# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 22:24:43 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)C(O)=O
#
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
 BYT  BYT  N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysine  ligand  52  25  .  2022-07-24  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_BYT
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
 BYT  N01  N  NH2    0  -0.785   -8.7679   1.0217   0.9222
 BYT  C02  C  CH1    0  -0.211   -8.5642   0.1461  -0.2227
 BYT  C03  C  CH2    0  -0.419   -7.1730  -0.4882  -0.1532
 BYT  C04  C  CH2    0  -0.407   -6.0292   0.5167  -0.1568
 BYT  C05  C  CH2    0  -0.475   -4.6670  -0.1575  -0.0566
 BYT  C06  C  CH2    0  -0.233   -3.5271   0.8479  -0.0677
 BYT  N07  N  NH1    0  -0.646   -2.2503   0.1741   0.0538
 BYT  C08  C  C      0   0.562   -1.0826   0.8238   0.1634
 BYT  O09  O  O      0  -0.511   -1.0071   2.0463   0.1222
 BYT  C10  C  CH2    0  -0.580    0.1295  -0.0575   0.3781
 BYT  C11  C  CH2    0  -0.414    1.3953   0.4824  -0.2734
 BYT  C12  C  CH2    0  -0.418    2.5938  -0.4185  -0.0066
 BYT  C13  C  CH2    0  -0.421    3.8805   0.1153  -0.6249
 BYT  C14  C  CH1    0  -0.360    5.0581  -0.8278  -0.4610
 BYT  S15  S  S2     0  -0.025    5.5198  -1.0868   1.2846
 BYT  C16  C  CH2    0  -0.570    7.0353  -1.9054   0.7284
 BYT  C17  C  CR15   0  -0.045    7.5559  -1.0889  -0.4596
 BYT  N18  N  NR15   0  -0.661    8.4048   0.0092  -0.0785
 BYT  C19  C  CR5    0   0.642    7.8643   1.2308  -0.3126
 BYT  O20  O  O      0  -0.529    8.3744   2.3119  -0.0609
 BYT  N21  N  NR15   0  -0.656    6.6485   1.0287  -0.8916
 BYT  C22  C  CR15   0  -0.065    6.3551  -0.3610  -1.1346
 BYT  C23  C  C      0   0.383   -9.6224  -0.9714  -0.4005
 BYT  O24  O  O      0  -0.609  -10.3811  -1.2087   0.5604
 BYT  O25  O  OC    -1  -0.625   -9.6119  -1.5638  -1.5005
 BYT  H1   H  HNH2   0   0.333   -9.6704   1.4724   0.8276
 BYT  H2   H  HNH2   0   0.321   -8.8680   0.4384   1.7458
 BYT  H4   H  HCH1   0   0.205   -8.5950   0.7717  -1.1237
 BYT  H5   H  HCH2   0   0.204   -7.1093  -1.1070   0.7513
 BYT  H6   H  HCH2   0   0.218   -7.0583  -1.1720  -0.9975
 BYT  H7   H  HCH2   0   0.207   -6.0762   1.1140  -1.0744
 BYT  H8   H  HCH2   0   0.218   -6.1563   1.2176   0.6716
 BYT  H9   H  HCH2   0   0.226   -4.6199  -0.7488   0.8642
 BYT  H10  H  HCH2   0   0.226   -4.5418  -0.8614  -0.8864
 BYT  H11  H  HCH2   0   0.227   -3.5569   1.4322  -0.9924
 BYT  H12  H  HCH2   0   0.227   -3.6520   1.5557   0.7564
 BYT  H13  H  HNH1   0   0.398   -2.2488  -0.8324   0.0865
 BYT  H14  H  HCH2   0   0.265    0.2822  -0.1377   1.4603
 BYT  H15  H  HCH2   0   0.248   -0.0687  -1.0734   0.0267
 BYT  H16  H  HCH2   0   0.225    1.2426   0.5742  -1.3530
