# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:32:47 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 3,4-dimethyl-5-(1~{H}-1,2,4-triazol-3-yl)thiophene-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(C)c(sc1C#N)c2n[nH]cn2
#
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
 8M8  8M8  3,4-dimethyl-5-(1~{H}-1,2,4-triazol-3-yl)thiophene-2-carbonitrile  ligand  22  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8M8
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
 8M8  C4  C  CR5   0  -0.312  -1.9241   0.3845   0.0133
 8M8  C5  C  CSP   0   0.027  -3.1970   0.9866   0.0261
 8M8  C6  C  CR5   0   0.330   1.9227   0.1323   0.0134
 8M8  N1  N  N     0  -0.466   2.8537  -0.8466  -0.0408
 8M8  C7  C  CR15  0   0.114   3.9858  -0.1825  -0.0101
 8M8  N2  N  NR15  0  -0.403   3.7367   1.1243   0.0576
 8M8  N3  N  N     0  -0.267   2.4285   1.3480   0.0743
 8M8  N   N  NS    0  -0.244  -4.2398   1.4815   0.0360
 8M8  C1  C  CR5   0   0.224  -1.6578  -0.9604  -0.0125
 8M8  C   C  CH3   0  -0.737  -2.6884  -2.0351  -0.0307
 8M8  S   S  S2    0   0.309  -0.4967   1.3476   0.0333
 8M8  C3  C  CR5   0  -0.285   0.4841  -0.0675   0.0062
 8M8  C2  C  CR5   0   0.154  -0.2557  -1.2239  -0.0168
 8M8  H2  H  HCR5  0   0.306   4.9803  -0.5985  -0.0351
 8M8  H3  H  HCH3  0   0.252  -0.0875  -3.1471  -0.9335
 8M8  H4  H  HCH3  0   0.277   1.3478  -2.6622  -0.0318
 8M8  H5  H  HCH3  0   0.252  -0.1057  -3.1838   0.8208
 8M8  H6  H  HCH3  0   0.264  -2.5765  -2.6631  -0.9157
 8M8  H7  H  HCH3  0   0.264  -2.5829  -2.6850   0.8393
 8M8  H8  H  HCH3  0   0.260  -3.7002  -1.6346  -0.0292
 8M8  H1  H  HNR5  0   0.442   4.3947   1.8883   0.0983
 8M8  C8  C  CH3   0  -0.760   0.2635  -2.6249  -0.0412

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
 8M8  C8  C2  single    1.494  0.020  1.494
 8M8  C   C1  single    1.489  0.020  1.489
 8M8  C2  C1  aromatic  1.427  0.020  1.427
 8M8  C2  C3  aromatic  1.373  0.020  1.373
 8M8  C1  C4  aromatic  1.371  0.020  1.371
 8M8  N1  C7  aromatic  1.313  0.020  1.313
 8M8  N1  C6  aromatic  1.352  0.020  1.352
 8M8  C3  C6  single    1.452  0.020  1.452
 8M8  C3  S   aromatic  1.722  0.020  1.722
 8M8  C4  C5  single    1.408  0.020  1.408
 8M8  C4  S   aromatic  1.722  0.020  1.722
 8M8  C7  N2  aromatic  1.332  0.020  1.332
 8M8  C6  N3  aromatic  1.318  0.020  1.318
 8M8  C5  N   triple    1.154  0.020  1.154
 8M8  N2  N3  aromatic  1.327  0.020  1.327
 8M8  C7  H2  single    0.930  0.020  1.080
 8M8  C8  H3  single    0.970  0.020  1.090
 8M8  C8  H4  single    0.970  0.020  1.090
 8M8  C8  H5  single    0.970  0.020  1.090
 8M8  C   H6  single    0.970  0.020  1.090
 8M8  C   H7  single    0.970  0.020  1.090
 8M8  C   H8  single    0.970  0.020  1.090
 8M8  N2  H1  single    0.860  0.020  1.020

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
 8M8  S   C4  C1  112.81  3.000
 8M8  S   C4  C5  120.67  3.000
 8M8  C1  C4  C5  126.52  3.000
 8M8  N   C5  C4  180.00  3.000
