# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 22:50:38 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(benzotriazol-1-yl)-1-[(4~{S})-4-methyl-6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N(CCc2sccc12)C(=O)Cn3nnc4ccccc34
#
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
 U7W  U7W  "2-(benzotriazol-1-yl)-1-[(4~{S})-4-methyl-6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-yl]ethanone"
  ligand  38  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U7W
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
 U7W  C4   C  CR15  0  -0.205  13.9503   2.0674  23.0716
 U7W  C14  C  CR16  0  -0.260   4.7507   2.5046  20.6044
 U7W  C5   C  CR15  0  -0.471  15.0517   1.2795  23.1761
 U7W  C6   C  CR5   0  -0.255  13.0248  -0.0007  22.5737
 U7W  C11  C  CR56  0   0.125   6.2794   1.8259  18.4190
 U7W  C7   C  CH2   0  -0.473  11.9837  -1.0090  22.2243
 U7W  C8   C  CH2   0  -0.346  10.6230  -0.4006  22.5389
 U7W  C10  C  CH2   0  -0.465   8.6823   0.2112  20.5051
 U7W  C12  C  CR16  0  -0.290   5.1119   2.5650  18.1989
 U7W  C13  C  CR16  0  -0.267   4.3620   2.8950  19.3043
 U7W  N1   N  NT    0  -0.472  10.5121   0.9336  21.9707
 U7W  N2   N  NR5   0  -0.378   7.7953   0.7517  19.5184
 U7W  C3   C  CR5   0   0.183  12.7800   1.3305  22.7215
 U7W  N3   N  N     0  -0.059   8.1102   0.7294  18.2264
 U7W  C1   C  CH3   0  -0.646  10.8627   2.5500  23.8035
 U7W  C2   C  CH1   0  -0.153  11.4211   1.9395  22.5197
 U7W  S1   S  S2    0   0.207  14.6822  -0.3669  22.8550
 U7W  O1   O  O     0  -0.474   9.5208   2.4401  20.6084
 U7W  N4   N  N     0  -0.318   7.2227   1.3505  17.5523
 U7W  C15  C  CR16  0  -0.290   5.8961   1.7773  20.8375
 U7W  C16  C  CR56  0   0.393   6.6507   1.4484  19.7098
 U7W  H1   H  HCR5  0   0.263  13.9666   3.1370  23.2321
 U7W  H3   H  HCR5  0   0.291  16.0599   1.5759  23.4209
 U7W  H4   H  HCH2  0   0.263  12.0400  -1.2828  21.1670
 U7W  H5   H  HCH2  0   0.264  12.1056  -1.9287  22.7996
 U7W  H6   H  HCH2  0   0.289   9.8323  -1.0481  22.1726
 U7W  H7   H  HCH2  0   0.269  10.4933  -0.3361  23.6223
 U7W  H8   H  HCH2  0   0.313   8.0807  -0.2185  21.3074
 U7W  H9   H  HCH2  0   0.325   9.2473  -0.6025  20.0487
 U7W  H10  H  HCR6  0   0.271   4.8149   2.8625  17.2021
 U7W  H11  H  HCR6  0   0.263   3.4524   3.4678  19.1823
 U7W  H12  H  HCH3  0   0.240  11.5450   3.3042  24.1955
 U7W  H13  H  HCH3  0   0.241   9.9041   3.0319  23.6128
 U7W  H14  H  HCH3  0   0.232  10.7242   1.7926  24.5757
 U7W  H15  H  HCH1  0   0.278  11.5127   2.7302  21.7745
 U7W  H16  H  HCR6  0   0.281   6.1896   1.4836  21.8366
 U7W  C9   C  C     0   0.563   9.6156   1.3030  21.0376
 U7W  H2   H  HCR6  0   0.267   4.1272   2.7894  21.4416

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
 U7W  N4   N3   aromatic  1.276  0.020  1.276
 U7W  N4   C11  aromatic  1.366  0.020  1.366
 U7W  C12  C11  aromatic  1.399  0.020  1.399
 U7W  C12  C13  aromatic  1.376  0.020  1.376
 U7W  N3   N2   aromatic  1.330  0.020  1.330