 BYT  H17  H  HCH2   0   0.225    1.6014   1.4887   0.0983
 BYT  H18  H  HCH2   0   0.221    2.7250  -0.5317   1.0745
 BYT  H19  H  HCH2   0   0.220    2.3932  -1.4223  -0.3958
 BYT  H20  H  HCH2   0   0.239    3.7245   0.2770  -1.6971
 BYT  H21  H  HCH2   0   0.233    4.1233   1.0891  -0.1917
 BYT  H22  H  HCH1   0   0.275    4.7969  -1.8051  -0.8818
 BYT  H23  H  HCH2   0   0.289    7.7591  -1.9607   1.5410
 BYT  H24  H  HCH2   0   0.274    6.8046  -2.9233   0.4096
 BYT  H25  H  HCR5   0   0.278    8.0704  -1.7548  -1.1562
 BYT  H26  H  HNR5   0   0.399    9.2250  -0.1075   0.4923
 BYT  H27  H  HNR5   0   0.399    6.2170   1.7610  -1.4296
 BYT  H28  H  HCR5   0   0.281    6.3016  -0.5724  -2.2063

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
 BYT  O24  C23  deloc   1.247  0.020  1.247
 BYT  O25  C23  deloc   1.249  0.020  1.249
 BYT  C23  C02  single  1.549  0.020  1.549
 BYT  C02  C03  single  1.531  0.020  1.531
 BYT  C02  N01  single  1.456  0.020  1.456
 BYT  C03  C04  single  1.523  0.020  1.523
 BYT  C05  C04  single  1.523  0.020  1.523
 BYT  C05  C06  single  1.520  0.020  1.520
 BYT  O09  C08  double  1.225  0.020  1.225
 BYT  C08  C10  single  1.514  0.020  1.514
 BYT  C08  N07  single  1.341  0.020  1.341
 BYT  C06  N07  single  1.449  0.020  1.449
 BYT  C10  C11  single  1.523  0.020  1.523
 BYT  C11  C12  single  1.523  0.020  1.523
 BYT  C12  C13  single  1.524  0.020  1.524
 BYT  C13  C14  single  1.518  0.020  1.518
 BYT  S15  C14  single  1.824  0.020  1.824
 BYT  S15  C16  single  1.810  0.020  1.810
 BYT  C14  C22  single  1.534  0.020  1.534
 BYT  N21  C22  single  1.441  0.020  1.441
 BYT  N21  C19  single  1.362  0.020  1.362
 BYT  C22  C17  single  1.558  0.020  1.558
 BYT  C16  C17  single  1.533  0.020  1.533
 BYT  O20  C19  double  1.222  0.020  1.222
 BYT  C19  N18  single  1.356  0.020  1.356
 BYT  C17  N18  single  1.439  0.020  1.439
 BYT  N01  H1   single  0.890  0.020  1.040
 BYT  N01  H2   single  0.890  0.020  1.040
 BYT  C02  H4   single  0.970  0.020  1.090
 BYT  C03  H5   single  0.970  0.020  1.090
 BYT  C03  H6   single  0.970  0.020  1.090
 BYT  C04  H7   single  0.970  0.020  1.090
 BYT  C04  H8   single  0.970  0.020  1.090
 BYT  C05  H9   single  0.970  0.020  1.090
 BYT  C05  H10  single  0.970  0.020  1.090
 BYT  C06  H11  single  0.970  0.020  1.090
 BYT  C06  H12  single  0.970  0.020  1.090
 BYT  N07  H13  single  0.860  0.020  1.020
 BYT  C10  H14  single  0.970  0.020  1.090
 BYT  C10  H15  single  0.970  0.020  1.090
 BYT  C11  H16  single  0.970  0.020  1.090
 BYT  C11  H17  single  0.970  0.020  1.090
 BYT  C12  H18  single  0.970  0.020  1.090
 BYT  C12  H19  single  0.970  0.020  1.090
 BYT  C13  H20  single  0.970  0.020  1.090
