# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 14:14:22 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-1-(4-methylpiperidin-1-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)C(=O)Cn2nnc3ccccc23
#
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
 SQ2  SQ2  "2-(1H-1,2,3-benzotriazol-1-yl)-1-(4-methylpiperidin-1-yl)ethan-1-one"
  ligand  37  19  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SQ2
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
 SQ2  N1   N  NT    0  -0.445  10.7328   0.6991  22.6971
 SQ2  N3   N  N     0  -0.060   8.8274   0.3424  18.6455
 SQ2  C4   C  CH2   0  -0.337  10.9367  -0.6756  23.1280
 SQ2  C5   C  C     0   0.545   9.9938   1.0680  21.6370
 SQ2  C6   C  CH2   0  -0.457   9.1213  -0.0187  21.0002
 SQ2  C7   C  CR56  0   0.123   7.1080   1.6148  18.5426
 SQ2  C8   C  CR16  0  -0.290   6.0544   2.4381  18.1314
 SQ2  C10  C  CR16  0  -0.261   5.4471   2.6461  20.4778
 SQ2  C13  C  CH2   0  -0.322  11.6975   1.6228  23.2759
 SQ2  C1   C  CH3   0  -0.650  14.7956  -0.6543  22.8068
 SQ2  C11  C  CR16  0  -0.290   6.4794   1.8380  20.8983
 SQ2  C12  C  CR56  0   0.397   7.3063   1.3290  19.8944
 SQ2  C14  C  CH2   0  -0.413  13.1114   1.2218  22.8764
 SQ2  C2   C  CH1   0  -0.244  13.4135  -0.2230  23.2726
 SQ2  C3   C  CH2   0  -0.406  12.3279  -1.1538  22.7331
 SQ2  C9   C  CR16  0  -0.268   5.2353   2.9445  19.1139
 SQ2  N2   N  NR5   0  -0.379   8.3885   0.5157  19.8896
 SQ2  N4   N  N     0  -0.320   8.0807   0.9755  17.8279
 SQ2  O1   O  O     0  -0.476   9.9682   2.2012  21.1862
 SQ2  H1   H  HCH2  0   0.253  10.8266  -0.7070  24.2160
 SQ2  H2   H  HCH2  0   0.276  10.1692  -1.3306  22.7235
 SQ2  H3   H  HCH2  0   0.312   8.4196  -0.4356  21.7256
 SQ2  H4   H  HCH2  0   0.319   9.7262  -0.8440  20.6236
 SQ2  H6   H  HCR6  0   0.266   4.7765   3.0696  21.2139
 SQ2  H7   H  HCH2  0   0.265  11.4664   2.6366  22.9610
 SQ2  H8   H  HCH2  0   0.243  11.5915   1.5832  24.3643
 SQ2  H9   H  HCH3  0   0.226  15.5719  -0.0039  23.2130
 SQ2  H10  H  HCH3  0   0.226  15.0179  -1.6755  23.1203
 SQ2  H11  H  HCH3  0   0.215  14.8669  -0.6171  21.7174
 SQ2  H12  H  HCR6  0   0.280   6.6366   1.6172  21.9456
 SQ2  H13  H  HCH2  0   0.222  13.2277   1.3403  21.7937
 SQ2  H14  H  HCH2  0   0.236  13.8261   1.9001  23.3495
 SQ2  H15  H  HCH1  0   0.218  13.3819  -0.2795  24.3685
 SQ2  H16  H  HCH2  0   0.238  12.4784  -2.1686  23.1101
 SQ2  H17  H  HCH2  0   0.222  12.3938  -1.2052  21.6406
 SQ2  H18  H  HCR6  0   0.262   4.4084   3.5873  18.8433
 SQ2  H5   H  HCR6  0   0.270   5.8952   2.6661  17.0859

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
 SQ2  N4   N3   aromatic  1.275  0.020  1.275
 SQ2  N4   C7   aromatic  1.366  0.020  1.366
 SQ2  N3   N2   aromatic  1.331  0.020  1.331
 SQ2  C8   C7   aromatic  1.399  0.020  1.399
