# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 14:14:31 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-1-(4-methylidenepiperidin-1-yl)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C=C1CCN(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
 SYH  SYH  "2-(1H-benzo[d][1,2,3]triazol-1-yl)-1-(4-methylenepiperidin-1-yl)ethan-1-one"
  ligand  35  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_SYH
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
 SYH  C4   C  CH2   0  -0.321  12.1477   1.4846  22.8389
 SYH  C14  C  CH2   0  -0.483  12.8036  -1.2630  22.1468
 SYH  C5   C  C     0   0.549  10.3805   0.9992  21.2420
 SYH  C6   C  CH2   0  -0.460   9.4836  -0.0591  20.5919
 SYH  C11  C  CR16  0  -0.290   6.6945   1.5011  20.9498
 SYH  C7   C  CR56  0   0.124   7.1379   1.6907  18.5483
 SYH  C8   C  CR16  0  -0.290   5.9784   2.4465  18.3434
 SYH  C9   C  CR16  0  -0.267   5.2027   2.7144  19.4478
 SYH  C10  C  CR16  0  -0.260   5.5580   2.2470  20.7320
 SYH  C12  C  CR56  0   0.393   7.4755   1.2352  19.8234
 SYH  C13  C  CH2   0  -0.333  11.4098  -0.8150  22.5903
 SYH  N1   N  NT    0  -0.452  11.1890   0.5761  22.2309
 SYH  N2   N  NR5   0  -0.378   8.6226   0.5463  19.6194
 SYH  C3   C  CH2   0  -0.487  13.5700   1.1211  22.4073
 SYH  N3   N  N     0  -0.059   8.9702   0.6007  18.3370
 SYH  C1   C  C2    0  -0.604  14.8838  -0.7434  23.4098
 SYH  C2   C  C     0   0.164  13.8446  -0.3280  22.6916
 SYH  N4   N  N     0  -0.319   8.1015   1.2644  17.6787
 SYH  O1   O  O     0  -0.473  10.3170   2.1565  20.8647
 SYH  H1   H  HCH2  0   0.271  11.9071   2.5077  22.5653
 SYH  H2   H  HCH2  0   0.253  12.0574   1.3995  23.9254
 SYH  H3   H  HCH2  0   0.253  12.9812  -2.2871  22.4784
 SYH  H4   H  HCH2  0   0.247  12.8352  -1.2596  21.0517
 SYH  H5   H  HCH2  0   0.312   8.8655  -0.5655  21.3350
 SYH  H6   H  HCH2  0   0.324  10.0780  -0.8221  20.0876
 SYH  H8   H  HCR6  0   0.271   5.7070   2.8035  17.3589
 SYH  H9   H  HCR6  0   0.263   4.2980   3.2971  19.3372
 SYH  H10  H  HCR6  0   0.266   4.9154   2.4859  21.5691
 SYH  H11  H  HCH2  0   0.261  11.3202  -0.9053  23.6762
 SYH  H12  H  HCH2  0   0.281  10.6489  -1.4610  22.1604
 SYH  H13  H  HCH2  0   0.246  13.6680   1.3149  21.3339
 SYH  H14  H  HCH2  0   0.251  14.2845   1.7649  22.9227
 SYH  H15  H  H     0   0.232  15.6105  -0.0472  23.8107
 SYH  H16  H  H     0   0.232  15.0458  -1.7943  23.6167
 SYH  H7   H  HCR6  0   0.281   6.9619   1.1474  21.9367

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
 SYH  N4   N3   aromatic  1.276  0.020  1.276
 SYH  N4   C7   aromatic  1.366  0.020  1.366
 SYH  N3   N2   aromatic  1.330  0.020  1.330
 SYH  C8   C7   aromatic  1.399  0.020  1.399
 SYH  C8   C9   aromatic  1.376  0.020  1.376
 SYH  C7   C12  aromatic  1.395  0.020  1.395
 SYH  C9   C10  aromatic  1.412  0.020  1.412
 SYH  N2   C12  aromatic  1.354  0.020  1.354
 SYH  N2   C6   single    1.433  0.020  1.433