 U7W  C11  C16  aromatic  1.395  0.020  1.395
 U7W  C13  C14  aromatic  1.412  0.020  1.412
 U7W  N2   C16  aromatic  1.354  0.020  1.354
 U7W  N2   C10  single    1.433  0.020  1.433
 U7W  C16  C15  aromatic  1.396  0.020  1.396
 U7W  C14  C15  aromatic  1.377  0.020  1.377
 U7W  C10  C9   single    1.532  0.020  1.532
 U7W  O1   C9   double    1.219  0.020  1.219
 U7W  C9   N1   single    1.346  0.020  1.346
 U7W  S1   C6   aromatic  1.721  0.020  1.721
 U7W  S1   C5   aromatic  1.718  0.020  1.718
 U7W  C7   C6   single    1.491  0.020  1.491
 U7W  C7   C8   single    1.523  0.020  1.523
 U7W  N1   C2   single    1.463  0.020  1.463
 U7W  N1   C8   single    1.454  0.020  1.454
 U7W  C6   C3   aromatic  1.362  0.020  1.362
 U7W  C3   C2   single    1.503  0.020  1.503
 U7W  C3   C4   aromatic  1.427  0.020  1.427
 U7W  C5   C4   aromatic  1.358  0.020  1.358
 U7W  C2   C1   single    1.527  0.020  1.527
 U7W  C4   H1   single    0.930  0.020  1.080
 U7W  C14  H2   single    0.930  0.020  1.080
 U7W  C5   H3   single    0.930  0.020  1.080
 U7W  C7   H4   single    0.970  0.020  1.090
 U7W  C7   H5   single    0.970  0.020  1.090
 U7W  C8   H6   single    0.970  0.020  1.090
 U7W  C8   H7   single    0.970  0.020  1.090
 U7W  C10  H8   single    0.970  0.020  1.090
 U7W  C10  H9   single    0.970  0.020  1.090
 U7W  C12  H10  single    0.930  0.020  1.080
 U7W  C13  H11  single    0.930  0.020  1.080
 U7W  C1   H12  single    0.970  0.020  1.090
 U7W  C1   H13  single    0.970  0.020  1.090
 U7W  C1   H14  single    0.970  0.020  1.090
 U7W  C2   H15  single    0.970  0.020  1.090
 U7W  C15  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
 U7W  H1   C4   C3   124.03  3.000
 U7W  H1   C4   C5   123.36  3.000
 U7W  C3   C4   C5   112.61  3.000
 U7W  H2   C14  C15  119.17  3.000
 U7W  H2   C14  C13  118.75  3.000
 U7W  C15  C14  C13  122.08  3.000
 U7W  H3   C5   S1   120.45  3.000
 U7W  H3   C5   C4   128.01  3.000
 U7W  S1   C5   C4   111.54  3.000
 U7W  S1   C6   C3   111.31  3.000
 U7W  C3   C6   C7   124.14  3.000
 U7W  S1   C6   C7   124.55  3.000
 U7W  C16  C11  N4   108.00  3.000
 U7W  C16  C11  C12  120.70  3.000
 U7W  N4   C11  C12  131.30  3.000
 U7W  H5   C7   H4   107.03  3.000
 U7W  H5   C7   C8   109.11  3.000
 U7W  H4   C7   C8   110.22  3.000
 U7W  H5   C7   C6   111.61  3.000
 U7W  H4   C7   C6   111.10  3.000
 U7W  C8   C7   C6   107.77  3.000
 U7W  H7   C8   H6   106.45  3.000
 U7W  H7   C8   N1   108.91  3.000
 U7W  H6   C8   N1   111.09  3.000
 U7W  H7   C8   C7   109.52  3.000
 U7W  H6   C8   C7   110.04  3.000
 U7W  N1   C8   C7   110.72  3.000
 U7W  H9   C10  H8   107.43  3.000
 U7W  H9   C10  N2   108.30  3.000
 U7W  H8   C10  N2   108.28  3.000
 U7W  H9   C10  C9   111.20  3.000
 U7W  H8   C10  C9   111.16  3.000
 U7W  N2   C10  C9   110.35  3.000
 U7W  H10  C12  C13  121.65  3.000
 U7W  H10  C12  C11  121.28  3.000
 U7W  C13  C12  C11  117.07  3.000
 U7W  H11  C13  C12  119.64  3.000
 U7W  H11  C13  C14  118.80  3.000
