# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:13:46 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-[(7S)-7-(thiophen-2-yl)-6,7-dihydro-1,4-thiazepin-4(5H)-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CC[C@H](SC=C1)c2sccc2
#
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
 QJA  QJA  1-[(7S)-7-(thiophen-2-yl)-6,7-dihydro-1,4-thiazepin-4(5H)-yl]ethan-1-one  ligand  28  15  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QJA
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
 QJA  C01  C  CH3   0  -0.800   4.2524  -0.4088   1.1123
 QJA  C02  C  C     0   0.520   3.2881  -0.9306   0.0787
 QJA  C04  C  C1    0   0.008   2.5281   1.3488  -0.1208
 QJA  C05  C  C1    0  -0.429   1.5056   2.0526   0.3559
 QJA  C07  C  CH1   0  -0.465  -0.6962   0.5385  -0.6889
 QJA  C08  C  CR5   0  -0.102  -2.1269   0.2355  -0.3961
 QJA  C09  C  CR15  0  -0.232  -3.2327   0.7743  -0.9837
 QJA  C10  C  CR15  0  -0.180  -4.4492   0.2588  -0.4583
 QJA  C11  C  CR15  0  -0.467  -4.2448  -0.6590   0.5250
 QJA  C13  C  CH2   0  -0.397   0.1091  -0.7051  -1.0406
 QJA  C14  C  CH2   0  -0.326   1.5202  -0.4128  -1.5253
 QJA  N03  N  NT    0  -0.477   2.4514  -0.0083  -0.4819
 QJA  O15  O  O     0  -0.482   3.2482  -2.1081  -0.2364
 QJA  S06  S  S2    0   0.044  -0.0816   1.4398   0.7922
 QJA  S12  S  S2    0   0.215  -2.5743  -0.9080   0.8173
 QJA  H1   H  HCH3  0   0.269   3.7388   0.1272   1.9105
 QJA  H2   H  HCH3  0   0.272   4.8051  -1.2390   1.5440
 QJA  H3   H  HCH3  0   0.271   4.9672   0.2840   0.6649
 QJA  H4   H  H     0   0.284   3.4802   1.8465  -0.2766
 QJA  H5   H  H     0   0.291   1.6609   3.1024   0.5725
 QJA  H6   H  HCH1  0   0.310  -0.6691   1.2392  -1.5274
 QJA  H7   H  HCR5  0   0.267  -3.1762   1.5168  -1.7674
 QJA  H8   H  HCR5  0   0.269  -5.4298   0.5581  -0.7989
 QJA  H9   H  HCR5  0   0.297  -4.9827  -1.2047   1.0924
 QJA  H10  H  HCH2  0   0.247   0.1401  -1.3986  -0.1965
 QJA  H11  H  HCH2  0   0.260  -0.4181  -1.2145  -1.8521
 QJA  H12  H  HCH2  0   0.272   1.9217  -1.3047  -2.0012
 QJA  H13  H  HCH2  0   0.258   1.4998   0.3714  -2.2845

