -30.7034
 DY3  N2   N  N     0  -0.300  -65.9502  -0.7371  -27.1549
 DY3  N    N  N     0  -0.336  -64.9466   0.0618  -26.7270
 DY3  C7   C  CR6   0   0.083  -62.4774  -0.7566  -31.7915
 DY3  C13  C  CH3   0  -0.742  -62.1333   0.2584  -32.8427
 DY3  C12  C  CH3   0  -0.746  -61.2790  -2.5083  -33.1266
 DY3  C3   C  CR6   0   0.081  -62.3883  -3.0157  -30.9141
 DY3  C14  C  CH3   0  -0.748  -61.9502  -4.4507  -30.9984
 DY3  H1   H  HCR6  0   0.262  -63.3541  -3.3057  -29.0199
 DY3  H2   H  HCR6  0   0.267  -63.5287   0.6692  -30.5773
 DY3  H3   H  HOH1  0   0.455  -63.5018   3.4211  -29.9821
 DY3  H4   H  HCH2  0   0.210  -63.6887   4.0203  -27.7270
 DY3  H5   H  HCH2  0   0.198  -64.6475   2.6085  -28.1558
 DY3  H6   H  HCH2  0   0.242  -61.8421   2.6074  -26.9509
 DY3  H7   H  HCH2  0   0.239  -63.3404   2.2457  -26.1228
 DY3  H8   H  HCH2  0   0.281  -62.0643   0.2015  -26.7000
 DY3  H9   H  HCH2  0   0.270  -62.0988   0.6100  -28.3935
 DY3  H10  H  HCH3  0   0.289  -67.4629  -2.2017  -31.2917
 DY3  H11  H  HCH3  0   0.280  -67.2892  -0.6239  -30.5036
 DY3  H12  H  HCH3  0   0.277  -65.8776  -1.4130  -31.2600
 DY3  H13  H  HCH3  0   0.249  -62.5784   0.0042  -33.8068
 DY3  H14  H  HCH3  0   0.251  -62.4909   1.2483  -32.5644
 DY3  H15  H  HCH3  0   0.248  -61.0555   0.3268  -33.0003
 DY3  H16  H  HCH3  0   0.253  -60.2335  -2.2038  -33.0314
 DY3  H17  H  HCH3  0   0.257  -61.2873  -3.5847  -33.2800
 DY3  H18  H  HCH3  0   0.249  -61.6600  -2.0470  -34.0375
 DY3  H19  H  HCH3  0   0.249  -60.8654  -4.5385  -31.0757
 DY3  H20  H  HCH3  0   0.254  -62.2645  -5.0064  -30.1163
 DY3  H21  H  HCH3  0   0.249  -62.3741  -4.9518  -31.8707

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
 DY3  C13  C7   single    1.501  0.020  1.501
 DY3  C12  C5   single    1.502  0.020  1.502
 DY3  C7   C5   aromatic  1.402  0.020  1.402
 DY3  C7   C6   aromatic  1.390  0.020  1.390
 DY3  C5   C3   aromatic  1.402  0.020  1.402
 DY3  C8   S    single    1.816  0.020  1.816
 DY3  C6   C4   aromatic  1.384  0.020  1.384
 DY3  C3   C14  single    1.503  0.020  1.503
 DY3  C3   C2   aromatic  1.391  0.020  1.391
 DY3  C4   C2   aromatic  1.383  0.020  1.383
 DY3  C4   N1   single    1.420  0.020  1.420
 DY3  S    C1   single    1.741  0.020  1.741
 DY3  N1   C1   aromatic  1.367  0.020  1.367
 DY3  N1   C    aromatic  1.360  0.020  1.360
 DY3  C1   N2   aromatic  1.301  0.020  1.301
 DY3  C11  O    single    1.412  0.020  1.412
 DY3  C11  C10  single    1.515  0.020  1.515
 DY3  C    C9   single    1.488  0.020  1.488
 DY3  C    N    aromatic  1.306  0.020  1.306
 DY3  C9   C10  single    1.529  0.020  1.529
 DY3  N2   N    aromatic  1.352  0.020  1.352
 DY3  C2   H1   single    0.930  0.020  1.080
 DY3  C6   H2   single    0.930  0.020  1.080
 DY3  O    H3   single    0.850  0.020  0.980
 DY3  C11  H4   single    0.970  0.020  1.090
 DY3  C11  H5   single    0.970  0.020  1.090