 SQ2  C8   C9   aromatic  1.376  0.020  1.376
 SQ2  C7   C12  aromatic  1.396  0.020  1.396
 SQ2  C9   C10  aromatic  1.412  0.020  1.412
 SQ2  N2   C12  aromatic  1.354  0.020  1.354
 SQ2  N2   C6   single    1.434  0.020  1.434
 SQ2  C12  C11  aromatic  1.397  0.020  1.397
 SQ2  C6   C5   single    1.532  0.020  1.532
 SQ2  C10  C11  aromatic  1.377  0.020  1.377
 SQ2  O1   C5   double    1.220  0.020  1.220
 SQ2  C5   N1   single    1.344  0.020  1.344
 SQ2  N1   C4   single    1.455  0.020  1.455
 SQ2  N1   C13  single    1.456  0.020  1.456
 SQ2  C3   C4   single    1.523  0.020  1.523
 SQ2  C3   C2   single    1.528  0.020  1.528
 SQ2  C13  C14  single    1.523  0.020  1.523
 SQ2  C14  C2   single    1.528  0.020  1.528
 SQ2  C2   C1   single    1.521  0.020  1.521
 SQ2  C4   H1   single    0.970  0.020  1.090
 SQ2  C4   H2   single    0.970  0.020  1.090
 SQ2  C6   H3   single    0.970  0.020  1.090
 SQ2  C6   H4   single    0.970  0.020  1.090
 SQ2  C8   H5   single    0.930  0.020  1.080
 SQ2  C10  H6   single    0.930  0.020  1.080
 SQ2  C13  H7   single    0.970  0.020  1.090
 SQ2  C13  H8   single    0.970  0.020  1.090
 SQ2  C1   H9   single    0.970  0.020  1.090
 SQ2  C1   H10  single    0.970  0.020  1.090
 SQ2  C1   H11  single    0.970  0.020  1.090
 SQ2  C11  H12  single    0.930  0.020  1.080
 SQ2  C14  H13  single    0.970  0.020  1.090
 SQ2  C14  H14  single    0.970  0.020  1.090
 SQ2  C2   H15  single    0.970  0.020  1.090
 SQ2  C3   H16  single    0.970  0.020  1.090
 SQ2  C3   H17  single    0.970  0.020  1.090
 SQ2  C9   H18  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
 SQ2  C13  N1   C5   120.26  3.000
 SQ2  C13  N1   C4   112.89  3.000
 SQ2  C5   N1   C4   124.75  3.000
 SQ2  N4   N3   N2   109.97  3.000
 SQ2  H2   C4   H1   106.36  3.000
 SQ2  H2   C4   C3   111.05  3.000
 SQ2  H1   C4   C3   109.92  3.000
 SQ2  H2   C4   N1   111.11  3.000
 SQ2  H1   C4   N1   107.91  3.000
 SQ2  C3   C4   N1   110.35  3.000
 SQ2  O1   C5   C6   119.56  3.000
 SQ2  O1   C5   N1   123.92  3.000
 SQ2  C6   C5   N1   116.51  3.000
 SQ2  H4   C6   H3   107.27  3.000
 SQ2  H4   C6   N2   107.35  3.000
 SQ2  H3   C6   N2   109.18  3.000
 SQ2  H4   C6   C5   111.37  3.000
 SQ2  H3   C6   C5   111.14  3.000
 SQ2  N2   C6   C5   110.40  3.000
 SQ2  N4   C7   C12  108.04  3.000
 SQ2  C12  C7   C8   120.81  3.000
 SQ2  N4   C7   C8   131.15  3.000
 SQ2  H5   C8   C9   121.67  3.000
 SQ2  H5   C8   C7   121.26  3.000
 SQ2  C9   C8   C7   117.07  3.000
 SQ2  H6   C10  C9   118.77  3.000
 SQ2  H6   C10  C11  119.12  3.000
 SQ2  C9   C10  C11  122.11  3.000
 SQ2  H8   C13  H7   107.55  3.000
 SQ2  H8   C13  C14  109.95  3.000
 SQ2  H7   C13  C14  111.54  3.000
 SQ2  H8   C13  N1   107.96  3.000
 SQ2  H7   C13  N1   109.63  3.000
