# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:47:08 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-methylpropyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)COC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
#
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
 BN7  BN7  '2-methylpropyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate'  ligand  44  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BN7
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
 BN7  O    O  O     0  -0.455  -3.5919   1.7525  -0.7433
 BN7  C7   C  C     0   0.604  -3.5863   0.5701  -0.5046
 BN7  O1   O  O2    0  -0.463  -4.6854  -0.1303  -0.2561
 BN7  C8   C  CH2   0  -0.146  -5.9457   0.5500  -0.2679
 BN7  C9   C  CH1   0  -0.287  -7.0263  -0.4275   0.1593
 BN7  C10  C  CH3   0  -0.653  -6.7970  -0.9468   1.5748
 BN7  C11  C  CH3   0  -0.661  -8.3827   0.2614   0.0424
 BN7  C6   C  CH2   0  -0.585  -2.3587  -0.3002  -0.4564
 BN7  C5   C  CH2   0  -0.419  -1.0574   0.4694  -0.6087
 BN7  C4   C  CH2   0  -0.419   0.1541  -0.4538  -0.5637
 BN7  C3   C  CH2   0  -0.420   1.4632   0.3165  -0.6826
 BN7  C2   C  CH1   0  -0.364   2.6928  -0.5717  -0.7267
 BN7  C12  C  CR15  0  -0.058   4.0124   0.1847  -0.9350
 BN7  N    N  NR15  0  -0.659   4.1152   1.3772  -0.1329
 BN7  C13  C  CR5   0   0.645   5.2004   1.3857   0.6895
 BN7  O2   O  O     0  -0.531   5.5545   2.3065   1.4106
 BN7  S    S  S2    0  -0.025   2.9423  -1.5174   0.8121
 BN7  C1   C  CH2   0  -0.566   4.6005  -1.9602   0.2346
 BN7  C    C  CR15  0  -0.046   5.1838  -0.6926  -0.3971
 BN7  N1   N  NR15  0  -0.662   5.8074   0.1822   0.5587
 BN7  H1   H  HCH2  0   0.224  -5.9159   1.4040   0.4160
 BN7  H2   H  HCH2  0   0.237  -6.1469   0.9301  -1.2732
 BN7  H3   H  HCH1  0   0.233  -7.0138  -1.2748  -0.5351
 BN7  H4   H  HCH3  0   0.230  -7.5861  -1.6426   1.8629
 BN7  H5   H  HCH3  0   0.233  -5.8461  -1.4705   1.6717
 BN7  H6   H  HCH3  0   0.216  -6.8031  -0.1240   2.2937
 BN7  H7   H  HCH3  0   0.220  -8.4512   1.1158   0.7200
 BN7  H8   H  HCH3  0   0.231  -8.5672   0.6216  -0.9710
 BN7  H9   H  HCH3  0   0.236  -9.1877  -0.4279   0.2992
 BN7  H10  H  HCH2  0   0.270  -2.3681  -0.8601   0.4838
 BN7  H11  H  HCH2  0   0.275  -2.4510  -1.0538  -1.2460
 BN7  H12  H  HCH2  0   0.228  -1.0582   1.0203  -1.5529
 BN7  H13  H  HCH2  0   0.228  -0.9724   1.2153   0.1859
 BN7  H14  H  HCH2  0   0.222   0.1416  -1.0238   0.3711
 BN7  H15  H  HCH2  0   0.222   0.0855  -1.1898  -1.3715
 BN7  H16  H  HCH2  0   0.240   1.4474   0.9139  -1.6013
 BN7  H17  H  HCH2  0   0.233   1.5512   1.0231   0.1468
 BN7  H18  H  HCH1  0   0.275   2.5877  -1.2919  -1.5452
 BN7  H19  H  HCR5  0   0.280   4.1311   0.4124  -1.9981
 BN7  H20  H  HNR5  0   0.399   3.6705   2.2396  -0.3985
 BN7  H21  H  HCH2  0   0.289   5.2071  -2.3228   1.0637
 BN7  H22  H  HCH2  0   0.273   4.5299  -2.7543  -0.5101
 BN7  H23  H  HCR5  0   0.278   5.8815  -0.9684  -1.1913