 DY3  C10  H6   single    0.970  0.020  1.090
 DY3  C10  H7   single    0.970  0.020  1.090
 DY3  C9   H8   single    0.970  0.020  1.090
 DY3  C9   H9   single    0.970  0.020  1.090
 DY3  C8   H10  single    0.970  0.020  1.090
 DY3  C8   H11  single    0.970  0.020  1.090
 DY3  C8   H12  single    0.970  0.020  1.090
 DY3  C13  H13  single    0.970  0.020  1.090
 DY3  C13  H14  single    0.970  0.020  1.090
 DY3  C13  H15  single    0.970  0.020  1.090
 DY3  C12  H16  single    0.970  0.020  1.090
 DY3  C12  H17  single    0.970  0.020  1.090
 DY3  C12  H18  single    0.970  0.020  1.090
 DY3  C14  H19  single    0.970  0.020  1.090
 DY3  C14  H20  single    0.970  0.020  1.090
 DY3  C14  H21  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
 DY3  C1   N1   C    104.95  3.000
 DY3  C    N1   C4   128.37  3.000
 DY3  C1   N1   C4   126.68  3.000
 DY3  H1   C2   C3   119.81  3.000
 DY3  H1   C2   C4   119.94  3.000
 DY3  C3   C2   C4   120.25  3.000
 DY3  C6   C4   C2   120.61  3.000
 DY3  C2   C4   N1   119.50  3.000
 DY3  C6   C4   N1   119.88  3.000
 DY3  C3   C5   C12  120.90  3.000
 DY3  C3   C5   C7   119.73  3.000
 DY3  C12  C5   C7   119.36  3.000
 DY3  N    C    C9   125.26  3.000
 DY3  N    C    N1   109.22  3.000
 DY3  C9   C    N1   125.51  3.000
 DY3  H2   C6   C7   120.05  3.000
 DY3  H2   C6   C4   119.94  3.000
 DY3  C7   C6   C4   120.01  3.000
 DY3  H3   O    C11  108.29  3.000
 DY3  H5   C11  H4   106.61  3.000
 DY3  H5   C11  C10  109.69  3.000
 DY3  H4   C11  C10  108.56  3.000
 DY3  H5   C11  O    111.31  3.000
 DY3  H4   C11  O    111.33  3.000
 DY3  C10  C11  O    109.27  3.000
 DY3  H7   C10  H6   106.47  3.000
 DY3  H7   C10  C9   109.69  3.000
 DY3  H6   C10  C9   108.30  3.000
 DY3  H7   C10  C11  108.01  3.000
 DY3  H6   C10  C11  109.76  3.000
 DY3  C9   C10  C11  114.32  3.000
 DY3  H9   C9   H8   105.94  3.000
 DY3  H9   C9   C10  110.38  3.000
 DY3  H8   C9   C10  108.98  3.000
 DY3  H9   C9   C    110.33  3.000
 DY3  H8   C9   C    108.24  3.000
 DY3  C10  C9   C    112.71  3.000
 DY3  N2   C1   S    124.97  3.000
 DY3  N2   C1   N1   109.61  3.000
 DY3  S    C1   N1   125.37  3.000
 DY3  C8   S    C1   101.26  3.000
 DY3  H12  C8   H11  110.39  3.000
 DY3  H12  C8   H10  108.99  3.000
 DY3  H11  C8   H10  109.13  3.000
 DY3  H12  C8   S    111.39  3.000
 DY3  H11  C8   S    110.73  3.000
 DY3  H10  C8   S    106.08  3.000
 DY3  N    N2   C1   107.81  3.000
 DY3  N2   N    C    108.41  3.000
 DY3  C13  C7   C6   119.29  3.000
 DY3  C6   C7   C5   119.82  3.000
 DY3  C13  C7   C5   120.89  3.000
 DY3  H15  C13  H14  107.71  3.000
 DY3  H15  C13  H13  106.84  3.000
 DY3  H14  C13  H13  107.66  3.000
 DY3  H15  C13  C7   111.71  3.000
 DY3  H14  C13  C7   111.13  3.000
 DY3  H13  C13  C7   111.56  3.000
 DY3  H18  C12  H17  107.36  3.000
 DY3  H18  C12  H16  106.81  3.000
 DY3  H17  C12  H16  107.18  3.000
 DY3  H18  C12  C5   111.67  3.000
 DY3  H17  C12  C5   112.52  3.000
