# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 06:57:10 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-(2-chlorophenyl)-2-ethyl-9-methyl-6,8-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2c(c1)C(=NCc3n[nH]c(C)[n+]23)c4ccccc4Cl
#
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
 H4C  H4C  4-(2-chlorophenyl)-2-ethyl-9-methyl-6,8-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium  ligand  39  23  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H4C
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
 H4C  C    C   CH3   0  -0.666   1.1028   5.0129   0.8940
 H4C  N    N   NR5   1  -0.575   2.0217  -0.7388   0.2467
 H4C  S    S   S2    0   0.308   1.9040   1.9731  -0.1075
 H4C  CL   CL  CL    0  -0.111  -1.3573  -0.4109  -2.1076
 H4C  C1   C   CH2   0  -0.502   0.2067   4.1922  -0.0296
 H4C  N1   N   NR15  0  -0.438   3.3423  -2.3158  -0.1885
 H4C  C2   C   CR5   0  -0.120   0.3651   2.7182   0.1433
 H4C  N2   N   N     0  -0.206   2.6556  -2.7340   0.8815
 H4C  C3   C   CR15  0  -0.248  -0.5713   1.8007   0.5026
 H4C  N3   N   N     0  -0.329  -0.5130  -1.6973   1.6179
 H4C  C4   C   CR5   0   0.115  -0.0693   0.4719   0.5840
 H4C  C5   C   CR5   0   0.004   1.2593   0.4310   0.2649
 H4C  C6   C   CR5   0   0.608   2.9844  -1.1242  -0.6091
 H4C  C7   C   CH3   0  -0.755   3.5226  -0.3895  -1.7644
 H4C  C8   C   CR5   0   0.445   1.8496  -1.7625   1.1519
 H4C  C9   C   CH2   0  -0.442   0.8145  -1.6835   2.2076
 H4C  C10  C   C     0   0.208  -0.8870  -0.7068   0.9146
 H4C  C11  C   CR6   0   0.125  -2.2879  -0.7031   0.4258
 H4C  C12  C   CR16  0  -0.293  -3.3248  -0.8678   1.3409
 H4C  C13  C   CR16  0  -0.233  -4.6473  -0.8525   0.9283
 H4C  C14  C   CR16  0  -0.263  -4.9483  -0.6826  -0.4157
 H4C  C15  C   CR16  0  -0.192  -3.9306  -0.5347  -1.3465
 H4C  C16  C   CR6   0  -0.102  -2.6123  -0.5439  -0.9197
 H4C  H    H   HCH3  0   0.247   0.9178   6.0766   0.7487
 H4C  HA   H   HCH3  0   0.238   0.9127   4.7756   1.9403
 H4C  HB   H   HCH3  0   0.230   2.1603   4.8351   0.6936
 H4C  H1   H   HCH2  0   0.267  -0.8409   4.4318   0.1591
 H4C  H1A  H   HCH2  0   0.268   0.4046   4.4613  -1.0701
 H4C  HN1  H   HNR5  0   0.475   4.0550  -2.9072  -0.5980
 H4C  H3   H   HCR5  0   0.284  -1.5981   2.0632   0.7149
 H4C  H7   H   HCH3  0   0.312   4.1494   0.4393  -1.4352
 H4C  H7A  H   HCH3  0   0.317   4.1287  -1.0547  -2.3735
 H4C  H7B  H   HCH3  0   0.302   2.7141   0.0068  -2.3773
 H4C  H9   H   HCH2  0   0.303   0.9794  -0.7788   2.8052
 H4C  H9A  H   HCH2  0   0.314   0.9246  -2.5432   2.8642
 H4C  H12  H   HCR6  0   0.272  -3.0835  -0.9932   2.3881
 H4C  H13  H   HCR6  0   0.271  -5.4396  -0.9713   1.6545
 H4C  H14  H   HCR6  0   0.275  -5.9778  -0.6688  -0.7476
 H4C  H15  H   HCR6  0   0.287  -4.1591  -0.4202  -2.3972

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
 H4C  C    C1   single    1.526  0.020  1.526
 H4C  N    C5   aromatic  1.396  0.020  1.396
 H4C  N    C6   aromatic  1.344  0.020  1.344
 H4C  N    C8   aromatic  1.377  0.020  1.377
 H4C  S    C2   aromatic  1.728  0.020  1.728
 H4C  S    C5   aromatic  1.712  0.020  1.712
 H4C  CL   C16  single    1.733  0.020  1.733
 H4C  C1   C2   single    1.493  0.020  1.493
 H4C  N1   N2   aromatic  1.338  0.020  1.338
 H4C  N1   C6   aromatic  1.313  0.020  1.313
 H4C  C2   C3   aromatic  1.359  0.020  1.359
 H4C  N2   C8   aromatic  1.291  0.020  1.291
 H4C  C3   C4   aromatic  1.423  0.020  1.423
