# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:02:32 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[C@H]1[C@H]2NC(=O)N[C@H]2C[S@]1=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
 BSO  BSO  '5-[(3aS,4S,5S,6aR)-5-oxido-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  32  17  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BSO
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
 BSO  C11   C  C      0   0.411   5.3091   0.3273  -0.1107
 BSO  O11   O  OC    -1  -0.634   6.3358  -0.3556  -0.3145
 BSO  O12   O  O      0  -0.609   5.2583   1.5698  -0.0204
 BSO  C10   C  CH2    0  -0.584   3.9969  -0.4616   0.0440
 BSO  C9    C  CH2    0  -0.404   2.7400   0.3660   0.2522
 BSO  C8    C  CH2    0  -0.415   1.4881  -0.4928   0.3819
 BSO  C7    C  CH2    0  -0.429   0.2361   0.3488   0.6023
 BSO  C2    C  CR15   0  -0.446  -1.0259  -0.4629   0.8370
 BSO  S1    S  S3     0   0.745  -1.4797  -1.4695  -0.6375
 BSO  C6    C  CH2    0  -0.591  -3.1709  -1.6217   0.0148
 BSO  C5    C  C      0  -0.135  -3.5094  -0.2282   0.4894
 BSO  N1    N  NR15   0  -0.655  -3.6306   0.7000  -0.6162
 BSO  C3    C  CR5    0   0.641  -3.0321   1.8998  -0.3357
 BSO  O3    O  O      0  -0.511  -3.1338   2.9267  -0.9829
 BSO  N2    N  NR15   0  -0.654  -2.3023   1.7221   0.7989
 BSO  C4    C  C      0  -0.033  -2.2788   0.3516   1.2337
 BSO  O10   O  O      0  -0.779  -0.8079  -2.8181  -0.5270
 BSO  H101  H  HCH2   0   0.217   3.8758  -1.1009  -0.8386
 BSO  H102  H  HCH2   0   0.218   4.1174  -1.1612   0.8801
 BSO  H9C1  H  HCH2   0   0.204   2.8463   0.9849   1.1483
 BSO  H9C2  H  HCH2   0   0.205   2.6124   1.0641  -0.5805
 BSO  H8C1  H  HCH2   0   0.217   1.3780  -1.1102  -0.5150
 BSO  H8C2  H  HCH2   0   0.214   1.6050  -1.1942   1.2151
 BSO  H7C1  H  HCH2   0   0.246   0.3936   0.9898   1.4766
 BSO  H7C2  H  HCH2   0   0.238   0.0921   1.0236  -0.2468
 BSO  H2    H  HCR5   0   0.307  -0.8510  -1.2188   1.6101
 BSO  H6C1  H  HCH2   0   0.300  -3.1392  -2.3369   0.8394
 BSO  H6C2  H  HCH2   0   0.309  -3.8406  -1.9919  -0.7606
 BSO  H5    H  H      0   0.300  -4.4019  -0.2320   1.1213
 BSO  H1    H  HNR5   0   0.403  -4.4609   0.6958  -1.1883
 BSO  HA    H  HNR5   0   0.405  -1.6144   2.3985   1.0866
 BSO  H4    H  H      0   0.297  -2.4029   0.2862   2.3140

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
 BSO  C11  O11   deloc   1.250  0.020  1.250
 BSO  C11  O12   deloc   1.247  0.020  1.247
 BSO  C11  C10   single  1.539  0.020  1.539
 BSO  C10  C9    single  1.519  0.020  1.519
 BSO  C10  H101  single  0.970  0.020  1.090
 BSO  C10  H102  single  0.970  0.020  1.090
 BSO  C9   C8    single  1.524  0.020  1.524
 BSO  C9   H9C1  single  0.970  0.020  1.090
 BSO  C9   H9C2  single  0.970  0.020  1.090
 BSO  C8   C7    single  1.525  0.020  1.525
 BSO  C8   H8C1  single  0.970  0.020  1.090
 BSO  C8   H8C2  single  0.970  0.020  1.090
 BSO  C7   C2    single  1.519  0.020  1.519
 BSO  C7   H7C1  single  0.970  0.020  1.090
 BSO  C7   H7C2  single  0.970  0.020  1.090
 BSO  C2   S1    single  1.842  0.020  1.842
 BSO  C2   C4    single  1.546  0.020  1.546
 BSO  C2   H2    single  0.970  0.020  1.090
 BSO  S1   C6    single  1.819  0.020  1.819
 BSO  S1   O10   double  1.511  0.020  1.511
 BSO  C6   C5    single  1.511  0.020  1.511
 BSO  C6   H6C1  single  0.970  0.020  1.090
 BSO  C6   H6C2  single  0.970  0.020  1.090
 BSO  C5   N1    single  1.449  0.020  1.449
 BSO  C5   C4    single  1.551  0.020  1.551
 BSO  C5   H5    single  0.970  0.020  1.090
 BSO  N1   C3    single  1.370  0.020  1.370
 BSO  N1   H1    single  0.890  0.020  1.040
 BSO  C3   O3    double  1.218  0.020  1.218
 BSO  C3   N2    single  1.361  0.020  1.361
