# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:33:24 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CCS[C@@H](CC1)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
 QJ1  QJ1  'methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate'  ligand  31  16  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QJ1
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
 QJ1  C10  C  CR5   0  -0.092  -2.1566  -0.4817  -0.3108
 QJ1  C13  C  CR15  0  -0.469  -4.6344  -0.5033  -0.2754
 QJ1  C15  C  CH2   0  -0.450  -0.3374  -0.2482   1.4059
 QJ1  C12  C  CR15  0  -0.181  -4.1136  -1.4995  -1.0409
 QJ1  C11  C  CR15  0  -0.235  -2.6909  -1.4852  -1.0616
 QJ1  C02  C  C     0   0.765   3.0462  -0.7910   0.2330
 QJ1  C04  C  CH3   0  -0.411   4.9257  -0.7497  -1.1809
 QJ1  C06  C  CH2   0  -0.309   1.9959   1.3993   0.5994
 QJ1  C07  C  CH2   0  -0.555   1.3286   1.7710  -0.7165
 QJ1  C09  C  CH1   0  -0.457  -0.7145  -0.1711  -0.0790
 QJ1  C16  C  CH2   0  -0.297   1.1036  -0.6741   1.6688
 QJ1  N05  N  NT    0  -0.492   2.0777  -0.0359   0.8022
 QJ1  O01  O  O     0  -0.525   3.1786  -1.9902   0.3858
 QJ1  O03  O  O2    0  -0.478   3.8612  -0.0622  -0.5324
 QJ1  S08  S  S2    0  -0.007  -0.4644   1.5069  -0.7840
 QJ1  S14  S  S2    0   0.209  -3.4018   0.4608   0.4269
 QJ1  H1   H  HCR5  0   0.295  -5.6732  -0.2796  -0.0879
 QJ1  H2   H  HCH2  0   0.250  -0.5695   0.7044   1.8855
 QJ1  H3   H  HCH2  0   0.273  -0.9690  -0.9926   1.8969
 QJ1  H4   H  HCR5  0   0.267  -4.7177  -2.2202  -1.5729
 QJ1  H5   H  HCR5  0   0.265  -2.0847  -2.1940  -1.6088
 QJ1  H6   H  HCH3  0   0.234   5.5906  -1.2331  -0.4651
 QJ1  H7   H  HCH3  0   0.234   4.5542  -1.4940  -1.8848
 QJ1  H8   H  HCH3  0   0.248   5.4798   0.0097  -1.7252
 QJ1  H9   H  HCH2  0   0.278   2.9903   1.8444   0.6305
 QJ1  H10  H  HCH2  0   0.267   1.4468   1.8297   1.4375
 QJ1  H11  H  HCH2  0   0.284   1.4466   2.8417  -0.8934
 QJ1  H12  H  HCH2  0   0.274   1.8098   1.2526  -1.5454
 QJ1  H13  H  HCH1  0   0.300  -0.1280  -0.8890  -0.6592
 QJ1  H14  H  HCH2  0   0.253   1.3421  -0.4760   2.7182
 QJ1  H15  H  HCH2  0   0.263   1.1830  -1.7481   1.5213

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
 QJ1  C12  C11  aromatic  1.423  0.020  1.423
 QJ1  C12  C13  aromatic  1.360  0.020  1.360
 QJ1  C11  C10  aromatic  1.362  0.020  1.362
 QJ1  C13  S14  aromatic  1.715  0.020  1.715
 QJ1  C10  S14  aromatic  1.727  0.020  1.727
 QJ1  C10  C09  single    1.493  0.020  1.493
 QJ1  S08  C09  single    1.837  0.020  1.837
 QJ1  S08  C07  single    1.814  0.020  1.814
 QJ1  C09  C15  single    1.534  0.020  1.534
 QJ1  C07  C06  single    1.522  0.020  1.522
 QJ1  C15  C16  single    1.525  0.020  1.525
 QJ1  C06  N05  single    1.452  0.020  1.452
 QJ1  N05  C16  single    1.452  0.020  1.452
 QJ1  N05  C02  single    1.354  0.020  1.354
 QJ1  O01  C02  double    1.216  0.020  1.216
 QJ1  C02  O03  single    1.335  0.020  1.335
 QJ1  O03  C04  single    1.423  0.020  1.423
 QJ1  C13  H1   single    0.930  0.020  1.080
 QJ1  C15  H2   single    0.970  0.020  1.090
 QJ1  C15  H3   single    0.970  0.020  1.090
 QJ1  C12  H4   single    0.930  0.020  1.080
 QJ1  C11  H5   single    0.930  0.020  1.080
 QJ1  C04  H6   single    0.970  0.020  1.090
 QJ1  C04  H7   single    0.970  0.020  1.090
 QJ1  C04  H8   single    0.970  0.020  1.090
 QJ1  C06  H9   single    0.970  0.020  1.090