 U7W  C12  C13  C14  121.56  3.000
 U7W  C2   N1   C9   119.04  3.000
 U7W  C2   N1   C8   115.91  3.000
 U7W  C9   N1   C8   125.00  3.000
 U7W  C16  N2   N3   110.25  3.000
 U7W  C16  N2   C10  128.34  3.000
 U7W  N3   N2   C10  121.07  3.000
 U7W  C2   C3   C6   122.97  3.000
 U7W  C2   C3   C4   124.43  3.000
 U7W  C6   C3   C4   112.60  3.000
 U7W  N4   N3   N2   109.90  3.000
 U7W  H14  C1   H13  108.63  3.000
 U7W  H14  C1   H12  107.79  3.000
 U7W  H13  C1   H12  107.92  3.000
 U7W  H14  C1   C2   111.35  3.000
 U7W  H13  C1   C2   110.56  3.000
 U7W  H12  C1   C2   110.49  3.000
 U7W  H15  C2   C1   108.38  3.000
 U7W  H15  C2   C3   108.04  3.000
 U7W  C1   C2   C3   112.31  3.000
 U7W  H15  C2   N1   107.13  3.000
 U7W  C1   C2   N1   111.29  3.000
 U7W  C3   C2   N1   109.49  3.000
 U7W  C6   S1   C5    91.94  3.000
 U7W  N3   N4   C11  108.33  3.000
 U7W  H16  C15  C16  122.37  3.000
 U7W  H16  C15  C14  121.70  3.000
 U7W  C16  C15  C14  115.93  3.000
 U7W  C15  C16  N2   133.83  3.000
 U7W  C15  C16  C11  122.66  3.000
 U7W  N2   C16  C11  103.51  3.000
 U7W  O1   C9   N1   123.51  3.000
 U7W  N1   C9   C10  116.82  3.000
 U7W  O1   C9   C10  119.67  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
 U7W  CONST_01  S1   C6   C3   C4      0.00   0.0  0
 U7W  CONST_02  C6   S1   C5   C4      0.00   0.0  0
 U7W  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 U7W  CONST_04  C11  C16  C15  C14     0.00   0.0  0
 U7W  CONST_05  N2   C16  C15  C14   180.00   0.0  0
 U7W  CONST_06  C3   C6   S1   C5      0.00   0.0  0
 U7W  CONST_07  C6   C3   C4   C5      0.00   0.0  0
 U7W  CONST_08  N2   N3   N4   C11     0.00   0.0  0
 U7W  CONST_09  N3   N2   C16  C11     0.00   0.0  0
 U7W  CONST_10  N3   N4   C11  C12   180.00   0.0  0
 U7W  CONST_11  N2   C16  C11  C12   180.00   0.0  0
 U7W  CONST_12  C15  C16  C11  C12     0.00   0.0  0
 U7W  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 U7W  CONST_14  N4   C11  C12  C13   180.00   0.0  0
 U7W  CONST_15  C16  C11  C12  C13     0.00   0.0  0
 U7W  CONST_16  C16  C15  C14  C13     0.00   0.0  0
 U7W  CONST_17  N4   C11  C16  N2      0.00   0.0  0
 U7W  CONST_18  S1   C5   C4   C3      0.00   0.0  0
 U7W  CONST_19  C16  C11  N4   N3      0.00   0.0  0
 U7W  CONST_20  C15  C16  N2   N3    180.00   0.0  0
 U7W  CONST_21  C16  N2   N3   N4      0.00   0.0  0
 U7W  CONST_22  C15  C16  C11  N4    180.00   0.0  0
 U7W  CONST_23  C10  N2   C16  C11   180.00   0.0  0
 U7W  CONST_24  N4   N3   N2   C10   180.00   0.0  0
 U7W  CONST_25  C15  C16  N2   C10     0.00   0.0  0
 U7W  CONST_26  H10  C12  C13  C14   180.00   0.0  0
 U7W  CONST_27  H3   C5   S1   C6    180.00   0.0  0
 U7W  CONST_28  H1   C4   C3   C6    180.00   0.0  0
 U7W  CONST_29  H11  C13  C12  C11   180.00   0.0  0
 U7W  CONST_30  H16  C15  C16  C11   180.00   0.0  0
 U7W  CONST_31  H2   C14  C13  C12   180.00   0.0  0
 U7W  CONST_32  H16  C15  C14  C13   180.00   0.0  0
 U7W  CONST_33  H16  C15  C16  N2      0.00   0.0  0
