# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 20:28:40 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{N}-methyl-4,5-dihydrobenzo[g][1]benzothiole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1sc2c(CCc3ccccc23)c1
#
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
 U5E  U5E  "N-methyl-4,5-dihydrobenzo[g]benzothiophene-2-carboxamide"
  ligand  30  17  .  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_U5E
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
 U5E  C01  C  CH3   0  -0.514   9.0758  -3.0124  5.9572
 U5E  C03  C  C     0   0.537   6.7129  -3.4069  5.5268
 U5E  C05  C  CR5   0  -0.291   5.5451  -4.2875  5.7134
 U5E  C06  C  CR15  0  -0.246   5.3934  -5.5012  6.3278
 U5E  C07  C  CR56  0   0.174   4.0638  -5.9761  6.2817
 U5E  C08  C  C     0  -0.503   3.5289  -7.2668  6.8197
 U5E  C09  C  C     0  -0.521   2.0731  -7.0869  7.2419
 U5E  C10  C  CR66  0   0.050   1.2426  -6.4085  6.1836
 U5E  C11  C  CR16  0  -0.309  -0.0946  -6.7270  5.9907
 U5E  C12  C  CR16  0  -0.252  -0.8659  -6.0457  5.0570
 U5E  C13  C  CR16  0  -0.255  -0.2986  -5.0301  4.2996
 U5E  C14  C  CR16  0  -0.326   1.0382  -4.7067  4.4716
 U5E  C15  C  CR66  0   0.166   1.8148  -5.3864  5.4086
 U5E  C16  C  CR56  0  -0.288   3.2261  -5.1102  5.6231
 U5E  N02  N  NH1   0  -0.647   7.8694  -3.7971  6.0777
 U5E  O04  O  O     0  -0.492   6.5936  -2.3648  4.8906
 U5E  S17  S  S2    0   0.262   4.0558  -3.7156  5.0657
 U5E  H1   H  HCH3  0   0.251   9.8605  -3.5049  6.5238
 U5E  H2   H  HCH3  0   0.240   9.4026  -2.9275  4.9201
 U5E  H3   H  HCH3  0   0.240   8.9427  -2.0073  6.3580
 U5E  H4   H  HCR5  0   0.269   6.1953  -6.0517  6.8030
 U5E  H5   H  H     0   0.254   3.6068  -8.0445  6.0524
 U5E  H6   H  H     0   0.260   4.1247  -7.6067  7.6678
 U5E  H7   H  H     0   0.254   2.0456  -6.4732  8.1496
 U5E  H8   H  H     0   0.260   1.6321  -8.0492  7.5044
 U5E  H9   H  HCR6  0   0.251  -0.5407  -7.5176  6.5827
 U5E  H10  H  HCR6  0   0.255  -1.9070  -6.3087  4.9220
 U5E  H11  H  HCR6  0   0.257  -0.8927  -4.4960  3.5699
 U5E  H12  H  HCR6  0   0.250   1.4803  -3.9265  3.8627
 U5E  H13  H  HNH1  0   0.413   7.9186  -4.6577  6.5959

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
 U5E  C13  C14  aromatic  1.386  0.020  1.386
 U5E  C13  C12  aromatic  1.388  0.020  1.388
 U5E  C14  C15  aromatic  1.394  0.020  1.394
 U5E  S17  C16  aromatic  1.716  0.020  1.716
 U5E  S17  C05  aromatic  1.722  0.020  1.722
 U5E  C12  C11  aromatic  1.390  0.020  1.390
 U5E  O04  C03  double    1.227  0.020  1.227
 U5E  C15  C16  aromatic  1.454  0.020  1.454
 U5E  C15  C10  aromatic  1.405  0.020  1.405
 U5E  C03  C05  single    1.475  0.020  1.475
 U5E  C03  N02  single    1.339  0.020  1.339
 U5E  C16  C07  aromatic  1.373  0.020  1.373
 U5E  C05  C06  aromatic  1.369  0.020  1.369
 U5E  C01  N02  single    1.444  0.020  1.444
 U5E  C11  C10  aromatic  1.388  0.020  1.388
 U5E  C10  C09  single    1.507  0.020  1.507
 U5E  C07  C06  aromatic  1.413  0.020  1.413
 U5E  C07  C08  single    1.497  0.020  1.497
 U5E  C08  C09  single    1.526  0.020  1.526
 U5E  C01  H1   single    0.970  0.020  1.090
 U5E  C01  H2   single    0.970  0.020  1.090