 BYT  C13  H21  single  0.970  0.020  1.090
 BYT  C14  H22  single  0.970  0.020  1.090
 BYT  C16  H23  single  0.970  0.020  1.090
 BYT  C16  H24  single  0.970  0.020  1.090
 BYT  C17  H25  single  0.970  0.020  1.090
 BYT  N18  H26  single  0.860  0.020  1.020
 BYT  N21  H27  single  0.890  0.020  1.040
 BYT  C22  H28  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
 BYT  H2   N01  H1   104.11  3.000
 BYT  H2   N01  C02  107.85  3.000
 BYT  H1   N01  C02  108.60  3.000
 BYT  H4   C02  C23  107.32  3.000
 BYT  H4   C02  C03  107.40  3.000
 BYT  C23  C02  C03  109.10  3.000
 BYT  H4   C02  N01  107.39  3.000
 BYT  C03  C02  N01  109.93  3.000
 BYT  C23  C02  N01  115.37  3.000
 BYT  H6   C03  H5   106.13  3.000
 BYT  H6   C03  C04  109.41  3.000
 BYT  H5   C03  C04  109.30  3.000
 BYT  H6   C03  C02  108.65  3.000
 BYT  H5   C03  C02  108.89  3.000
 BYT  C04  C03  C02  114.15  3.000
 BYT  H8   C04  H7   106.27  3.000
 BYT  H8   C04  C05  109.77  3.000
 BYT  H7   C04  C05  109.55  3.000
 BYT  H8   C04  C03  109.52  3.000
 BYT  H7   C04  C03  109.24  3.000
 BYT  C05  C04  C03  112.31  3.000
 BYT  H10  C05  H9   106.56  3.000
 BYT  H10  C05  C06  109.51  3.000
 BYT  H9   C05  C06  109.33  3.000
 BYT  H10  C05  C04  109.69  3.000
 BYT  H9   C05  C04  109.43  3.000
 BYT  C06  C05  C04  112.18  3.000
 BYT  H12  C06  H11  106.74  3.000
 BYT  H12  C06  N07  109.79  3.000
 BYT  H11  C06  N07  110.07  3.000
 BYT  H12  C06  C05  109.69  3.000
 BYT  H11  C06  C05  109.81  3.000
 BYT  N07  C06  C05  110.65  3.000
 BYT  H13  N07  C08  118.71  3.000
 BYT  H13  N07  C06  117.96  3.000
 BYT  C08  N07  C06  123.30  3.000
 BYT  C10  C08  O09  122.42  3.000
 BYT  C10  C08  N07  115.26  3.000
 BYT  O09  C08  N07  122.30  3.000
 BYT  H15  C10  H14  105.95  3.000
 BYT  H15  C10  C11  110.04  3.000
 BYT  H14  C10  C11  109.43  3.000
 BYT  H15  C10  C08  110.50  3.000
 BYT  H14  C10  C08  107.11  3.000
 BYT  C11  C10  C08  113.48  3.000
 BYT  H17  C11  H16  106.54  3.000
 BYT  H17  C11  C12  109.68  3.000
 BYT  H16  C11  C12  109.41  3.000
 BYT  H17  C11  C10  109.75  3.000
 BYT  H16  C11  C10  109.63  3.000
 BYT  C12  C11  C10  111.69  3.000
 BYT  H19  C12  H18  106.14  3.000
 BYT  H19  C12  C13  109.36  3.000
 BYT  H18  C12  C13  109.61  3.000
 BYT  H19  C12  C11  109.62  3.000
 BYT  H18  C12  C11  109.17  3.000
 BYT  C13  C12  C11  112.71  3.000
 BYT  H21  C13  H20  106.74  3.000
 BYT  H21  C13  C14  109.78  3.000
 BYT  H20  C13  C14  107.93  3.000
 BYT  H21  C13  C12  109.81  3.000
 BYT  H20  C13  C12  109.18  3.000
 BYT  C14  C13  C12  113.18  3.000
 BYT  H22  C14  C22  107.72  3.000
 BYT  H22  C14  S15  107.53  3.000
 BYT  C22  C14  S15  104.44  3.000
 BYT  H22  C14  C13  109.14  3.000
 BYT  C22  C14  C13  114.80  3.000
 BYT  S15  C14  C13  112.83  3.000
