# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:55:43 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: N'-acetyl-4,5,6,7-tetrahydro-1-benzothiophene-2-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NNC(=O)c1sc2CCCCc2c1
#
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
 U1D  U1D  N'-acetyl-4,5,6,7-tetrahydro-1-benzothiophene-2-carbohydrazide  ligand  30  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U1D
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
 U1D  N1   N  NH1   0  -0.530   8.4007  -3.7442  21.1484
 U1D  C4   C  CR15  0  -0.243  10.7379  -2.0819  21.9382
 U1D  C5   C  CR56  0   0.192  11.6258  -1.1902  22.5911
 U1D  C6   C  C     0  -0.489  13.0806  -1.0112  22.2735
 U1D  C7   C  C     0  -0.450  13.8073  -0.3146  23.4208
 U1D  C8   C  C     0  -0.449  13.0346   0.9110  23.8976
 U1D  C10  C  CR56  0  -0.238  11.0032  -0.4749  23.5796
 U1D  N    N  NH1   0  -0.457   7.3587  -4.5515  20.8207
 U1D  C    C  CH3   0  -0.783   6.7754  -3.0308  19.0087
 U1D  O    O  O     0  -0.473   5.4823  -4.9419  19.6716
 U1D  C1   C  C     0   0.502   6.4631  -4.2419  19.8435
 U1D  C2   C  C     0   0.546   8.2489  -2.7641  22.0811
 U1D  C3   C  CR5   0  -0.301   9.4662  -2.0316  22.4385
 U1D  C9   C  C     0  -0.483  11.6721   0.5213  24.4710
 U1D  O1   O  O     0  -0.459   7.1720  -2.4992  22.5851
 U1D  S    S  S2    0   0.259   9.3426  -0.8798  23.7135
 U1D  H4   H  HNH1  0   0.423   9.3138  -4.0384  20.8384
 U1D  H5   H  HCR5  0   0.268  11.0518  -2.7264  21.1266
 U1D  H6   H  H     0   0.251  13.5388  -1.9796  22.0597
 U1D  H7   H  H     0   0.244  13.1815  -0.4184  21.3585
 U1D  H8   H  H     0   0.226  13.9289  -1.0136  24.2542
 U1D  H9   H  H     0   0.241  14.8104  -0.0288  23.1003
 U1D  H10  H  H     0   0.244  13.6032   1.4492  24.6576
 U1D  H11  H  H     0   0.229  12.8954   1.6023  23.0612
 U1D  H3   H  HNH1  0   0.407   7.1406  -5.3095  21.4543
 U1D  H    H  HCH3  0   0.268   6.0580  -2.9625  18.1952
 U1D  H1   H  HCH3  0   0.270   6.7119  -2.1179  19.6018
 U1D  H2   H  HCH3  0   0.267   7.7812  -3.0781  18.5925
 U1D  H12  H  H     0   0.257  11.7990   0.0855  25.4671
 U1D  H13  H  H     0   0.261  11.0464   1.4065  24.6024

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
 U1D  C1   C    single    1.504  0.020  1.504
 U1D  C1   O    double    1.217  0.020  1.217
 U1D  N    C1   single    1.361  0.020  1.361
 U1D  N1   N    single    1.358  0.020  1.358
 U1D  C2   N1   single    1.361  0.020  1.361
 U1D  O1   C2   double    1.218  0.020  1.218
 U1D  C2   C3   single    1.465  0.020  1.465
 U1D  C3   C4   aromatic  1.367  0.020  1.367
 U1D  C5   C4   aromatic  1.418  0.020  1.418
 U1D  C5   C6   single    1.500  0.020  1.500
 U1D  C7   C6   single    1.526  0.020  1.526
 U1D  C8   C7   single    1.525  0.020  1.525
 U1D  C9   C8   single    1.529  0.020  1.529
 U1D  C10  C9   single    1.495  0.020  1.495
 U1D  C10  C5   aromatic  1.370  0.020  1.370
 U1D  S    C10  aromatic  1.714  0.020  1.714
 U1D  C3   S    aromatic  1.723  0.020  1.723
 U1D  N1   H4   single    0.860  0.020  1.020
 U1D  C4   H5   single    0.930  0.020  1.080
 U1D  C6   H6   single    0.970  0.020  1.090
 U1D  C6   H7   single    0.970  0.020  1.090
 U1D  C7   H8   single    0.970  0.020  1.090
 U1D  C7   H9   single    0.970  0.020  1.090
 U1D  C8   H10  single    0.970  0.020  1.090
 U1D  C8   H11  single    0.970  0.020  1.090
 U1D  N    H3   single    0.860  0.020  1.020
 U1D  C    H    single    0.970  0.020  1.090
 U1D  C    H1   single    0.970  0.020  1.090
 U1D  C    H2   single    0.970  0.020  1.090
 U1D  C9   H12  single    0.970  0.020  1.090
 U1D  C9   H13  single    0.970  0.020  1.090

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