 U5E  C01  H3   single    0.970  0.020  1.090
 U5E  C06  H4   single    0.930  0.020  1.080
 U5E  C08  H5   single    0.970  0.020  1.090
 U5E  C08  H6   single    0.970  0.020  1.090
 U5E  C09  H7   single    0.970  0.020  1.090
 U5E  C09  H8   single    0.970  0.020  1.090
 U5E  C11  H9   single    0.930  0.020  1.080
 U5E  C12  H10  single    0.930  0.020  1.080
 U5E  C13  H11  single    0.930  0.020  1.080
 U5E  C14  H12  single    0.930  0.020  1.080
 U5E  N02  H13  single    0.860  0.020  1.020

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
 U5E  H3   C01  H2   108.32  3.000
 U5E  H3   C01  H1   108.33  3.000
 U5E  H2   C01  H1   108.35  3.000
 U5E  H3   C01  N02  111.61  3.000
 U5E  H2   C01  N02  111.84  3.000
 U5E  H1   C01  N02  108.28  3.000
 U5E  O04  C03  N02  123.02  3.000
 U5E  N02  C03  C05  117.25  3.000
 U5E  O04  C03  C05  119.73  3.000
 U5E  S17  C05  C06  111.56  3.000
 U5E  C06  C05  C03  132.39  3.000
 U5E  S17  C05  C03  116.05  3.000
 U5E  H4   C06  C07  122.72  3.000
 U5E  H4   C06  C05  124.46  3.000
 U5E  C07  C06  C05  112.82  3.000
 U5E  C16  C07  C08  119.87  3.000
 U5E  C08  C07  C06  127.91  3.000
 U5E  C16  C07  C06  112.20  3.000
 U5E  H6   C08  H5   106.53  3.000
 U5E  H6   C08  C09  110.04  3.000
 U5E  H5   C08  C09  110.21  3.000
 U5E  H6   C08  C07  110.67  3.000
 U5E  H5   C08  C07  109.57  3.000
 U5E  C09  C08  C07  109.79  3.000
 U5E  H8   C09  H7   106.54  3.000
 U5E  H8   C09  C10  110.09  3.000
 U5E  H7   C09  C10  108.41  3.000
 U5E  H8   C09  C08  110.38  3.000
 U5E  H7   C09  C08  108.60  3.000
 U5E  C10  C09  C08  112.61  3.000
 U5E  C15  C10  C11  118.87  3.000
 U5E  C11  C10  C09  121.69  3.000
 U5E  C15  C10  C09  119.38  3.000
 U5E  H9   C11  C12  119.75  3.000
 U5E  H9   C11  C10  119.21  3.000
 U5E  C12  C11  C10  121.04  3.000
 U5E  H10  C12  C13  120.19  3.000
 U5E  H10  C12  C11  119.91  3.000
 U5E  C13  C12  C11  119.90  3.000
 U5E  H11  C13  C14  119.88  3.000
 U5E  H11  C13  C12  120.31  3.000
 U5E  C14  C13  C12  119.81  3.000
 U5E  H12  C14  C15  120.09  3.000
 U5E  H12  C14  C13  119.45  3.000
 U5E  C15  C14  C13  120.46  3.000
 U5E  C16  C15  C14  123.18  3.000
 U5E  C16  C15  C10  116.89  3.000
 U5E  C14  C15  C10  119.91  3.000
 U5E  S17  C16  C15  125.16  3.000
 U5E  C15  C16  C07  122.90  3.000
 U5E  S17  C16  C07  111.92  3.000
 U5E  H13  N02  C03  120.24  3.000
 U5E  H13  N02  C01  117.84  3.000
 U5E  C03  N02  C01  121.92  3.000
 U5E  C16  S17  C05   91.50  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
 U5E  CONST_01  C15  C16  S17  C05   180.00   0.0  0
 U5E  CONST_02  C07  C16  S17  C05     0.00   0.0  0
 U5E  CONST_03  C16  C07  C06  C05     0.00   0.0  0
 U5E  CONST_04  C16  S17  C05  C06     0.00   0.0  0
 U5E  CONST_05  S17  C16  C07  C06     0.00   0.0  0
 U5E  CONST_06  C15  C16  C07  C06   180.00   0.0  0
 U5E  CONST_09  S17  C05  C06  C07     0.00   0.0  0
 U5E  CONST_11  C13  C14  C15  C10     0.00   0.0  0
 U5E  CONST_12  S17  C16  C15  C10   180.00   0.0  0
 U5E  CONST_13  C13  C12  C11  C10     0.00   0.0  0
 U5E  CONST_14  C14  C13  C12  C11     0.00   0.0  0
 U5E  CONST_15  C14  C15  C10  C11     0.00   0.0  0