 SYH  C12  C11  aromatic  1.396  0.020  1.396
 SYH  C6   C5   single    1.532  0.020  1.532
 SYH  C10  C11  aromatic  1.377  0.020  1.377
 SYH  O1   C5   double    1.219  0.020  1.219
 SYH  C5   N1   single    1.346  0.020  1.346
 SYH  N1   C13  single    1.454  0.020  1.454
 SYH  N1   C4   single    1.454  0.020  1.454
 SYH  C14  C13  single    1.530  0.020  1.530
 SYH  C14  C2   single    1.502  0.020  1.502
 SYH  C3   C4   single    1.530  0.020  1.530
 SYH  C3   C2   single    1.502  0.020  1.502
 SYH  C2   C1   double    1.330  0.020  1.330
 SYH  C4   H1   single    0.970  0.020  1.090
 SYH  C4   H2   single    0.970  0.020  1.090
 SYH  C14  H3   single    0.970  0.020  1.090
 SYH  C14  H4   single    0.970  0.020  1.090
 SYH  C6   H5   single    0.970  0.020  1.090
 SYH  C6   H6   single    0.970  0.020  1.090
 SYH  C11  H7   single    0.930  0.020  1.080
 SYH  C8   H8   single    0.930  0.020  1.080
 SYH  C9   H9   single    0.930  0.020  1.080
 SYH  C10  H10  single    0.930  0.020  1.080
 SYH  C13  H11  single    0.970  0.020  1.090
 SYH  C13  H12  single    0.970  0.020  1.090
 SYH  C3   H13  single    0.970  0.020  1.090
 SYH  C3   H14  single    0.970  0.020  1.090
 SYH  C1   H15  single    0.930  0.020  1.080
 SYH  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
 SYH  H2   C4   H1   107.77  3.000
 SYH  H2   C4   C3   109.79  3.000
 SYH  H1   C4   C3   111.02  3.000
 SYH  H2   C4   N1   108.20  3.000
 SYH  H1   C4   N1   109.70  3.000
 SYH  C3   C4   N1   110.28  3.000
 SYH  H4   C14  H3   107.58  3.000
 SYH  H4   C14  C2   109.92  3.000
 SYH  H3   C14  C2   111.18  3.000
 SYH  H4   C14  C13  108.38  3.000
 SYH  H3   C14  C13  109.58  3.000
 SYH  C2   C14  C13  110.13  3.000
 SYH  O1   C5   N1   123.87  3.000
 SYH  N1   C5   C6   116.51  3.000
 SYH  O1   C5   C6   119.61  3.000
 SYH  H6   C6   H5   107.40  3.000
 SYH  H6   C6   N2   108.01  3.000
 SYH  H5   C6   N2   108.53  3.000
 SYH  H6   C6   C5   111.13  3.000
 SYH  H5   C6   C5   111.30  3.000
 SYH  N2   C6   C5   110.35  3.000
 SYH  H7   C11  C12  122.37  3.000
 SYH  H7   C11  C10  121.70  3.000
 SYH  C12  C11  C10  115.93  3.000
 SYH  N4   C7   C12  108.01  3.000
 SYH  C12  C7   C8   120.71  3.000
 SYH  N4   C7   C8   131.29  3.000
 SYH  H8   C8   C9   121.66  3.000
 SYH  H8   C8   C7   121.29  3.000
 SYH  C9   C8   C7   117.05  3.000
 SYH  H9   C9   C10  118.80  3.000
 SYH  H9   C9   C8   119.62  3.000
 SYH  C10  C9   C8   121.58  3.000
 SYH  H10  C10  C9   118.76  3.000
 SYH  H10  C10  C11  119.18  3.000
 SYH  C9   C10  C11  122.07  3.000
 SYH  N2   C12  C7   103.50  3.000
 SYH  N2   C12  C11  133.83  3.000
 SYH  C7   C12  C11  122.66  3.000
 SYH  H12  C13  H11  106.65  3.000
 SYH  H12  C13  N1   111.39  3.000
 SYH  H11  C13  N1   108.19  3.000
 SYH  H12  C13  C14  110.43  3.000
 SYH  H11  C13  C14  109.78  3.000
 SYH  N1   C13  C14  110.30  3.000
 SYH  C13  N1   C5   125.02  3.000