 U1D  H4   N1   C2   121.45  3.000
 U1D  H4   N1   N    116.56  3.000
 U1D  C2   N1   N    120.51  3.000
 U1D  H5   C4   C3   124.45  3.000
 U1D  H5   C4   C5   122.55  3.000
 U1D  C3   C4   C5   113.00  3.000
 U1D  C10  C5   C6   122.09  3.000
 U1D  C10  C5   C4   112.10  3.000
 U1D  C6   C5   C4   125.81  3.000
 U1D  H7   C6   H6   106.12  3.000
 U1D  H7   C6   C7   109.71  3.000
 U1D  H6   C6   C7   110.61  3.000
 U1D  H7   C6   C5   109.33  3.000
 U1D  H6   C6   C5   110.03  3.000
 U1D  C7   C6   C5   110.93  3.000
 U1D  H9   C7   H8   106.79  3.000
 U1D  H9   C7   C8   110.31  3.000
 U1D  H8   C7   C8   109.36  3.000
 U1D  H9   C7   C6   109.66  3.000
 U1D  H8   C7   C6   109.50  3.000
 U1D  C8   C7   C6   111.13  3.000
 U1D  H11  C8   H10  106.69  3.000
 U1D  H11  C8   C9   109.54  3.000
 U1D  H10  C8   C9   109.20  3.000
 U1D  H11  C8   C7   109.47  3.000
 U1D  H10  C8   C7   110.49  3.000
 U1D  C9   C8   C7   111.34  3.000
 U1D  S    C10  C9   122.97  3.000
 U1D  S    C10  C5   111.91  3.000
 U1D  C9   C10  C5   125.10  3.000
 U1D  H3   N    C1   118.57  3.000
 U1D  H3   N    N1   117.36  3.000
 U1D  C1   N    N1   122.87  3.000
 U1D  H2   C    H1   107.32  3.000
 U1D  H2   C    H    109.04  3.000
 U1D  H1   C    H    108.42  3.000
 U1D  H2   C    C1   111.64  3.000
 U1D  H1   C    C1   111.11  3.000
 U1D  H    C    C1   109.22  3.000
 U1D  O    C1   C    123.51  3.000
 U1D  O    C1   N    120.05  3.000
 U1D  C    C1   N    116.43  3.000
 U1D  O1   C2   C3   121.67  3.000
 U1D  C3   C2   N1   115.75  3.000
 U1D  O1   C2   N1   122.58  3.000
 U1D  S    C3   C2   117.08  3.000
 U1D  S    C3   C4   111.23  3.000
 U1D  C2   C3   C4   131.69  3.000
 U1D  H13  C9   H12  106.24  3.000
 U1D  H13  C9   C10  110.83  3.000
 U1D  H12  C9   C10  109.22  3.000
 U1D  H13  C9   C8   110.44  3.000
 U1D  H12  C9   C8   109.84  3.000
 U1D  C10  C9   C8   110.19  3.000
 U1D  C3   S    C10   91.75  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
 U1D  CONST_01  C10  S    C3   C4      0.00   0.0  0
 U1D  CONST_02  S    C10  C5   C4      0.00   0.0  0
 U1D  CONST_03  S    C3   C4   C5      0.00   0.0  0
 U1D  CONST_04  C3   S    C10  C5      0.00   0.0  0
 U1D  CONST_05  C3   C4   C5   C10     0.00   0.0  0
 U1D  CONST_06  C2   C3   C4   C5    180.00   0.0  0
 U1D  CONST_07  C2   C3   S    C10   180.00   0.0  0
 U1D  CONST_08  H5   C4   C5   C6      0.00   0.0  0
 U1D  CONST_09  C3   C2   N1   N     180.00   0.0  0
 U1D  CONST_10  H4   N1   C2   C3      0.00   0.0  0
 U1D  CONST_11  C    C1   N    N1      0.00   0.0  0
 U1D  CONST_12  O    C1   N    N1    180.00   0.0  0
 U1D  CONST_13  O1   C2   N1   N       0.00   0.0  0
 U1D  CONST_14  H3   N    C1   C     180.00   0.0  0
 U1D  Var_01    C7   C6   C5   C4   -162.51  30.0  1
 U1D  Var_02    C8   C7   C6   C5    -47.34  30.0  1
 U1D  Var_03    C8   C9   C10  C5     15.21  30.0  1
 U1D  Var_04    C9   C8   C7   C6     63.33  30.0  1
 U1D  Var_05    C10  C9   C8   C7    -44.76  30.0  1
 U1D  Var_06    C4   C3   C2   N1      5.30  30.0  2
 U1D  Var_07    C2   N1   N    C1     88.35  30.0  1
 U1D  Var_08    H    C    C1   N     173.11  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
 U1D  plan-1  N1   0.020
 U1D  plan-1  N    0.020
 U1D  plan-1  C    0.020
 U1D  plan-1  O    0.020
 U1D  plan-1  C1   0.020
 U1D  plan-1  H3   0.020
 U1D  plan-2  C4   0.020
 U1D  plan-2  C5   0.020
 U1D  plan-2  C6   0.020
 U1D  plan-2  C10  0.020
 U1D  plan-2  C2   0.020
 U1D  plan-2  C3   0.020
 U1D  plan-2  C9   0.020
 U1D  plan-2  S    0.020
 U1D  plan-2  H5   0.020
 U1D  plan-3  N1   0.020
 U1D  plan-3  N    0.020
 U1D  plan-3  C2   0.020
 U1D  plan-3  C3   0.020
 U1D  plan-3  O1   0.020
 U1D  plan-3  H4   0.020