 U5E  CONST_16  C16  C15  C10  C11   180.00   0.0  0
 U5E  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 U5E  CONST_18  C15  C10  C11  C12     0.00   0.0  0
 U5E  CONST_19  C16  C15  C14  C13   180.00   0.0  0
 U5E  CONST_21  C16  S17  C05  C03   180.00   0.0  0
 U5E  CONST_22  C07  C06  C05  C03   180.00   0.0  0
 U5E  CONST_23  H4   C06  C07  C08     0.00   0.0  0
 U5E  CONST_24  H9   C11  C10  C09     0.00   0.0  0
 U5E  CONST_25  H12  C14  C15  C10   180.00   0.0  0
 U5E  CONST_26  H10  C12  C11  C10   180.00   0.0  0
 U5E  CONST_27  H11  C13  C12  C11   180.00   0.0  0
 U5E  CONST_28  H12  C14  C13  C12   180.00   0.0  0
 U5E  CONST_29  H9   C11  C12  C13   180.00   0.0  0
 U5E  CONST_30  H10  C12  C13  C14   180.00   0.0  0
 U5E  CONST_31  H11  C13  C14  C15   180.00   0.0  0
 U5E  CONST_32  H9   C11  C10  C15   180.00   0.0  0
 U5E  CONST_33  H12  C14  C15  C16     0.00   0.0  0
 U5E  CONST_34  H4   C06  C07  C16   180.00   0.0  0
 U5E  CONST_35  H4   C06  C05  S17   180.00   0.0  0
 U5E  CONST_36  C05  C03  N02  C01   180.00   0.0  0
 U5E  CONST_37  H13  N02  C03  C05     0.00   0.0  0
 U5E  CONST_38  O04  C03  N02  C01     0.00   0.0  0
 U5E  CONST_39  H13  N02  C03  O04   180.00   0.0  0
 U5E  Var_01    C09  C08  C07  C06   149.70  30.0  1
 U5E  Var_02    C15  C10  C09  C08   -36.81  30.0  1
 U5E  Var_03    C11  C10  C09  C08   146.01  30.0  1
 U5E  Var_04    C16  C07  C08  C09   -31.97  30.0  1
 U5E  Var_05    H5   C08  C07  C06   -89.14  30.0  1
 U5E  Var_06    H6   C08  C07  C06    28.04  30.0  1
 U5E  Var_07    H7   C09  C08  C07   -71.42  30.0  1
 U5E  Var_08    H8   C09  C08  C07   172.13  30.0  1
 U5E  Var_09    H5   C08  C09  C10   -72.12  30.0  1
 U5E  Var_10    H6   C08  C09  C10   170.69  30.0  1
 U5E  Var_11    H7   C09  C10  C11   -93.80  30.0  1
 U5E  Var_12    H8   C09  C10  C11    22.38  30.0  1
 U5E  Var_13    H7   C09  C10  C15    83.38  30.0  1
 U5E  Var_14    H8   C09  C10  C15  -160.44  30.0  1
 U5E  Var_15    H5   C08  C07  C16    89.19  30.0  1
 U5E  Var_16    H6   C08  C07  C16  -153.63  30.0  1
 U5E  Var_17    O04  C03  C05  C06   177.81  30.0  2
 U5E  Var_18    N02  C03  C05  C06    -2.41  30.0  2
 U5E  Var_19    S17  C05  C03  N02   176.81  30.0  2
 U5E  Var_20    S17  C05  C03  O04    -2.97  30.0  2
 U5E  Var_21    H1   C01  N02  C03   177.21  30.0  3
 U5E  Var_22    H2   C01  N02  C03   -63.48  30.0  3
 U5E  Var_23    H3   C01  N02  C03    58.06  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
 U5E  plan-1  C01  0.020
 U5E  plan-1  C03  0.020
 U5E  plan-1  C05  0.020
 U5E  plan-1  N02  0.020
 U5E  plan-1  O04  0.020
 U5E  plan-1  H13  0.020
 U5E  plan-2  C03  0.020
 U5E  plan-2  C05  0.020
 U5E  plan-2  C06  0.020
 U5E  plan-2  C07  0.020
 U5E  plan-2  C08  0.020
 U5E  plan-2  C15  0.020
 U5E  plan-2  C16  0.020
 U5E  plan-2  S17  0.020
 U5E  plan-2  H4   0.020
 U5E  plan-3  C09  0.020
 U5E  plan-3  C10  0.020
 U5E  plan-3  C11  0.020
 U5E  plan-3  C12  0.020
 U5E  plan-3  C13  0.020
 U5E  plan-3  C14  0.020
 U5E  plan-3  C15  0.020
 U5E  plan-3  C16  0.020
 U5E  plan-3  H9   0.020
 U5E  plan-3  H10  0.020
 U5E  plan-3  H11  0.020
 U5E  plan-3  H12  0.020