 U7W  CONST_34  H3   C5   C4   C3    180.00   0.0  0
 U7W  CONST_35  H1   C4   C3   C2      0.00   0.0  0
 U7W  CONST_36  H1   C4   C5   S1    180.00   0.0  0
 U7W  CONST_37  H10  C12  C11  N4      0.00   0.0  0
 U7W  CONST_38  H11  C13  C14  C15   180.00   0.0  0
 U7W  CONST_39  H10  C12  C11  C16   180.00   0.0  0
 U7W  CONST_40  H2   C14  C15  C16   180.00   0.0  0
 U7W  CONST_41  C10  C9   N1   C8      0.00   0.0  0
 U7W  CONST_42  O1   C9   N1   C8    180.00   0.0  0
 U7W  CONST_43  C2   N1   C9   C10   180.00   0.0  0
 U7W  CONST_44  O1   C9   N1   C2      0.00   0.0  0
 U7W  Var_01    N1   C8   C7   C6     49.06  30.0  1
 U7W  Var_02    C2   N1   C8   C7    -64.85  30.0  1
 U7W  Var_03    S1   C6   C7   C8    160.33  30.0  1
 U7W  Var_04    C3   C6   C7   C8    -19.11  30.0  1
 U7W  Var_05    C9   N1   C8   C7    117.91  30.0  1
 U7W  Var_06    H6   C8   C7   C6    172.25  30.0  1
 U7W  Var_07    H7   C8   C7   C6    -71.06  30.0  1
 U7W  Var_08    H4   C7   C8   N1    -72.33  30.0  1
 U7W  Var_09    H5   C7   C8   N1    170.42  30.0  1
 U7W  Var_10    H4   C7   C6   C3    101.73  30.0  1
 U7W  Var_11    H5   C7   C6   C3   -138.90  30.0  1
 U7W  Var_12    H6   C8   N1   C2    172.56  30.0  1
 U7W  Var_13    H7   C8   N1   C2     55.63  30.0  1
 U7W  Var_14    H4   C7   C6   S1    -78.83  30.0  1
 U7W  Var_15    H5   C7   C6   S1     40.54  30.0  1
 U7W  Var_16    N3   N2   C10  C9     91.85  30.0  3
 U7W  Var_17    C16  N2   C10  C9    -80.88  30.0  3
 U7W  Var_18    N2   C10  C9   N1   -179.65  30.0  1
 U7W  Var_19    H6   C8   N1   C9     -4.68  30.0  1
 U7W  Var_20    H7   C8   N1   C9   -121.61  30.0  1
 U7W  Var_21    H8   C10  N2   N3   -146.28  30.0  2
 U7W  Var_22    H9   C10  N2   N3    -30.08  30.0  2
 U7W  Var_23    H8   C10  N2   C16    41.00  30.0  2
 U7W  Var_24    H9   C10  N2   C16   157.20  30.0  2
 U7W  Var_25    O1   C9   C10  N2      0.19  30.0  3
 U7W  Var_26    H8   C10  C9   N1     60.20  30.0  1
 U7W  Var_27    H9   C10  C9   N1    -59.45  30.0  1
 U7W  Var_28    H8   C10  C9   O1   -119.96  30.0  1
 U7W  Var_29    H9   C10  C9   O1    120.39  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
 U7W  chir_01  C2  N1  C3  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
 U7W  plan-1  C14  0.020
 U7W  plan-1  C11  0.020
 U7W  plan-1  C10  0.020
 U7W  plan-1  C12  0.020
 U7W  plan-1  C13  0.020
 U7W  plan-1  N2   0.020
 U7W  plan-1  N3   0.020
 U7W  plan-1  N4   0.020
 U7W  plan-1  C15  0.020
 U7W  plan-1  C16  0.020
 U7W  plan-1  H10  0.020
 U7W  plan-1  H11  0.020
 U7W  plan-1  H16  0.020
 U7W  plan-1  H2   0.020
 U7W  plan-2  C4   0.020
 U7W  plan-2  C5   0.020
 U7W  plan-2  C6   0.020
 U7W  plan-2  C7   0.020
 U7W  plan-2  C3   0.020
 U7W  plan-2  C2   0.020
 U7W  plan-2  S1   0.020
 U7W  plan-2  H1   0.020
 U7W  plan-2  H3   0.020
 U7W  plan-3  C8   0.020
 U7W  plan-3  C10  0.020
 U7W  plan-3  N1   0.020
 U7W  plan-3  C2   0.020
 U7W  plan-3  O1   0.020
 U7W  plan-3  C9   0.020