 BN7  H24  H  HNR5  0   0.400   6.6295  -0.0658   1.0816

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
 BN7  N1   C    single  1.438  0.020  1.438
 BN7  N1   C13  single  1.354  0.020  1.354
 BN7  C1   C    single  1.532  0.020  1.532
 BN7  C1   S    single  1.811  0.020  1.811
 BN7  O2   C13  double  1.222  0.020  1.222
 BN7  C    C12  single  1.559  0.020  1.559
 BN7  C13  N    single  1.362  0.020  1.362
 BN7  S    C2   single  1.823  0.020  1.823
 BN7  N    C12  single  1.441  0.020  1.441
 BN7  C12  C2   single  1.535  0.020  1.535
 BN7  C2   C3   single  1.517  0.020  1.517
 BN7  C3   C4   single  1.524  0.020  1.524
 BN7  C4   C5   single  1.524  0.020  1.524
 BN7  C5   C6   single  1.520  0.020  1.520
 BN7  C6   C7   single  1.506  0.020  1.506
 BN7  C7   O1   single  1.327  0.020  1.327
 BN7  C7   O    double  1.206  0.020  1.206
 BN7  O1   C8   single  1.432  0.020  1.432
 BN7  C9   C10  single  1.525  0.020  1.525
 BN7  C9   C8   single  1.518  0.020  1.518
 BN7  C9   C11  single  1.526  0.020  1.526
 BN7  C8   H1   single  0.970  0.020  1.090
 BN7  C8   H2   single  0.970  0.020  1.090
 BN7  C9   H3   single  0.970  0.020  1.090
 BN7  C10  H4   single  0.970  0.020  1.090
 BN7  C10  H5   single  0.970  0.020  1.090
 BN7  C10  H6   single  0.970  0.020  1.090
 BN7  C11  H7   single  0.970  0.020  1.090
 BN7  C11  H8   single  0.970  0.020  1.090
 BN7  C11  H9   single  0.970  0.020  1.090
 BN7  C6   H10  single  0.970  0.020  1.090
 BN7  C6   H11  single  0.970  0.020  1.090
 BN7  C5   H12  single  0.970  0.020  1.090
 BN7  C5   H13  single  0.970  0.020  1.090
 BN7  C4   H14  single  0.970  0.020  1.090
 BN7  C4   H15  single  0.970  0.020  1.090
 BN7  C3   H16  single  0.970  0.020  1.090
 BN7  C3   H17  single  0.970  0.020  1.090
 BN7  C2   H18  single  0.970  0.020  1.090
 BN7  C12  H19  single  0.970  0.020  1.090
 BN7  N    H20  single  0.890  0.020  1.040
 BN7  C1   H21  single  0.970  0.020  1.090
 BN7  C1   H22  single  0.970  0.020  1.090
 BN7  C    H23  single  0.970  0.020  1.090
 BN7  N1   H24  single  0.860  0.020  1.020

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
 BN7  C6   C7   O1   111.36  3.000
 BN7  O1   C7   O    123.42  3.000
 BN7  C6   C7   O    125.22  3.000
 BN7  C8   O1   C7   118.47  3.000
 BN7  H2   C8   H1   107.96  3.000
 BN7  H2   C8   C9   110.58  3.000
 BN7  H1   C8   C9   110.23  3.000
 BN7  H2   C8   O1   109.55  3.000
 BN7  H1   C8   O1   109.97  3.000
 BN7  C9   C8   O1   108.55  3.000
 BN7  H3   C9   C11  108.11  3.000
 BN7  H3   C9   C10  108.86  3.000
 BN7  C11  C9   C10  111.01  3.000
 BN7  H3   C9   C8   108.15  3.000
 BN7  C11  C9   C8   108.69  3.000
 BN7  C10  C9   C8   111.92  3.000
 BN7  H6   C10  H5   107.95  3.000
 BN7  H6   C10  H4   107.61  3.000
 BN7  H5   C10  H4   107.53  3.000
 BN7  H6   C10  C9   110.70  3.000
 BN7  H5   C10  C9   112.17  3.000
 BN7  H4   C10  C9   110.71  3.000
 BN7  H9   C11  H8   107.61  3.000