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
 QJA  C10  C09  aromatic  1.422  0.020  1.422
 QJA  C10  C11  aromatic  1.361  0.020  1.361
 QJA  C09  C08  aromatic  1.363  0.020  1.363
 QJA  C11  S12  aromatic  1.714  0.020  1.714
 QJA  C08  S12  aromatic  1.726  0.020  1.726
 QJA  C08  C07  single    1.491  0.020  1.491
 QJA  S06  C07  single    1.839  0.020  1.839
 QJA  S06  C05  single    1.756  0.020  1.756
 QJA  C07  C13  single    1.523  0.020  1.523
 QJA  C05  C04  double    1.330  0.020  1.330
 QJA  C13  C14  single    1.520  0.020  1.520
 QJA  C04  N03  single    1.406  0.020  1.406
 QJA  O15  C02  double    1.220  0.020  1.220
 QJA  N03  C02  single    1.366  0.020  1.366
 QJA  N03  C14  single    1.456  0.020  1.456
 QJA  C02  C01  single    1.507  0.020  1.507
 QJA  C01  H1   single    0.970  0.020  1.090
 QJA  C01  H2   single    0.970  0.020  1.090
 QJA  C01  H3   single    0.970  0.020  1.090
 QJA  C04  H4   single    0.930  0.020  1.080
 QJA  C05  H5   single    0.930  0.020  1.080
 QJA  C07  H6   single    0.970  0.020  1.090
 QJA  C09  H7   single    0.930  0.020  1.080
 QJA  C10  H8   single    0.930  0.020  1.080
 QJA  C11  H9   single    0.930  0.020  1.080
 QJA  C13  H10  single    0.970  0.020  1.090
 QJA  C13  H11  single    0.970  0.020  1.090
 QJA  C14  H12  single    0.970  0.020  1.090
 QJA  C14  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
 QJA  H3   C01  H2   108.34  3.000
 QJA  H3   C01  H1   107.26  3.000
 QJA  H2   C01  H1   108.93  3.000
 QJA  H3   C01  C02  110.96  3.000
 QJA  H2   C01  C02  109.47  3.000
 QJA  H1   C01  C02  111.78  3.000
 QJA  O15  C02  N03  121.73  3.000
 QJA  N03  C02  C01  116.09  3.000
 QJA  O15  C02  C01  122.18  3.000
 QJA  H4   C04  N03  116.96  3.000
 QJA  H4   C04  C05  118.90  3.000
 QJA  N03  C04  C05  124.11  3.000
 QJA  H5   C05  S06  114.71  3.000
 QJA  H5   C05  C04  118.32  3.000
 QJA  S06  C05  C04  126.82  3.000
 QJA  H6   C07  S06  107.17  3.000
 QJA  H6   C07  C13  109.47  3.000
 QJA  S06  C07  C13  114.17  3.000
 QJA  H6   C07  C08  107.74  3.000
 QJA  C13  C07  C08  112.75  3.000
 QJA  S06  C07  C08  105.19  3.000
 QJA  S12  C08  C09  110.77  3.000
 QJA  S12  C08  C07  121.41  3.000
 QJA  C09  C08  C07  127.82  3.000
 QJA  H7   C09  C10  124.17  3.000
 QJA  H7   C09  C08  122.78  3.000
 QJA  C10  C09  C08  113.05  3.000
 QJA  H8   C10  C11  123.45  3.000
 QJA  H8   C10  C09  124.03  3.000
 QJA  C11  C10  C09  112.52  3.000
 QJA  H9   C11  S12  120.22  3.000
 QJA  H9   C11  C10  128.20  3.000
 QJA  S12  C11  C10  111.57  3.000
 QJA  H11  C13  H10  106.94  3.000
 QJA  H11  C13  C14  107.48  3.000
 QJA  H10  C13  C14  109.99  3.000
 QJA  H11  C13  C07  107.27  3.000
 QJA  H10  C13  C07  110.79  3.000
 QJA  C14  C13  C07  114.04  3.000
 QJA  H13  C14  H12  106.95  3.000
 QJA  H13  C14  N03  108.10  3.000
 QJA  H12  C14  N03  107.78  3.000
 QJA  H13  C14  C13  110.03  3.000
 QJA  H12  C14  C13  108.93  3.000
 QJA  N03  C14  C13  114.75  3.000
 QJA  C14  N03  C04  119.15  3.000
 QJA  C14  N03  C02  119.90  3.000
 QJA  C04  N03  C02  120.86  3.000
 QJA  C07  S06  C05  105.84  3.000
 QJA  C11  S12  C08   92.09  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
 QJA  CONST_01  C11  C10  C09  C08    0.00   0.0  0
 QJA  CONST_02  C10  C11  S12  C08    0.00   0.0  0
 QJA  CONST_03  S12  C11  C10  C09    0.00   0.0  0
 QJA  CONST_04  C11  S12  C08  C09    0.00   0.0  0
 QJA  CONST_05  S12  C08  C09  C10    0.00   0.0  0
 QJA  CONST_06  C10  C09  C08  C07  180.00   0.0  0
 QJA  CONST_07  C11  S12  C08  C07  180.00   0.0  0
 QJA  CONST_08  H7   C09  C08  C07    0.00   0.0  0
 QJA  CONST_09  H8   C10  C09  C08  180.00   0.0  0
 QJA  CONST_10  H9   C11  S12  C08  180.00   0.0  0
 QJA  Var_01    H1   C01  C02  N03   54.58  30.0  3

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
 QJA  chir_01  C07  C08  S06  C13  negativ

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
 QJA  plan-1  C07  0.020
 QJA  plan-1  C08  0.020
 QJA  plan-1  C09  0.020
 QJA  plan-1  C10  0.020
 QJA  plan-1  C11  0.020
 QJA  plan-1  S12  0.020
 QJA  plan-1  H7   0.020
 QJA  plan-1  H8   0.020
 QJA  plan-1  H9   0.020
 QJA  plan-2  C01  0.020
 QJA  plan-2  C02  0.020
 QJA  plan-2  C04  0.020
 QJA  plan-2  C14  0.020
 QJA  plan-2  N03  0.020
 QJA  plan-2  O15  0.020