 H4C  N3   C9   single    1.453  0.020  1.453
 H4C  N3   C10  double    1.271  0.020  1.271
 H4C  C4   C5   aromatic  1.367  0.020  1.367
 H4C  C4   C10  single    1.472  0.020  1.472
 H4C  C6   C7   single    1.471  0.020  1.471
 H4C  C8   C9   single    1.481  0.020  1.481
 H4C  C10  C11  single    1.484  0.020  1.484
 H4C  C11  C12  aromatic  1.393  0.020  1.393
 H4C  C11  C16  aromatic  1.393  0.020  1.393
 H4C  C12  C13  aromatic  1.385  0.020  1.385
 H4C  C13  C14  aromatic  1.388  0.020  1.388
 H4C  C14  C15  aromatic  1.387  0.020  1.387
 H4C  C15  C16  aromatic  1.386  0.020  1.386
 H4C  C    H    single    0.970  0.020  1.090
 H4C  C    HA   single    0.970  0.020  1.090
 H4C  C    HB   single    0.970  0.020  1.090
 H4C  C1   H1   single    0.970  0.020  1.090
 H4C  C1   H1A  single    0.970  0.020  1.090
 H4C  N1   HN1  single    0.860  0.020  1.020
 H4C  C3   H3   single    0.930  0.020  1.080
 H4C  C7   H7   single    0.970  0.020  1.090
 H4C  C7   H7A  single    0.970  0.020  1.090
 H4C  C7   H7B  single    0.970  0.020  1.090
 H4C  C9   H9   single    0.970  0.020  1.090
 H4C  C9   H9A  single    0.970  0.020  1.090
 H4C  C12  H12  single    0.930  0.020  1.080
 H4C  C13  H13  single    0.930  0.020  1.080
 H4C  C14  H14  single    0.930  0.020  1.080
 H4C  C15  H15  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
 H4C  HB   C    HA   108.06  3.000
 H4C  HB   C    H    107.42  3.000
 H4C  HA   C    H    108.13  3.000
 H4C  HB   C    C1   111.74  3.000
 H4C  HA   C    C1   111.19  3.000
 H4C  H    C    C1   110.16  3.000
 H4C  C8   N    C6   107.15  3.000
 H4C  C8   N    C5   123.08  3.000
 H4C  C6   N    C5   129.74  3.000
 H4C  C5   S    C2    91.23  3.000
 H4C  H1A  C1   H1   106.53  3.000
 H4C  H1A  C1   C2   109.53  3.000
 H4C  H1   C1   C2   107.38  3.000
 H4C  H1A  C1   C    109.72  3.000
 H4C  H1   C1   C    109.94  3.000
 H4C  C2   C1   C    113.49  3.000
 H4C  HN1  N1   C6   126.31  3.000
 H4C  HN1  N1   N2   120.13  3.000
 H4C  C6   N1   N2   113.56  3.000
 H4C  C3   C2   C1   128.62  3.000
 H4C  C3   C2   S    111.15  3.000
 H4C  C1   C2   S    120.23  3.000
 H4C  C8   N2   N1   104.64  3.000
 H4C  H3   C3   C4   123.42  3.000
 H4C  H3   C3   C2   122.85  3.000
 H4C  C4   C3   C2   113.73  3.000
 H4C  C10  N3   C9   119.08  3.000
 H4C  C10  C4   C5   124.63  3.000
 H4C  C10  C4   C3   124.38  3.000
 H4C  C5   C4   C3   110.95  3.000
 H4C  C4   C5   S    112.94  3.000
 H4C  C4   C5   N    123.97  3.000
 H4C  S    C5   N    123.09  3.000
 H4C  C7   C6   N1   127.23  3.000
 H4C  C7   C6   N    128.22  3.000
 H4C  N1   C6   N    104.56  3.000
 H4C  H7B  C7   H7A  108.75  3.000
 H4C  H7B  C7   H7   108.68  3.000
 H4C  H7A  C7   H7   108.30  3.000
 H4C  H7B  C7   C6   110.61  3.000
 H4C  H7A  C7   C6   109.79  3.000
 H4C  H7   C7   C6   110.66  3.000
 H4C  C9   C8   N2   128.76  3.000
 H4C  C9   C8   N    121.09  3.000
 H4C  N2   C8   N    110.09  3.000
 H4C  H9A  C9   H9   107.94  3.000
 H4C  H9A  C9   C8   108.51  3.000
 H4C  H9   C9   C8   109.11  3.000
 H4C  H9A  C9   N3   109.28  3.000
 H4C  H9   C9   N3   111.50  3.000
 H4C  C8   C9   N3   110.42  3.000
 H4C  C11  C10  C4   116.64  3.000
 H4C  C11  C10  N3   117.52  3.000
 H4C  C4   C10  N3   125.79  3.000
 H4C  C16  C11  C12  118.34  3.000
 H4C  C16  C11  C10  122.57  3.000
 H4C  C12  C11  C10  119.09  3.000
 H4C  H12  C12  C13  120.16  3.000
 H4C  H12  C12  C11  118.93  3.000
 H4C  C13  C12  C11  120.91  3.000
 H4C  H13  C13  C14  120.32  3.000