 BSO  N2   C4    single  1.438  0.020  1.438
 BSO  N2   HA    single  0.860  0.020  1.020
 BSO  C4   H4    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
 BSO  C10   C11  O12   117.96  3.000
 BSO  C10   C11  O11   115.89  3.000
 BSO  O12   C11  O11   126.15  3.000
 BSO  H102  C10  H101  104.70  3.000
 BSO  H102  C10  C9    109.50  3.000
 BSO  H101  C10  C9    109.66  3.000
 BSO  H102  C10  C11   108.06  3.000
 BSO  H101  C10  C11   108.19  3.000
 BSO  C9    C10  C11   116.10  3.000
 BSO  H9C2  C9   H9C1  105.88  3.000
 BSO  H9C2  C9   C8    109.18  3.000
 BSO  H9C1  C9   C8    109.20  3.000
 BSO  H9C2  C9   C10   109.87  3.000
 BSO  H9C1  C9   C10   109.87  3.000
 BSO  C8    C9   C10   112.61  3.000
 BSO  H8C2  C8   H8C1  105.84  3.000
 BSO  H8C2  C8   C7    109.34  3.000
 BSO  H8C1  C8   C7    110.32  3.000
 BSO  H8C2  C8   C9    109.75  3.000
 BSO  H8C1  C8   C9    109.32  3.000
 BSO  C7    C8   C9    112.08  3.000
 BSO  H7C2  C7   H7C1  106.11  3.000
 BSO  H7C2  C7   C2    109.89  3.000
 BSO  H7C1  C7   C2    107.99  3.000
 BSO  H7C2  C7   C8    109.65  3.000
 BSO  H7C1  C7   C8    108.68  3.000
 BSO  C2    C7   C8    114.18  3.000
 BSO  H2    C2   C4    108.17  3.000
 BSO  H2    C2   S1    103.13  3.000
 BSO  C4    C2   S1    107.07  3.000
 BSO  H2    C2   C7    110.20  3.000
 BSO  C4    C2   C7    115.56  3.000
 BSO  S1    C2   C7    111.91  3.000
 BSO  O10   S1   C6    108.21  3.000
 BSO  O10   S1   C2    108.65  3.000
 BSO  C6    S1   C2     89.30  3.000
 BSO  H6C2  C6   H6C1  109.44  3.000
 BSO  H6C2  C6   C5    113.53  3.000
 BSO  H6C1  C6   C5    111.93  3.000
 BSO  H6C2  C6   S1    110.16  3.000
 BSO  H6C1  C6   S1    107.37  3.000
 BSO  C5    C6   S1    104.12  3.000
 BSO  H5    C5   C4    111.81  3.000
 BSO  H5    C5   N1    112.02  3.000
 BSO  C4    C5   N1    101.13  3.000
 BSO  H5    C5   C6    111.18  3.000
 BSO  C4    C5   C6    108.54  3.000
 BSO  N1    C5   C6    111.72  3.000
 BSO  H1    N1   C3    118.66  3.000
 BSO  H1    N1   C5    119.95  3.000
 BSO  C3    N1   C5    111.62  3.000
 BSO  N2    C3   O3    126.72  3.000
 BSO  N2    C3   N1    106.90  3.000
 BSO  O3    C3   N1    126.38  3.000
 BSO  HA    N2   C4    122.87  3.000
 BSO  HA    N2   C3    121.13  3.000
 BSO  C4    N2   C3    112.67  3.000
 BSO  H4    C4   N2    110.81  3.000
 BSO  H4    C4   C5    111.29  3.000
 BSO  N2    C4   C5    101.43  3.000
 BSO  H4    C4   C2    108.37  3.000
 BSO  N2    C4   C2    115.96  3.000
 BSO  C5    C4   C2    108.84  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
 BSO  CONST_01  N2  C3   N1   C5      0.00   0.0  0
 BSO  CONST_02  C4  N2   C3   N1      0.00   0.0  0
 BSO  CONST_03  O3  C3   N1   C5    180.00   0.0  0
 BSO  CONST_04  C4  N2   C3   O3    180.00   0.0  0
 BSO  CONST_05  HA  N2   C3   N1    180.00   0.0  0
 BSO  Var_01    C5  C6   S1   C2     44.01  30.0  1
 BSO  Var_02    C2  C7   C8   C9   -175.86  30.0  3
 BSO  Var_03    C8  C9   C10  C11   179.44  30.0  3
 BSO  Var_04    C9  C10  C11  O11  -178.31  30.0  3
 BSO  Var_05    C7  C8   C9   C10   179.51  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
 BSO  chir_01  C2  C7  S1  C4  positiv
 BSO  chir_03  C5  C6  N1  C4  positiv
 BSO  chir_04  C4  N2  C2  C5  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
 BSO  plan-1  C5   0.020
 BSO  plan-1  N1   0.020
 BSO  plan-1  C3   0.020
 BSO  plan-1  O3   0.020
 BSO  plan-1  N2   0.020
 BSO  plan-1  C4   0.020
 BSO  plan-1  H1   0.020
 BSO  plan-1  HA   0.020
 BSO  plan-2  C11  0.020
 BSO  plan-2  O11  0.020
 BSO  plan-2  O12  0.020
 BSO  plan-2  C10  0.020
 BSO  plan-3  C2   0.020
 BSO  plan-3  S1   0.020
 BSO  plan-3  C6   0.020
 BSO  plan-3  O10  0.020

