# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 15:50:16 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 1-[4-(3-chlorophenyl)piperazin-1-yl]-2-(1~{H}-1,2,4-triazol-3-ylsulfanyl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)N2CCN(CC2)C(=O)CSc3n[nH]cn3
#
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
 I2W  I2W  "2-((4H-1,2,4-triazol-3-yl)thio)-1-(4-(3-chlorophenyl)piperazin-1-yl)ethan-1-one"
  ligand  38  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I2W
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
 I2W  N1   N   NT    0  -0.466   2.8117  44.7642  -52.6959
 I2W  N3   N   NR15  0  -0.409  -2.1477  48.7459  -51.1322
 I2W  C4   C   CR6   0   0.411   6.7380  44.1890  -51.2119
 I2W  C5   C   CR16  0  -0.321   6.9876  44.0247  -49.8371
 I2W  C6   C   CH2   0  -0.320   5.1696  44.2480  -53.0982
 I2W  C7   C   CH2   0  -0.299   3.7295  43.8318  -53.3329
 I2W  C8   C   CH2   0  -0.309   3.3115  45.4659  -51.5239
 I2W  C10  C   C     0   0.592   1.5906  44.9602  -53.2202
 I2W  C13  C   CR15  0   0.114  -3.1359  48.6730  -52.0182
 I2W  O    O   O     0  -0.486   1.1763  44.3518  -54.1968
 I2W  C11  C   CH2   0  -0.723   0.7222  45.9972  -52.5369
 I2W  S    S   S2    0   0.079  -0.7796  46.1692  -53.5293
 I2W  C12  C   CR5   0   0.189  -1.6110  47.3685  -52.5720
 I2W  N4   N   N     0  -0.463  -2.8315  47.8031  -52.9556
 I2W  N2   N   N     0  -0.265  -1.1537  47.9141  -51.4684
 I2W  C9   C   CH2   0  -0.310   4.3552  44.6312  -50.8040
 I2W  N    N   NT    0  -0.526   5.4614  44.3173  -51.6819
 I2W  C    C   CR6   0  -0.019   8.2877  43.9080  -49.3812
 I2W  CL   CL  CL    0  -0.138   8.5448  43.7060  -47.6738
 I2W  C3   C   CR16  0  -0.356   7.8459  44.2105  -52.0797
 I2W  C2   C   CR16  0  -0.243   9.1313  44.0807  -51.5854
 I2W  C1   C   CR16  0  -0.269   9.3832  43.9316  -50.2278
 I2W  H2   H   HCR6  0   0.285   6.1753  43.9631  -49.1269
 I2W  H3   H   HCH2  0   0.266   5.7994  43.4926  -53.5710
 I2W  H4   H   HCH2  0   0.241   5.3723  45.1993  -53.6060
 I2W  H5   H   HCH2  0   0.273   3.5443  43.8124  -54.4053
 I2W  H6   H   HCH2  0   0.254   3.5707  42.8177  -52.9543
 I2W  H7   H   HCH2  0   0.260   3.7410  46.4333  -51.8021
 I2W  H8   H   HCH2  0   0.280   2.5046  45.6552  -50.8171
 I2W  H9   H   HCR5  0   0.306  -4.0418  49.2550  -51.9490
 I2W  H10  H   HCH2  0   0.315   1.2339  46.9576  -52.4559
 I2W  H11  H   HCH2  0   0.317   0.4602  45.6785  -51.5255
 I2W  H12  H   HCH2  0   0.244   3.8878  43.7296  -50.3903
 I2W  H13  H   HCH2  0   0.267   4.7052  45.2246  -49.9580
 I2W  H14  H   HCR6  0   0.271   7.7117  44.3537  -53.1424
 I2W  H15  H   HCR6  0   0.260   9.9633  44.1096  -52.2773
 I2W  H16  H   HCR6  0   0.266  10.3906  43.8373  -49.8483
 I2W  H1   H   HNR5  0   0.435  -2.0844  49.3189  -50.3038

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
 I2W  O    C10  double    1.223  0.020  1.223
 I2W  S    C11  single    1.808  0.020  1.808
 I2W  S    C12  single    1.745  0.020  1.745
 I2W  C10  N1   single    1.343  0.020  1.343
 I2W  C10  C11  single    1.515  0.020  1.515