 H4C  H13  C13  C12  119.89  3.000
 H4C  C14  C13  C12  119.79  3.000
 H4C  H14  C14  C15  119.40  3.000
 H4C  H14  C14  C13  120.35  3.000
 H4C  C15  C14  C13  120.25  3.000
 H4C  H15  C15  C16  120.07  3.000
 H4C  H15  C15  C14  120.54  3.000
 H4C  C16  C15  C14  119.38  3.000
 H4C  C15  C16  C11  121.32  3.000
 H4C  C15  C16  CL   118.50  3.000
 H4C  C11  C16  CL   120.14  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
 H4C  CONST_01  C2   S    C5   N     180.00   0.0  0
 H4C  CONST_02  C3   C4   C5   N     180.00   0.0  0
 H4C  CONST_03  N2   N1   C6   N       0.00   0.0  0
 H4C  CONST_04  N1   N2   C8   N       0.00   0.0  0
 H4C  CONST_05  C4   C3   C2   S       0.00   0.0  0
 H4C  CONST_08  C3   C4   C5   S       0.00   0.0  0
 H4C  CONST_09  C5   N    C6   N1    180.00   0.0  0
 H4C  CONST_10  C8   N    C6   N1      0.00   0.0  0
 H4C  CONST_11  C4   C5   S    C2      0.00   0.0  0
 H4C  CONST_12  C5   C4   C3   C2      0.00   0.0  0
 H4C  CONST_13  C5   N    C8   N2    180.00   0.0  0
 H4C  CONST_14  C6   N    C8   N2      0.00   0.0  0
 H4C  CONST_15  C5   S    C2   C3      0.00   0.0  0
 H4C  CONST_18  C8   N2   N1   C6      0.00   0.0  0
 H4C  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 H4C  CONST_20  C14  C15  C16  C11     0.00   0.0  0
 H4C  CONST_21  C15  C16  C11  C12     0.00   0.0  0
 H4C  CONST_22  C15  C14  C13  C12     0.00   0.0  0
 H4C  CONST_23  C16  C11  C12  C13     0.00   0.0  0
 H4C  CONST_24  C16  C15  C14  C13     0.00   0.0  0
 H4C  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 H4C  CONST_26  C15  C16  C11  C10   180.00   0.0  0
 H4C  CONST_27  C10  C11  C16  CL      0.00   0.0  0
 H4C  CONST_28  C12  C11  C16  CL    180.00   0.0  0
 H4C  CONST_29  C14  C15  C16  CL    180.00   0.0  0
 H4C  CONST_30  C5   S    C2   C1    180.00   0.0  0
 H4C  CONST_31  C4   C3   C2   C1    180.00   0.0  0
 H4C  CONST_32  C7   C6   N1   N2    180.00   0.0  0
 H4C  CONST_33  C7   C6   N    C5      0.00   0.0  0
 H4C  CONST_34  C8   N    C6   C7    180.00   0.0  0
 H4C  CONST_35  HN1  N1   C6   N     180.00   0.0  0
 H4C  CONST_36  H3   C3   C2   S     180.00   0.0  0
 H4C  CONST_37  H12  C12  C11  C10     0.00   0.0  0
 H4C  CONST_38  H13  C13  C12  C11   180.00   0.0  0
 H4C  CONST_39  H15  C15  C16  C11   180.00   0.0  0
 H4C  CONST_40  H14  C14  C13  C12   180.00   0.0  0
 H4C  Var_01    N3   C9   C8   N      66.06  30.0  1
 H4C  Var_02    N3   C10  C4   C3   -142.77  30.0  1
 H4C  Var_03    C12  C11  C10  N3     53.47  30.0  2
 H4C  Var_04    S    C2   C1   C     -59.36  30.0  2
 H4C  Var_05    H7   C7   C6   N      72.86  30.0  2
 H4C  Var_06    H    C    C1   C2   -177.94  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
 H4C  plan-1  CL   0.020
 H4C  plan-1  C10  0.020
 H4C  plan-1  C11  0.020
 H4C  plan-1  C12  0.020
 H4C  plan-1  C13  0.020
 H4C  plan-1  C14  0.020
 H4C  plan-1  C15  0.020
 H4C  plan-1  C16  0.020
 H4C  plan-1  H12  0.020
 H4C  plan-1  H13  0.020
 H4C  plan-1  H14  0.020
 H4C  plan-1  H15  0.020
 H4C  plan-2  N    0.020
 H4C  plan-2  N1   0.020
 H4C  plan-2  N2   0.020
 H4C  plan-2  C5   0.020
 H4C  plan-2  C6   0.020
 H4C  plan-2  C7   0.020
 H4C  plan-2  C8   0.020
 H4C  plan-2  C9   0.020
 H4C  plan-2  HN1  0.020
 H4C  plan-3  N    0.020
 H4C  plan-3  S    0.020
 H4C  plan-3  C1   0.020
 H4C  plan-3  C2   0.020
 H4C  plan-3  C3   0.020
 H4C  plan-3  C4   0.020
 H4C  plan-3  C5   0.020
 H4C  plan-3  C10  0.020
 H4C  plan-3  H3   0.020