 SYH  C13  N1   C4   113.23  3.000
 SYH  C5   N1   C4   120.47  3.000
 SYH  N3   N2   C12  110.25  3.000
 SYH  C12  N2   C6   128.46  3.000
 SYH  N3   N2   C6   120.97  3.000
 SYH  H14  C3   H13  107.45  3.000
 SYH  H14  C3   C2   111.11  3.000
 SYH  H13  C3   C2   109.87  3.000
 SYH  H14  C3   C4   109.59  3.000
 SYH  H13  C3   C4   108.52  3.000
 SYH  C2   C3   C4   110.23  3.000
 SYH  N4   N3   N2   109.93  3.000
 SYH  H16  C1   H15  116.91  3.000
 SYH  H16  C1   C2   121.54  3.000
 SYH  H15  C1   C2   121.56  3.000
 SYH  C1   C2   C3   123.13  3.000
 SYH  C1   C2   C14  122.90  3.000
 SYH  C3   C2   C14  113.91  3.000
 SYH  N3   N4   C7   108.30  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
 SYH  CONST_01  N4   C7   C12  C11   180.00   0.0  0
 SYH  CONST_02  C8   C7   C12  C11     0.00   0.0  0
 SYH  CONST_03  N3   N2   C12  C11   180.00   0.0  0
 SYH  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 SYH  CONST_05  N2   N3   N4   C7      0.00   0.0  0
 SYH  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 SYH  CONST_07  N3   N2   C12  C7      0.00   0.0  0
 SYH  CONST_08  C10  C11  C12  C7      0.00   0.0  0
 SYH  CONST_09  N3   N4   C7   C8    180.00   0.0  0
 SYH  CONST_10  N2   C12  C7   C8    180.00   0.0  0
 SYH  CONST_11  N4   C7   C8   C9    180.00   0.0  0
 SYH  CONST_12  C12  C7   C8   C9      0.00   0.0  0
 SYH  CONST_13  C12  C11  C10  C9      0.00   0.0  0
 SYH  CONST_14  N2   C12  C11  C10   180.00   0.0  0
 SYH  CONST_15  N3   N4   C7   C12     0.00   0.0  0
 SYH  CONST_16  N4   N3   N2   C12     0.00   0.0  0
 SYH  CONST_17  N4   C7   C12  N2      0.00   0.0  0
 SYH  CONST_18  N4   N3   N2   C6    180.00   0.0  0
 SYH  CONST_19  C7   C12  N2   C6    180.00   0.0  0
 SYH  CONST_20  C11  C12  N2   C6      0.00   0.0  0
 SYH  CONST_21  H9   C9   C10  C11   180.00   0.0  0
 SYH  CONST_22  H9   C9   C8   C7    180.00   0.0  0
 SYH  CONST_23  H7   C11  C12  C7    180.00   0.0  0
 SYH  CONST_24  H10  C10  C9   C8    180.00   0.0  0
 SYH  CONST_25  H7   C11  C10  C9    180.00   0.0  0
 SYH  CONST_26  H8   C8   C9   C10   180.00   0.0  0
 SYH  CONST_27  H8   C8   C7   C12   180.00   0.0  0
 SYH  CONST_28  H10  C10  C11  C12   180.00   0.0  0
 SYH  CONST_29  H7   C11  C12  N2      0.00   0.0  0
 SYH  CONST_30  H8   C8   C7   N4      0.00   0.0  0
 SYH  CONST_31  C6   C5   N1   C4    180.00   0.0  0
 SYH  CONST_32  O1   C5   N1   C4      0.00   0.0  0
 SYH  CONST_33  C13  N1   C5   C6      0.00   0.0  0
 SYH  CONST_34  O1   C5   N1   C13   180.00   0.0  0
 SYH  Var_01    C14  C13  N1   C4    -59.81  30.0  1
 SYH  Var_02    C14  C2   C3   C4     51.47  30.0  1
 SYH  Var_03    C3   C4   N1   C13    59.66  30.0  1
 SYH  Var_04    C3   C2   C14  C13   -51.55  30.0  1
 SYH  Var_05    C2   C14  C13  N1     53.78  30.0  1
 SYH  Var_06    C2   C3   C4   N1    -53.55  30.0  1
 SYH  Var_07    C1   C2   C3   C4   -125.77  30.0  1
 SYH  Var_08    C5   N1   C13  C14   107.22  30.0  1