 I2W  C6   C7   single    1.517  0.020  1.517
 I2W  C6   N    single    1.448  0.020  1.448
 I2W  C7   N1   single    1.455  0.020  1.455
 I2W  N1   C8   single    1.455  0.020  1.455
 I2W  N4   C12  aromatic  1.351  0.020  1.351
 I2W  N4   C13  aromatic  1.315  0.020  1.315
 I2W  C12  N2   aromatic  1.313  0.020  1.313
 I2W  C3   C4   aromatic  1.407  0.020  1.407
 I2W  C3   C2   aromatic  1.383  0.020  1.383
 I2W  N    C4   single    1.366  0.020  1.366
 I2W  N    C9   single    1.447  0.020  1.447
 I2W  C13  N3   aromatic  1.329  0.020  1.329
 I2W  C8   C9   single    1.518  0.020  1.518
 I2W  C4   C5   aromatic  1.407  0.020  1.407
 I2W  N2   N3   aromatic  1.339  0.020  1.339
 I2W  C2   C1   aromatic  1.389  0.020  1.389
 I2W  C5   C    aromatic  1.383  0.020  1.383
 I2W  C1   C    aromatic  1.385  0.020  1.385
 I2W  C    CL   single    1.738  0.020  1.738
 I2W  N3   H1   single    0.860  0.020  1.020
 I2W  C5   H2   single    0.930  0.020  1.080
 I2W  C6   H3   single    0.970  0.020  1.090
 I2W  C6   H4   single    0.970  0.020  1.090
 I2W  C7   H5   single    0.970  0.020  1.090
 I2W  C7   H6   single    0.970  0.020  1.090
 I2W  C8   H7   single    0.970  0.020  1.090
 I2W  C8   H8   single    0.970  0.020  1.090
 I2W  C13  H9   single    0.930  0.020  1.080
 I2W  C11  H10  single    0.970  0.020  1.090
 I2W  C11  H11  single    0.970  0.020  1.090
 I2W  C9   H12  single    0.970  0.020  1.090
 I2W  C9   H13  single    0.970  0.020  1.090
 I2W  C3   H14  single    0.930  0.020  1.080
 I2W  C2   H15  single    0.930  0.020  1.080
 I2W  C1   H16  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
 I2W  C10  N1   C8   123.81  3.000
 I2W  C8   N1   C7   116.43  3.000
 I2W  C10  N1   C7   119.73  3.000
 I2W  H1   N3   N2   120.81  3.000
 I2W  H1   N3   C13  128.67  3.000
 I2W  N2   N3   C13  110.52  3.000
 I2W  C3   C4   N    121.46  3.000
 I2W  N    C4   C5   120.85  3.000
 I2W  C3   C4   C5   117.69  3.000
 I2W  H2   C5   C    119.02  3.000
 I2W  H2   C5   C4   121.03  3.000
 I2W  C    C5   C4   119.93  3.000
 I2W  H4   C6   H3   107.04  3.000
 I2W  H4   C6   N    111.97  3.000
 I2W  H3   C6   N    109.92  3.000
 I2W  H4   C6   C7   109.97  3.000
 I2W  H3   C6   C7   106.91  3.000
 I2W  N    C6   C7   110.84  3.000
 I2W  H6   C7   H5   107.44  3.000
 I2W  H6   C7   C6   109.79  3.000
 I2W  H5   C7   C6   108.59  3.000
 I2W  H6   C7   N1   110.54  3.000
 I2W  H5   C7   N1   109.60  3.000
 I2W  C6   C7   N1   110.80  3.000
 I2W  H8   C8   H7   107.58  3.000
 I2W  H8   C8   C9   107.29  3.000
 I2W  H7   C8   C9   109.68  3.000
 I2W  H8   C8   N1   110.62  3.000
 I2W  H7   C8   N1   110.88  3.000
 I2W  C9   C8   N1   110.67  3.000
 I2W  C11  C10  O    120.42  3.000
 I2W  C11  C10  N1   116.41  3.000
 I2W  O    C10  N1   123.17  3.000
 I2W  H9   C13  N4   126.66  3.000
 I2W  H9   C13  N3   123.50  3.000
 I2W  N4   C13  N3   109.84  3.000
 I2W  H11  C11  H10  107.49  3.000
 I2W  H11  C11  S    109.68  3.000
 I2W  H10  C11  S    110.27  3.000
 I2W  H11  C11  C10  110.82  3.000
 I2W  H10  C11  C10  111.53  3.000
 I2W  S    C11  C10  107.07  3.000
