# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 17:53:34 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: ethyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=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
 QKD  QKD  'ethyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate'  ligand  34  17  .  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_QKD
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
 QKD  C10  C  CH2   0  -0.273   1.9886   1.8710   0.2578
 QKD  C13  C  C     0   0.774   2.4927  -0.3029  -0.8046
 QKD  C17  C  CH3   0  -0.689   5.1229  -1.4935   1.3881
 QKD  C01  C  CR5   0  -0.096  -2.6226   0.1494  -0.1556
 QKD  C02  C  CR15  0  -0.237  -3.9178   0.5616  -0.2546
 QKD  C03  C  CR15  0  -0.180  -4.8549  -0.4632   0.0537
 QKD  C04  C  CR15  0  -0.469  -4.2534  -1.6365   0.3877
 QKD  C06  C  CH1   0  -0.466  -1.3843   0.9464  -0.3962
 QKD  C07  C  CH2   0  -0.390  -0.5254   0.3571  -1.5119
 QKD  C08  C  CH2   0  -0.336   0.7933   1.0750  -1.7847
 QKD  C11  C  CH2   0  -0.607   0.6719   2.3995   0.8099
 QKD  C16  C  CH2   0  -0.168   4.1934  -1.5979   0.2034
 QKD  N09  N  NT    0  -0.478   1.8020   0.8570  -0.7619
 QKD  O14  O  O     0  -0.533   2.3146  -1.1693  -1.6418
 QKD  O15  O  O2    0  -0.482   3.4086  -0.4011   0.1594
 QKD  S05  S  S2    0   0.209  -2.5445  -1.5075   0.3244
 QKD  S12  S  S2    0   0.009  -0.5234   1.1014   1.2168
 QKD  H1   H  HCH2  0   0.250   2.5586   2.7169  -0.1427
 QKD  H2   H  HCH2  0   0.268   2.5668   1.4549   1.0767
 QKD  H3   H  HCH3  0   0.238   5.7415  -2.3893   1.4348
 QKD  H4   H  HCH3  0   0.235   5.7852  -0.6320   1.3041
 QKD  H5   H  HCH3  0   0.235   4.5725  -1.4191   2.3262
 QKD  H6   H  HCR5  0   0.265  -4.1918   1.5677  -0.5406
 QKD  H7   H  HCR5  0   0.267  -5.9267  -0.3292   0.0286
 QKD  H8   H  HCR5  0   0.296  -4.7183  -2.5697   0.6653
 QKD  H9   H  HCH1  0   0.299  -1.6978   1.9557  -0.6784
 QKD  H10  H  HCH2  0   0.241  -0.3213  -0.6965  -1.3119
 QKD  H11  H  HCH2  0   0.253  -1.1241   0.3873  -2.4271
 QKD  H12  H  HCH2  0   0.269   1.1785   0.7392  -2.7470
 QKD  H13  H  HCH2  0   0.259   0.6367   2.1509  -1.8845
 QKD  H14  H  HCH2  0   0.301   0.8761   2.9513   1.7283
 QKD  H15  H  HCH2  0   0.277   0.1898   3.1022   0.1282
 QKD  H16  H  HCH2  0   0.229   4.7608  -1.7037  -0.7236
 QKD  H17  H  HCH2  0   0.229   3.5426  -2.4694   0.2986

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
 QKD  C03  C02  aromatic  1.423  0.020  1.423
 QKD  C03  C04  aromatic  1.360  0.020  1.360
 QKD  C02  C01  aromatic  1.363  0.020  1.363
 QKD  C04  S05  aromatic  1.715  0.020  1.715
 QKD  S12  C11  single    1.811  0.020  1.811
 QKD  S12  C06  single    1.835  0.020  1.835
 QKD  C01  S05  aromatic  1.727  0.020  1.727
 QKD  C01  C06  single    1.492  0.020  1.492
 QKD  C11  C10  single    1.523  0.020  1.523
 QKD  C06  C07  single    1.526  0.020  1.526
 QKD  C10  N09  single    1.450  0.020  1.450
 QKD  C07  C08  single    1.526  0.020  1.526
 QKD  N09  C08  single    1.453  0.020  1.453
 QKD  N09  C13  single    1.351  0.020  1.351
 QKD  O14  C13  double    1.218  0.020  1.218
 QKD  C13  O15  single    1.333  0.020  1.333
 QKD  O15  C16  single    1.432  0.020  1.432
 QKD  C16  C17  single    1.510  0.020  1.510
 QKD  C10  H1   single    0.970  0.020  1.090
 QKD  C10  H2   single    0.970  0.020  1.090
 QKD  C17  H3   single    0.970  0.020  1.090
 QKD  C17  H4   single    0.970  0.020  1.090
 QKD  C17  H5   single    0.970  0.020  1.090
 QKD  C02  H6   single    0.930  0.020  1.080
 QKD  C03  H7   single    0.930  0.020  1.080
 QKD  C04  H8   single    0.930  0.020  1.080
 QKD  C06  H9   single    0.970  0.020  1.090
 QKD  C07  H10  single    0.970  0.020  1.090