 8M8  C3  C6  N3  120.48  3.000
 8M8  N3  C6  N1  113.91  3.000
 8M8  C3  C6  N1  125.61  3.000
 8M8  C7  N1  C6  103.10  3.000
 8M8  H2  C7  N2  123.51  3.000
 8M8  H2  C7  N1  126.84  3.000
 8M8  N2  C7  N1  109.64  3.000
 8M8  H1  N2  N3  120.97  3.000
 8M8  H1  N2  C7  128.53  3.000
 8M8  N3  N2  C7  110.50  3.000
 8M8  N2  N3  C6  102.84  3.000
 8M8  C2  C1  C   123.15  3.000
 8M8  C2  C1  C4  111.84  3.000
 8M8  C   C1  C4  125.00  3.000
 8M8  H8  C   H7  107.94  3.000
 8M8  H8  C   H6  107.96  3.000
 8M8  H7  C   H6  107.10  3.000
 8M8  H8  C   C1  112.20  3.000
 8M8  H7  C   C1  110.68  3.000
 8M8  H6  C   C1  110.76  3.000
 8M8  C3  S   C4   90.71  3.000
 8M8  C2  C3  S   112.67  3.000
 8M8  S   C3  C6  116.81  3.000
 8M8  C2  C3  C6  130.52  3.000
 8M8  C3  C2  C1  111.96  3.000
 8M8  C3  C2  C8  127.06  3.000
 8M8  C1  C2  C8  120.98  3.000
 8M8  H5  C8  H4  108.28  3.000
 8M8  H5  C8  H3  106.96  3.000
 8M8  H4  C8  H3  108.18  3.000
 8M8  H5  C8  C2  110.46  3.000
 8M8  H4  C8  C2  112.30  3.000
 8M8  H3  C8  C2  110.49  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
 8M8  CONST_01  C3  C2  C1  C4    0.00   0.0  0
 8M8  CONST_02  C2  C3  S   C4    0.00   0.0  0
 8M8  CONST_03  C6  C3  S   C4  180.00   0.0  0
 8M8  CONST_04  N2  C7  N1  C6    0.00   0.0  0
 8M8  CONST_05  C1  C2  C3  C6  180.00   0.0  0
 8M8  CONST_06  C7  N2  N3  C6    0.00   0.0  0
 8M8  CONST_07  N3  N2  C7  N1    0.00   0.0  0
 8M8  CONST_08  C2  C3  C6  N1    0.00   0.0  0
 8M8  CONST_09  S   C3  C6  N1  180.00   0.0  0
 8M8  CONST_10  N2  N3  C6  N1    0.00   0.0  0
 8M8  CONST_11  C3  C6  N1  C7  180.00   0.0  0
 8M8  CONST_12  N3  C6  N1  C7    0.00   0.0  0
 8M8  CONST_13  C3  C6  N3  N2  180.00   0.0  0
 8M8  CONST_14  C2  C3  C6  N3  180.00   0.0  0
 8M8  CONST_15  S   C3  C6  N3    0.00   0.0  0
 8M8  CONST_16  S   C3  C2  C1    0.00   0.0  0
 8M8  CONST_17  C3  S   C4  C1    0.00   0.0  0
 8M8  CONST_18  C2  C1  C4  S     0.00   0.0  0
 8M8  CONST_19  C8  C2  C1  C4  180.00   0.0  0
 8M8  CONST_20  C2  C1  C4  C5  180.00   0.0  0
 8M8  CONST_21  C3  S   C4  C5  180.00   0.0  0
 8M8  CONST_22  C8  C2  C3  C6    0.00   0.0  0
 8M8  CONST_23  S   C3  C2  C8  180.00   0.0  0
 8M8  CONST_24  C3  C2  C1  C   180.00   0.0  0
 8M8  CONST_25  S   C4  C1  C   180.00   0.0  0
 8M8  CONST_26  H2  C7  N1  C6  180.00   0.0  0
 8M8  CONST_27  H1  N2  N3  C6  180.00   0.0  0
 8M8  Var_01    H6  C   C1  C4  121.17  30.0  2
 8M8  Var_02    H3  C8  C2  C1   59.69  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
 8M8  plan-1  C6  0.020
 8M8  plan-1  N1  0.020
 8M8  plan-1  C7  0.020
 8M8  plan-1  N2  0.020
 8M8  plan-1  N3  0.020
 8M8  plan-1  C3  0.020
 8M8  plan-1  H2  0.020
 8M8  plan-1  H1  0.020
 8M8  plan-2  C4  0.020
 8M8  plan-2  C5  0.020
 8M8  plan-2  C6  0.020
 8M8  plan-2  N   0.020
 8M8  plan-2  C1  0.020
 8M8  plan-2  C   0.020
 8M8  plan-2  S   0.020
 8M8  plan-2  C3  0.020
 8M8  plan-2  C2  0.020
 8M8  plan-2  C8  0.020