 I2W  C12  S    C11   99.20  3.000
 I2W  N2   C12  N4   114.80  3.000
 I2W  N2   C12  S    125.49  3.000
 I2W  N4   C12  S    119.71  3.000
 I2W  C12  N4   C13  102.68  3.000
 I2W  C12  N2   N3   102.15  3.000
 I2W  H13  C9   H12  106.94  3.000
 I2W  H13  C9   N    110.08  3.000
 I2W  H12  C9   N    112.12  3.000
 I2W  H13  C9   C8   106.81  3.000
 I2W  H12  C9   C8   109.75  3.000
 I2W  N    C9   C8   110.93  3.000
 I2W  C9   N    C6   116.74  3.000
 I2W  C9   N    C4   121.74  3.000
 I2W  C6   N    C4   121.35  3.000
 I2W  C1   C    CL   119.04  3.000
 I2W  CL   C    C5   118.21  3.000
 I2W  C1   C    C5   122.74  3.000
 I2W  H14  C3   C2   118.64  3.000
 I2W  H14  C3   C4   120.70  3.000
 I2W  C2   C3   C4   120.64  3.000
 I2W  H15  C2   C1   119.23  3.000
 I2W  H15  C2   C3   118.90  3.000
 I2W  C1   C2   C3   121.87  3.000
 I2W  H16  C1   C2   121.45  3.000
 I2W  H16  C1   C    121.43  3.000
 I2W  C2   C1   C    117.13  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
 I2W  CONST_01  C12  N4   C13  N3      0.00   0.0  0
 I2W  CONST_02  N4   C12  N2   N3      0.00   0.0  0
 I2W  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 I2W  CONST_04  C1   C    C5   C4      0.00   0.0  0
 I2W  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 I2W  CONST_06  C2   C1   C    C5      0.00   0.0  0
 I2W  CONST_07  N2   C12  N4   C13     0.00   0.0  0
 I2W  CONST_08  C12  N2   N3   C13     0.00   0.0  0
 I2W  CONST_09  N2   N3   C13  N4      0.00   0.0  0
 I2W  CONST_10  C3   C4   C5   C       0.00   0.0  0
 I2W  CONST_11  C3   C2   C1   C       0.00   0.0  0
 I2W  CONST_12  C2   C3   C4   N     180.00   0.0  0
 I2W  CONST_13  C    C5   C4   N     180.00   0.0  0
 I2W  CONST_14  S    C12  N2   N3    180.00   0.0  0
 I2W  CONST_15  CL   C    C5   C4    180.00   0.0  0
 I2W  CONST_16  S    C12  N4   C13   180.00   0.0  0
 I2W  CONST_17  C2   C1   C    CL    180.00   0.0  0
 I2W  CONST_18  H15  C2   C3   C4    180.00   0.0  0
 I2W  CONST_19  H14  C3   C4   C5    180.00   0.0  0
 I2W  CONST_20  H16  C1   C    C5    180.00   0.0  0
 I2W  CONST_21  H9   C13  N4   C12   180.00   0.0  0
 I2W  CONST_22  H1   N3   N2   C12   180.00   0.0  0
 I2W  CONST_23  H1   N3   C13  N4    180.00   0.0  0
 I2W  CONST_24  H9   C13  N3   N2    180.00   0.0  0
 I2W  CONST_25  H14  C3   C4   N       0.00   0.0  0
 I2W  CONST_26  H2   C5   C4   N       0.00   0.0  0
 I2W  CONST_27  H15  C2   C1   C     180.00   0.0  0
 I2W  CONST_28  H2   C5   C4   C3    180.00   0.0  0
 I2W  CONST_29  H16  C1   C2   C3    180.00   0.0  0
 I2W  CONST_30  H14  C3   C2   C1    180.00   0.0  0
 I2W  CONST_31  H2   C5   C    C1    180.00   0.0  0
 I2W  CONST_32  O    C10  N1   C7      0.00   0.0  0
 I2W  CONST_33  C11  C10  N1   C7    180.00   0.0  0
 I2W  CONST_34  O    C10  N1   C8    180.00   0.0  0
 I2W  CONST_35  C11  C10  N1   C8      0.00   0.0  0
 I2W  Var_01    N    C6   C7   N1     58.37  30.0  1
 I2W  Var_02    N    C9   C8   N1     58.47  30.0  1
 I2W  Var_03    C7   C6   N    C4    156.00  30.0  1
 I2W  Var_04    C8   C9   N    C4    147.40  30.0  1