 SQ2  C14  C13  N1   110.11  3.000
 SQ2  H11  C1   H10  107.77  3.000
 SQ2  H11  C1   H9   107.73  3.000
 SQ2  H10  C1   H9   107.81  3.000
 SQ2  H11  C1   C2   110.80  3.000
 SQ2  H10  C1   C2   111.25  3.000
 SQ2  H9   C1   C2   111.31  3.000
 SQ2  H12  C11  C12  122.38  3.000
 SQ2  H12  C11  C10  121.63  3.000
 SQ2  C12  C11  C10  115.99  3.000
 SQ2  N2   C12  C11  134.01  3.000
 SQ2  C11  C12  C7   122.51  3.000
 SQ2  N2   C12  C7   103.48  3.000
 SQ2  H14  C14  H13  106.93  3.000
 SQ2  H14  C14  C2   110.19  3.000
 SQ2  H13  C14  C2   109.73  3.000
 SQ2  H14  C14  C13  109.28  3.000
 SQ2  H13  C14  C13  109.23  3.000
 SQ2  C2   C14  C13  111.37  3.000
 SQ2  H15  C2   C3   107.49  3.000
 SQ2  H15  C2   C14  107.57  3.000
 SQ2  C3   C2   C14  110.11  3.000
 SQ2  H15  C2   C1   108.50  3.000
 SQ2  C14  C2   C1   111.61  3.000
 SQ2  C3   C2   C1   111.39  3.000
 SQ2  H17  C3   H16  106.98  3.000
 SQ2  H17  C3   C2   109.74  3.000
 SQ2  H16  C3   C2   110.24  3.000
 SQ2  H17  C3   C4   109.16  3.000
 SQ2  H16  C3   C4   109.14  3.000
 SQ2  C2   C3   C4   111.47  3.000
 SQ2  H18  C9   C10  118.81  3.000
 SQ2  H18  C9   C8   119.68  3.000
 SQ2  C10  C9   C8   121.51  3.000
 SQ2  C12  N2   C6   129.03  3.000
 SQ2  C6   N2   N3   120.47  3.000
 SQ2  C12  N2   N3   110.19  3.000
 SQ2  C7   N4   N3   108.29  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
 SQ2  CONST_01  C8   C7   N4   N3    180.00   0.0  0
 SQ2  CONST_02  C12  C7   N4   N3      0.00   0.0  0
 SQ2  CONST_03  C7   C12  N2   N3      0.00   0.0  0
 SQ2  CONST_04  C11  C12  N2   N3    180.00   0.0  0
 SQ2  CONST_05  N2   N3   N4   C7      0.00   0.0  0
 SQ2  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 SQ2  CONST_07  C10  C11  C12  C7      0.00   0.0  0
 SQ2  CONST_08  N2   C12  C7   C8    180.00   0.0  0
 SQ2  CONST_09  C11  C12  C7   C8      0.00   0.0  0
 SQ2  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 SQ2  CONST_11  N2   C12  C11  C10   180.00   0.0  0
 SQ2  CONST_12  N4   C7   C12  C11   180.00   0.0  0
 SQ2  CONST_13  C9   C8   C7   C12     0.00   0.0  0
 SQ2  CONST_14  N4   N3   N2   C12     0.00   0.0  0
 SQ2  CONST_15  C9   C10  C11  C12     0.00   0.0  0
 SQ2  CONST_16  N4   C7   C8   C9    180.00   0.0  0
 SQ2  CONST_17  N4   C7   C12  N2      0.00   0.0  0
 SQ2  CONST_18  N4   N3   N2   C6    180.00   0.0  0
 SQ2  CONST_19  C7   C12  N2   C6    180.00   0.0  0
 SQ2  CONST_20  C11  C12  N2   C6      0.00   0.0  0
 SQ2  CONST_21  H18  C9   C8   C7    180.00   0.0  0
 SQ2  CONST_22  H12  C11  C12  C7    180.00   0.0  0
 SQ2  CONST_23  H6   C10  C9   C8    180.00   0.0  0
 SQ2  CONST_24  H5   C8   C9   C10   180.00   0.0  0
 SQ2  CONST_25  H18  C9   C10  C11   180.00   0.0  0
 SQ2  CONST_26  H5   C8   C7   C12   180.00   0.0  0
 SQ2  CONST_27  H6   C10  C11  C12   180.00   0.0  0