 SYH  Var_09    C3   C4   N1   C5   -108.03  30.0  1
 SYH  Var_10    C1   C2   C14  C13   125.70  30.0  1
 SYH  Var_11    H11  C13  N1   C4     60.28  30.0  1
 SYH  Var_12    H12  C13  N1   C4    177.19  30.0  1
 SYH  Var_13    H13  C3   C2   C14   -68.07  30.0  1
 SYH  Var_14    H14  C3   C2   C14   173.16  30.0  1
 SYH  Var_15    H1   C4   N1   C13  -177.76  30.0  1
 SYH  Var_16    H2   C4   N1   C13   -60.43  30.0  1
 SYH  Var_17    H3   C14  C13  N1    176.39  30.0  1
 SYH  Var_18    H4   C14  C13  N1    -66.49  30.0  1
 SYH  Var_19    H13  C3   C4   N1     66.81  30.0  1
 SYH  Var_20    H14  C3   C4   N1   -176.13  30.0  1
 SYH  Var_21    H3   C14  C2   C3   -173.20  30.0  1
 SYH  Var_22    H4   C14  C2   C3     67.78  30.0  1
 SYH  Var_23    H11  C13  C14  C2    -65.34  30.0  1
 SYH  Var_24    H12  C13  C14  C2    177.34  30.0  1
 SYH  Var_25    H1   C4   C3   C2   -175.36  30.0  1
 SYH  Var_26    H2   C4   C3   C2     65.58  30.0  1
 SYH  Var_27    N3   N2   C6   C5     93.49  30.0  2
 SYH  Var_28    C12  N2   C6   C5    -79.35  30.0  2
 SYH  Var_29    N2   C6   C5   N1    176.40  30.0  1
 SYH  Var_30    H15  C1   C2   C14  -178.64   0.0  2
 SYH  Var_31    H16  C1   C2   C14     1.69   0.0  2
 SYH  Var_32    H15  C1   C2   C3     -1.64   0.0  2
 SYH  Var_33    H16  C1   C2   C3    178.68   0.0  2
 SYH  Var_34    H11  C13  N1   C5   -132.69  30.0  1
 SYH  Var_35    H12  C13  N1   C5    -15.78  30.0  1
 SYH  Var_36    H1   C4   N1   C5     14.55  30.0  1
 SYH  Var_37    H2   C4   N1   C5    131.88  30.0  1
 SYH  Var_38    H5   C6   N2   C12    42.86  30.0  2
 SYH  Var_39    H6   C6   N2   C12   159.00  30.0  2
 SYH  Var_40    H5   C6   N2   N3   -144.30  30.0  2
 SYH  Var_41    H6   C6   N2   N3    -28.17  30.0  2
 SYH  Var_42    H3   C14  C2   C1      4.04  30.0  1
 SYH  Var_43    H4   C14  C2   C1   -114.97  30.0  1
 SYH  Var_44    H13  C3   C2   C1    114.69  30.0  1
 SYH  Var_45    H14  C3   C2   C1     -4.08  30.0  1
 SYH  Var_46    O1   C5   C6   N2     -2.54  30.0  3
 SYH  Var_47    H5   C6   C5   N1     55.84  30.0  1
 SYH  Var_48    H6   C6   C5   N1    -63.81  30.0  1
 SYH  Var_49    H5   C6   C5   O1   -123.10  30.0  1
 SYH  Var_50    H6   C6   C5   O1    117.25  30.0  1

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
 SYH  plan-1  C6   0.020
 SYH  plan-1  C11  0.020
 SYH  plan-1  C7   0.020
 SYH  plan-1  C8   0.020
 SYH  plan-1  C9   0.020
 SYH  plan-1  C10  0.020
 SYH  plan-1  C12  0.020
 SYH  plan-1  N2   0.020
 SYH  plan-1  N3   0.020
 SYH  plan-1  N4   0.020
 SYH  plan-1  H8   0.020
 SYH  plan-1  H9   0.020
 SYH  plan-1  H10  0.020
 SYH  plan-1  H7   0.020
 SYH  plan-2  C4   0.020
 SYH  plan-2  C5   0.020
 SYH  plan-2  C6   0.020
 SYH  plan-2  C13  0.020
 SYH  plan-2  N1   0.020
 SYH  plan-2  O1   0.020
 SYH  plan-3  C14  0.020
 SYH  plan-3  C3   0.020
 SYH  plan-3  C1   0.020
 SYH  plan-3  C2   0.020
 SYH  plan-3  H15  0.020
 SYH  plan-3  H16  0.020