 I2W  Var_05    C6   N    C4   C5   -168.86  30.0  3
 I2W  Var_06    C9   N    C4   C5     16.02  30.0  3
 I2W  Var_07    C8   N1   C7   C6    -27.70  30.0  1
 I2W  Var_08    C3   C4   N    C6     10.87  30.0  2
 I2W  Var_09    C8   C9   N    C6    -27.93  30.0  1
 I2W  Var_10    C9   N    C6   C7    -28.65  30.0  1
 I2W  Var_11    C9   C8   N1   C7    -28.60  30.0  1
 I2W  Var_12    C3   C4   N    C9   -164.24  30.0  2
 I2W  Var_13    C10  N1   C7   C6    150.57  30.0  1
 I2W  Var_14    C9   C8   N1   C10   153.21  30.0  1
 I2W  Var_15    H3   C6   C7   N1    178.15  30.0  1
 I2W  Var_16    H4   C6   C7   N1    -65.98  30.0  1
 I2W  Var_17    H12  C9   C8   N1    -65.98  30.0  1
 I2W  Var_18    H13  C9   C8   N1    178.43  30.0  1
 I2W  Var_19    H3   C6   N    C4     38.03  30.0  1
 I2W  Var_20    H4   C6   N    C4    -80.80  30.0  1
 I2W  Var_21    H12  C9   N    C4    -89.50  30.0  1
 I2W  Var_22    H13  C9   N    C4     29.40  30.0  1
 I2W  Var_23    H12  C9   N    C6     95.16  30.0  1
 I2W  Var_24    H13  C9   N    C6   -145.93  30.0  1
 I2W  Var_25    H7   C8   N1   C7     93.35  30.0  1
 I2W  Var_26    H8   C8   N1   C7   -147.38  30.0  1
 I2W  Var_27    H5   C7   N1   C8   -147.52  30.0  1
 I2W  Var_28    H6   C7   N1   C8     94.25  30.0  1
 I2W  Var_29    H3   C6   N    C9   -146.62  30.0  1
 I2W  Var_30    H4   C6   N    C9     94.55  30.0  1
 I2W  Var_31    H5   C7   C6   N     178.79  30.0  1
 I2W  Var_32    H6   C7   C6   N     -64.01  30.0  1
 I2W  Var_33    H7   C8   C9   N     -64.19  30.0  1
 I2W  Var_34    H8   C8   C9   N     179.24  30.0  1
 I2W  Var_35    N4   C12  S    C11  -179.46  30.0  2
 I2W  Var_36    N2   C12  S    C11     0.42  30.0  2
 I2W  Var_37    H5   C7   N1   C10    30.75  30.0  1
 I2W  Var_38    H6   C7   N1   C10   -87.49  30.0  1
 I2W  Var_39    H7   C8   N1   C10   -84.84  30.0  1
 I2W  Var_40    H8   C8   N1   C10    34.43  30.0  1
 I2W  Var_41    S    C11  C10  N1    174.69  30.0  3
 I2W  Var_42    C12  S    C11  C10   179.53  30.0  1
 I2W  Var_43    H10  C11  C10  N1     53.98  30.0  3
 I2W  Var_44    H11  C11  C10  N1    -65.73  30.0  3
 I2W  Var_45    H10  C11  S    C12   -58.96  30.0  3
 I2W  Var_46    H11  C11  S    C12    59.22  30.0  3
 I2W  Var_47    S    C11  C10  O      -5.18  30.0  3
 I2W  Var_48    H10  C11  C10  O    -125.88  30.0  3
 I2W  Var_49    H11  C11  C10  O     114.41  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
 I2W  plan-1  N3   0.020
 I2W  plan-1  C13  0.020
 I2W  plan-1  S    0.020
 I2W  plan-1  C12  0.020
 I2W  plan-1  N4   0.020
 I2W  plan-1  N2   0.020
 I2W  plan-1  H9   0.020
 I2W  plan-1  H1   0.020
 I2W  plan-2  C4   0.020
 I2W  plan-2  C5   0.020
 I2W  plan-2  N    0.020
 I2W  plan-2  C    0.020
 I2W  plan-2  CL   0.020
 I2W  plan-2  C3   0.020
 I2W  plan-2  C2   0.020
 I2W  plan-2  C1   0.020
 I2W  plan-2  H2   0.020
 I2W  plan-2  H14  0.020
 I2W  plan-2  H15  0.020
 I2W  plan-2  H16  0.020
 I2W  plan-3  N1   0.020
 I2W  plan-3  C7   0.020
 I2W  plan-3  C8   0.020
 I2W  plan-3  C10  0.020
 I2W  plan-3  O    0.020
 I2W  plan-3  C11  0.020