 QJ1  C06  H10  single    0.970  0.020  1.090
 QJ1  C07  H11  single    0.970  0.020  1.090
 QJ1  C07  H12  single    0.970  0.020  1.090
 QJ1  C09  H13  single    0.970  0.020  1.090
 QJ1  C16  H14  single    0.970  0.020  1.090
 QJ1  C16  H15  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
 QJ1  S14  C10  C09  121.10  3.000
 QJ1  C09  C10  C11  128.13  3.000
 QJ1  S14  C10  C11  110.77  3.000
 QJ1  H1   C13  S14  120.28  3.000
 QJ1  H1   C13  C12  128.20  3.000
 QJ1  S14  C13  C12  111.53  3.000
 QJ1  H3   C15  H2   105.91  3.000
 QJ1  H3   C15  C16  106.16  3.000
 QJ1  H2   C15  C16  111.64  3.000
 QJ1  H3   C15  C09  109.10  3.000
 QJ1  H2   C15  C09  109.22  3.000
 QJ1  C16  C15  C09  114.40  3.000
 QJ1  H4   C12  C11  123.96  3.000
 QJ1  H4   C12  C13  123.48  3.000
 QJ1  C11  C12  C13  112.57  3.000
 QJ1  H5   C11  C12  124.15  3.000
 QJ1  H5   C11  C10  122.81  3.000
 QJ1  C12  C11  C10  113.04  3.000
 QJ1  O03  C02  O01  122.96  3.000
 QJ1  O03  C02  N05  111.93  3.000
 QJ1  O01  C02  N05  125.11  3.000
 QJ1  H8   C04  H7   109.13  3.000
 QJ1  H8   C04  H6   109.14  3.000
 QJ1  H7   C04  H6   109.22  3.000
 QJ1  H8   C04  O03  105.79  3.000
 QJ1  H7   C04  O03  111.67  3.000
 QJ1  H6   C04  O03  111.79  3.000
 QJ1  H10  C06  H9   106.04  3.000
 QJ1  H10  C06  N05  108.13  3.000
 QJ1  H9   C06  N05  110.39  3.000
 QJ1  H10  C06  C07  110.33  3.000
 QJ1  H9   C06  C07  108.97  3.000
 QJ1  N05  C06  C07  112.76  3.000
 QJ1  H12  C07  H11  107.20  3.000
 QJ1  H12  C07  S08  109.82  3.000
 QJ1  H11  C07  S08  104.11  3.000
 QJ1  H12  C07  C06  110.37  3.000
 QJ1  H11  C07  C06  109.41  3.000
 QJ1  S08  C07  C06  115.48  3.000
 QJ1  H13  C09  S08  108.85  3.000
 QJ1  H13  C09  C15  110.40  3.000
 QJ1  S08  C09  C15  112.58  3.000
 QJ1  H13  C09  C10  107.40  3.000
 QJ1  C15  C09  C10  112.16  3.000
 QJ1  S08  C09  C10  105.19  3.000
 QJ1  H15  C16  H14  107.04  3.000
 QJ1  H15  C16  N05  107.72  3.000
 QJ1  H14  C16  N05  110.29  3.000
 QJ1  H15  C16  C15  108.75  3.000
 QJ1  H14  C16  C15  108.70  3.000
 QJ1  N05  C16  C15  114.10  3.000
 QJ1  C16  N05  C06  118.70  3.000
 QJ1  C16  N05  C02  119.08  3.000
 QJ1  C06  N05  C02  122.21  3.000
 QJ1  C04  O03  C02  117.01  3.000
 QJ1  C09  S08  C07  104.68  3.000
 QJ1  C13  S14  C10   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
 QJ1  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 QJ1  CONST_02  C12  C13  S14  C10    0.00   0.0  0
 QJ1  CONST_03  C11  C10  S14  C13    0.00   0.0  0
 QJ1  CONST_04  S14  C10  C11  C12    0.00   0.0  0
 QJ1  CONST_05  S14  C13  C12  C11    0.00   0.0  0
 QJ1  CONST_06  C09  C10  S14  C13  180.00   0.0  0
 QJ1  CONST_07  C09  C10  C11  C12  180.00   0.0  0
 QJ1  CONST_08  H4   C12  C11  C10  180.00   0.0  0
 QJ1  CONST_09  H1   C13  S14  C10  180.00   0.0  0
 QJ1  CONST_10  H5   C11  C12  C13  180.00   0.0  0
 QJ1  Var_01    N05  C02  O03  C04  179.75  30.0  1
 QJ1  Var_02    H6   C04  O03  C02  -59.90  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
 QJ1  chir_01  C09  C10  S08  C15  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
 QJ1  plan-1  C10  0.020
 QJ1  plan-1  C13  0.020
 QJ1  plan-1  C12  0.020
 QJ1  plan-1  C11  0.020
 QJ1  plan-1  C09  0.020
 QJ1  plan-1  S14  0.020
 QJ1  plan-1  H1   0.020
 QJ1  plan-1  H4   0.020
 QJ1  plan-1  H5   0.020
 QJ1  plan-2  C02  0.020
 QJ1  plan-2  N05  0.020
 QJ1  plan-2  O01  0.020
 QJ1  plan-2  O03  0.020