 BYT  C16  S15  C14   88.97  3.000
 BYT  H24  C16  H23  108.12  3.000
 BYT  H24  C16  C17  110.02  3.000
 BYT  H23  C16  C17  112.30  3.000
 BYT  H24  C16  S15  109.55  3.000
 BYT  H23  C16  S15  110.48  3.000
 BYT  C17  C16  S15  106.36  3.000
 BYT  H25  C17  C22  111.81  3.000
 BYT  H25  C17  N18  110.86  3.000
 BYT  C22  C17  N18  102.29  3.000
 BYT  H25  C17  C16  109.24  3.000
 BYT  N18  C17  C16  113.68  3.000
 BYT  C22  C17  C16  108.84  3.000
 BYT  H26  N18  C19  121.83  3.000
 BYT  H26  N18  C17  122.85  3.000
 BYT  C19  N18  C17  113.98  3.000
 BYT  N21  C19  O20  126.29  3.000
 BYT  O20  C19  N18  126.53  3.000
 BYT  N21  C19  N18  107.19  3.000
 BYT  H27  N21  C22  121.64  3.000
 BYT  H27  N21  C19  120.15  3.000
 BYT  C22  N21  C19  113.37  3.000
 BYT  H28  C22  N21  111.20  3.000
 BYT  H28  C22  C17  111.84  3.000
 BYT  N21  C22  C17  102.74  3.000
 BYT  H28  C22  C14  109.27  3.000
 BYT  C17  C22  C14  108.62  3.000
 BYT  N21  C22  C14  113.05  3.000
 BYT  O25  C23  O24  126.39  3.000
 BYT  O25  C23  C02  115.93  3.000
 BYT  O24  C23  C02  117.67  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
 BYT  CONST_01  N21  C19  N18  C17     0.00   0.0  0
 BYT  CONST_02  C22  N21  C19  N18     0.00   0.0  0
 BYT  CONST_03  O20  C19  N18  C17   180.00   0.0  0
 BYT  CONST_04  C22  N21  C19  O20   180.00   0.0  0
 BYT  CONST_06  H26  N18  C19  N21   180.00   0.0  0
 BYT  CONST_07  O09  C08  N07  C06     0.00   0.0  0
 BYT  CONST_08  C10  C08  N07  C06   180.00   0.0  0
 BYT  CONST_09  H13  N07  C08  O09   180.00   0.0  0
 BYT  Var_01    C17  C16  S15  C14    40.79  30.0  1
 BYT  Var_02    C14  C13  C12  C11  -175.40  30.0  3
 BYT  Var_03    C05  C04  C03  C02   178.78  30.0  3
 BYT  Var_04    C06  C05  C04  C03   179.71  30.0  1
 BYT  Var_05    N07  C06  C05  C04   178.94  30.0  3
 BYT  Var_06    C08  N07  C06  C05  -175.27  30.0  3
 BYT  Var_07    C11  C10  C08  N07   146.39  30.0  3
 BYT  Var_08    C12  C11  C10  C08   178.75  30.0  3
 BYT  Var_09    C13  C12  C11  C10  -178.83  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
 BYT  chir_01  C02  C23  C03  N01  positiv
 BYT  chir_02  C14  C13  S15  C22  positiv
 BYT  chir_03  C17  N18  C16  C22  negativ
 BYT  chir_04  C22  N21  C14  C17  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
 BYT  plan-1  C06  0.020
 BYT  plan-1  N07  0.020
 BYT  plan-1  C08  0.020
 BYT  plan-1  O09  0.020
 BYT  plan-1  C10  0.020
 BYT  plan-1  H13  0.020
 BYT  plan-2  C17  0.020
 BYT  plan-2  N18  0.020
 BYT  plan-2  C19  0.020
 BYT  plan-2  O20  0.020
 BYT  plan-2  N21  0.020
 BYT  plan-2  C22  0.020
 BYT  plan-2  H26  0.020
 BYT  plan-2  H27  0.020
 BYT  plan-3  C02  0.020
 BYT  plan-3  C23  0.020
 BYT  plan-3  O24  0.020
 BYT  plan-3  O25  0.020