 DY3  H16  C12  C5   111.00  3.000
 DY3  C14  C3   C5   121.51  3.000
 DY3  C14  C3   C2   118.93  3.000
 DY3  C5   C3   C2   119.56  3.000
 DY3  H21  C14  H20  107.52  3.000
 DY3  H21  C14  H19  107.01  3.000
 DY3  H20  C14  H19  107.65  3.000
 DY3  H21  C14  C3   111.71  3.000
 DY3  H20  C14  C3   110.96  3.000
 DY3  H19  C14  C3   111.76  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
 DY3  CONST_01  C7   C6   C4   N1    180.00   0.0  0
 DY3  CONST_02  C3   C2   C4   N1    180.00   0.0  0
 DY3  CONST_03  N    N2   C1   N1      0.00   0.0  0
 DY3  CONST_04  N2   N    C    N1      0.00   0.0  0
 DY3  CONST_05  C7   C5   C3   C2      0.00   0.0  0
 DY3  CONST_06  C7   C6   C4   C2      0.00   0.0  0
 DY3  CONST_09  C5   C7   C6   C4      0.00   0.0  0
 DY3  CONST_10  C5   C3   C2   C4      0.00   0.0  0
 DY3  CONST_11  N2   C1   N1   C4    180.00   0.0  0
 DY3  CONST_12  N    C    N1   C4    180.00   0.0  0
 DY3  CONST_14  N2   C1   N1   C       0.00   0.0  0
 DY3  CONST_15  C1   N2   N    C       0.00   0.0  0
 DY3  CONST_16  C3   C5   C7   C6      0.00   0.0  0
 DY3  CONST_17  C3   C2   C4   C6      0.00   0.0  0
 DY3  CONST_19  N    C    N1   C1      0.00   0.0  0
 DY3  CONST_20  C12  C5   C3   C2    180.00   0.0  0
 DY3  CONST_21  C13  C7   C6   C4    180.00   0.0  0
 DY3  CONST_22  C14  C3   C2   C4    180.00   0.0  0
 DY3  CONST_23  S    C1   N1   C4      0.00   0.0  0
 DY3  CONST_24  C9   C    N1   C4      0.00   0.0  0
 DY3  CONST_25  S    C1   N1   C     180.00   0.0  0
 DY3  CONST_26  C12  C5   C7   C6    180.00   0.0  0
 DY3  CONST_27  C1   N1   C    C9    180.00   0.0  0
 DY3  CONST_28  N2   N    C    C9    180.00   0.0  0
 DY3  CONST_29  N    N2   C1   S     180.00   0.0  0
 DY3  CONST_30  C14  C3   C5   C7    180.00   0.0  0
 DY3  CONST_31  C3   C5   C7   C13   180.00   0.0  0
 DY3  CONST_32  H2   C6   C4   N1      0.00   0.0  0
 DY3  CONST_33  H1   C2   C4   N1      0.00   0.0  0
 DY3  Var_01    C10  C9   C    N1    136.08  30.0  2
 DY3  Var_02    N2   C1   S    C8    115.34  30.0  2
 DY3  Var_03    H19  C14  C3   C2   -121.19  30.0  2
 DY3  Var_04    H13  C13  C7   C5     62.03  30.0  2
 DY3  Var_05    H16  C12  C5   C7     77.73  30.0  2
 DY3  Var_06    C11  C10  C9   C     -61.40  30.0  3
 DY3  Var_07    H10  C8   S    C1   -174.47  30.0  3
 DY3  Var_08    C9   C10  C11  O     -58.67  30.0  3

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
 DY3  plan-1  N1   0.020
 DY3  plan-1  C4   0.020
 DY3  plan-1  C    0.020
 DY3  plan-1  C9   0.020
 DY3  plan-1  C1   0.020
 DY3  plan-1  S    0.020
 DY3  plan-1  N2   0.020
 DY3  plan-1  N    0.020
 DY3  plan-2  N1   0.020
 DY3  plan-2  C2   0.020
 DY3  plan-2  C4   0.020
 DY3  plan-2  C5   0.020
 DY3  plan-2  C6   0.020
 DY3  plan-2  C7   0.020
 DY3  plan-2  C13  0.020
 DY3  plan-2  C12  0.020
 DY3  plan-2  C3   0.020
 DY3  plan-2  C14  0.020
 DY3  plan-2  H1   0.020
 DY3  plan-2  H2   0.020