 SQ2  CONST_28  H12  C11  C10  C9    180.00   0.0  0
 SQ2  CONST_29  H12  C11  C12  N2      0.00   0.0  0
 SQ2  CONST_30  H5   C8   C7   N4      0.00   0.0  0
 SQ2  CONST_31  C6   C5   N1   C4      0.00   0.0  0
 SQ2  CONST_32  O1   C5   N1   C4    180.00   0.0  0
 SQ2  CONST_33  C13  N1   C5   C6    180.00   0.0  0
 SQ2  CONST_34  O1   C5   N1   C13     0.00   0.0  0
 SQ2  Var_01    C2   C3   C4   N1     55.14  30.0  1
 SQ2  Var_02    C2   C14  C13  N1    -55.83  30.0  1
 SQ2  Var_03    C14  C13  N1   C4     59.82  30.0  1
 SQ2  Var_04    C3   C4   N1   C13   -59.51  30.0  1
 SQ2  Var_05    C3   C4   N1   C5    103.95  30.0  1
 SQ2  Var_06    C14  C13  N1   C5   -104.47  30.0  1
 SQ2  Var_07    H16  C3   C4   N1    177.15  30.0  1
 SQ2  Var_08    H17  C3   C4   N1    -66.25  30.0  1
 SQ2  Var_09    H13  C14  C13  N1     65.53  30.0  1
 SQ2  Var_10    H14  C14  C13  N1   -177.81  30.0  1
 SQ2  Var_11    H7   C13  N1   C4   -177.11  30.0  1
 SQ2  Var_12    H8   C13  N1   C4    -60.23  30.0  1
 SQ2  Var_13    H1   C4   N1   C13    60.61  30.0  1
 SQ2  Var_14    H2   C4   N1   C13   176.85  30.0  1
 SQ2  Var_15    H1   C4   C3   C2    -63.76  30.0  1
 SQ2  Var_16    H2   C4   C3   C2    178.81  30.0  1
 SQ2  Var_17    H7   C13  C14  C2   -177.78  30.0  1
 SQ2  Var_18    H8   C13  C14  C2     63.01  30.0  1
 SQ2  Var_19    N2   C6   C5   N1    179.78  30.0  1
 SQ2  Var_20    C5   C6   N2   N3     98.28  30.0  2
 SQ2  Var_21    C12  N2   C6   C5    -74.72  30.0  2
 SQ2  Var_22    H3   C6   N2   N3   -139.26  30.0  2
 SQ2  Var_23    H4   C6   N2   N3    -23.29  30.0  2
 SQ2  Var_24    H1   C4   N1   C5   -135.93  30.0  1
 SQ2  Var_25    H2   C4   N1   C5    -19.69  30.0  1
 SQ2  Var_26    H7   C13  N1   C5     18.61  30.0  1
 SQ2  Var_27    H8   C13  N1   C5    135.49  30.0  1
 SQ2  Var_28    H3   C6   N2   C12    47.74  30.0  2
 SQ2  Var_29    H4   C6   N2   C12   163.71  30.0  2
 SQ2  Var_30    O1   C5   C6   N2      1.04  30.0  3
 SQ2  Var_31    H3   C6   C5   N1     58.48  30.0  1
 SQ2  Var_32    H4   C6   C5   N1    -61.07  30.0  1
 SQ2  Var_33    H3   C6   C5   O1   -120.26  30.0  1
 SQ2  Var_34    H4   C6   C5   O1    120.19  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SQ2  chir_01  C2  C3  C14  C1  positiv

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
 SQ2  plan-1  N3   0.020
 SQ2  plan-1  C6   0.020
 SQ2  plan-1  C7   0.020
 SQ2  plan-1  C8   0.020
 SQ2  plan-1  C10  0.020
 SQ2  plan-1  C11  0.020
 SQ2  plan-1  C12  0.020
 SQ2  plan-1  C9   0.020
 SQ2  plan-1  N2   0.020
 SQ2  plan-1  N4   0.020
 SQ2  plan-1  H6   0.020
 SQ2  plan-1  H12  0.020
 SQ2  plan-1  H18  0.020
 SQ2  plan-1  H5   0.020
 SQ2  plan-2  N1   0.020
 SQ2  plan-2  C4   0.020
 SQ2  plan-2  C5   0.020
 SQ2  plan-2  C6   0.020
 SQ2  plan-2  C13  0.020
 SQ2  plan-2  O1   0.020