 QKD  C07  H11  single    0.970  0.020  1.090
 QKD  C08  H12  single    0.970  0.020  1.090
 QKD  C08  H13  single    0.970  0.020  1.090
 QKD  C11  H14  single    0.970  0.020  1.090
 QKD  C11  H15  single    0.970  0.020  1.090
 QKD  C16  H16  single    0.970  0.020  1.090
 QKD  C16  H17  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
 QKD  H2   C10  H1   107.14  3.000
 QKD  H2   C10  N09  109.33  3.000
 QKD  H1   C10  N09  110.48  3.000
 QKD  H2   C10  C11  108.67  3.000
 QKD  H1   C10  C11  108.33  3.000
 QKD  N09  C10  C11  112.73  3.000
 QKD  O15  C13  O14  123.03  3.000
 QKD  O15  C13  N09  113.06  3.000
 QKD  O14  C13  N09  123.91  3.000
 QKD  H5   C17  H4   108.62  3.000
 QKD  H5   C17  H3   107.81  3.000
 QKD  H4   C17  H3   107.95  3.000
 QKD  H5   C17  C16  111.66  3.000
 QKD  H4   C17  C16  111.61  3.000
 QKD  H3   C17  C16  109.05  3.000
 QKD  S05  C01  C06  121.32  3.000
 QKD  C06  C01  C02  127.98  3.000
 QKD  S05  C01  C02  110.70  3.000
 QKD  H6   C02  C03  124.11  3.000
 QKD  H6   C02  C01  122.79  3.000
 QKD  C03  C02  C01  113.10  3.000
 QKD  H7   C03  C04  123.47  3.000
 QKD  H7   C03  C02  123.99  3.000
 QKD  C04  C03  C02  112.54  3.000
 QKD  H8   C04  S05  120.26  3.000
 QKD  H8   C04  C03  128.22  3.000
 QKD  S05  C04  C03  111.51  3.000
 QKD  H9   C06  S12  106.46  3.000
 QKD  H9   C06  C07  109.21  3.000
 QKD  S12  C06  C07  114.28  3.000
 QKD  H9   C06  C01  107.25  3.000
 QKD  C07  C06  C01  112.25  3.000
 QKD  S12  C06  C01  107.02  3.000
 QKD  H11  C07  H10  106.40  3.000
 QKD  H11  C07  C08  108.08  3.000
 QKD  H10  C07  C08  108.98  3.000
 QKD  H11  C07  C06  107.03  3.000
 QKD  H10  C07  C06  110.11  3.000
 QKD  C08  C07  C06  115.80  3.000
 QKD  H13  C08  H12  105.88  3.000
 QKD  H13  C08  N09  108.17  3.000
 QKD  H12  C08  N09  109.27  3.000
 QKD  H13  C08  C07  110.85  3.000
 QKD  H12  C08  C07  108.56  3.000
 QKD  N09  C08  C07  113.79  3.000
 QKD  H15  C11  H14  106.44  3.000
 QKD  H15  C11  S12  108.09  3.000
 QKD  H14  C11  S12  107.28  3.000
 QKD  H15  C11  C10  112.27  3.000
 QKD  H14  C11  C10  108.60  3.000
 QKD  S12  C11  C10  113.80  3.000
 QKD  H17  C16  H16  107.84  3.000
 QKD  H17  C16  O15  110.07  3.000
 QKD  H16  C16  O15  109.86  3.000
 QKD  H17  C16  C17  110.72  3.000
 QKD  H16  C16  C17  110.67  3.000
 QKD  O15  C16  C17  107.69  3.000
 QKD  C08  N09  C13  117.49  3.000
 QKD  C13  N09  C10  123.84  3.000
 QKD  C08  N09  C10  118.65  3.000
 QKD  C16  O15  C13  117.41  3.000
 QKD  C04  S05  C01   92.14  3.000
 QKD  C11  S12  C06   99.94  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
 QKD  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 QKD  CONST_02  C03  C04  S05  C01     0.00   0.0  0
 QKD  CONST_03  S05  C04  C03  C02     0.00   0.0  0
 QKD  CONST_04  C04  S05  C01  C02     0.00   0.0  0
 QKD  CONST_05  S05  C01  C02  C03     0.00   0.0  0
 QKD  CONST_06  C06  C01  C02  C03   180.00   0.0  0
 QKD  CONST_07  C06  C01  S05  C04   180.00   0.0  0
 QKD  CONST_08  H7   C03  C02  C01   180.00   0.0  0
 QKD  CONST_09  H8   C04  S05  C01   180.00   0.0  0
 QKD  CONST_10  H6   C02  C03  C04   180.00   0.0  0
 QKD  Var_01    N09  C13  O15  C16   179.82  30.0  1
 QKD  Var_02    C17  C16  O15  C13  -178.49  30.0  3
 QKD  Var_03    H3   C17  C16  O15  -179.25  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
 QKD  chir_01  C06  S12  C01  C07  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
 QKD  plan-1  C01  0.020
 QKD  plan-1  C02  0.020
 QKD  plan-1  C03  0.020
 QKD  plan-1  C04  0.020
 QKD  plan-1  C06  0.020
 QKD  plan-1  S05  0.020
 QKD  plan-1  H6   0.020
 QKD  plan-1  H7   0.020
 QKD  plan-1  H8   0.020
 QKD  plan-2  C13  0.020
 QKD  plan-2  N09  0.020
 QKD  plan-2  O14  0.020
 QKD  plan-2  O15  0.020