 BN7  H9   C11  H7   107.58  3.000
 BN7  H8   C11  H7   107.89  3.000
 BN7  H9   C11  C9   110.66  3.000
 BN7  H8   C11  C9   111.74  3.000
 BN7  H7   C11  C9   111.18  3.000
 BN7  H11  C6   H10  105.46  3.000
 BN7  H11  C6   C5   110.39  3.000
 BN7  H10  C6   C5   110.64  3.000
 BN7  H11  C6   C7   107.82  3.000
 BN7  H10  C6   C7   108.44  3.000
 BN7  C5   C6   C7   113.72  3.000
 BN7  H13  C5   H12  106.50  3.000
 BN7  H13  C5   C4   109.28  3.000
 BN7  H12  C5   C4   109.35  3.000
 BN7  H13  C5   C6   109.84  3.000
 BN7  H12  C5   C6   109.95  3.000
 BN7  C4   C5   C6   111.79  3.000
 BN7  H15  C4   H14  106.21  3.000
 BN7  H15  C4   C3   109.64  3.000
 BN7  H14  C4   C3   109.85  3.000
 BN7  H15  C4   C5   109.61  3.000
 BN7  H14  C4   C5   109.36  3.000
 BN7  C3   C4   C5   112.00  3.000
 BN7  H17  C3   H16  106.55  3.000
 BN7  H17  C3   C2   109.58  3.000
 BN7  H16  C3   C2   107.84  3.000
 BN7  H17  C3   C4   109.68  3.000
 BN7  H16  C3   C4   109.18  3.000
 BN7  C2   C3   C4   113.74  3.000
 BN7  H18  C2   S    107.62  3.000
 BN7  H18  C2   C12  107.77  3.000
 BN7  S    C2   C12  104.62  3.000
 BN7  H18  C2   C3   109.20  3.000
 BN7  C12  C2   C3   114.33  3.000
 BN7  S    C2   C3   112.95  3.000
 BN7  H19  C12  C    111.77  3.000
 BN7  H19  C12  N    111.16  3.000
 BN7  C    C12  N    102.71  3.000
 BN7  H19  C12  C2   109.13  3.000
 BN7  N    C12  C2   113.18  3.000
 BN7  C    C12  C2   108.77  3.000
 BN7  H20  N    C13  120.43  3.000
 BN7  H20  N    C12  122.07  3.000
 BN7  C13  N    C12  113.47  3.000
 BN7  N1   C13  O2   126.64  3.000
 BN7  O2   C13  N    126.30  3.000
 BN7  N1   C13  N    107.06  3.000
 BN7  C1   S    C2    89.03  3.000
 BN7  H22  C1   H21  108.26  3.000
 BN7  H22  C1   C    110.21  3.000
 BN7  H21  C1   C    112.17  3.000
 BN7  H22  C1   S    109.66  3.000
 BN7  H21  C1   S    110.40  3.000
 BN7  C    C1   S    106.13  3.000
 BN7  H23  C    N1   111.09  3.000
 BN7  H23  C    C1   109.52  3.000
 BN7  N1   C    C1   113.23  3.000
 BN7  H23  C    C12  111.78  3.000
 BN7  C1   C    C12  108.77  3.000
 BN7  N1   C    C12  102.29  3.000
 BN7  H24  N1   C    123.38  3.000
 BN7  H24  N1   C13  122.38  3.000
 BN7  C    N1   C13  114.23  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
 BN7  CONST_01  N1   C13  N    C12     0.00   0.0  0
 BN7  CONST_02  C    N1   C13  N       0.00   0.0  0
 BN7  CONST_03  O2   C13  N    C12   180.00   0.0  0
 BN7  CONST_04  C    N1   C13  O2    180.00   0.0  0
 BN7  CONST_05  H24  N1   C13  N     180.00   0.0  0
 BN7  Var_01    C    C1   S    C2     41.40  30.0  1
 BN7  Var_02    C2   C3   C4   C5   -176.50  30.0  2
 BN7  Var_03    C5   C6   C7   O       5.60  30.0  2
 BN7  Var_04    C4   C5   C6   C7   -179.59  30.0  1
 BN7  Var_05    C9   C8   O1   C7   -175.13  30.0  3
 BN7  Var_06    C10  C9   C8   O1     61.44  30.0  2
 BN7  Var_07    C6   C7   O1   C8   -179.80  30.0  1
 BN7  Var_08    C3   C4   C5   C6   -178.64  30.0  1
 BN7  Var_09    H4   C10  C9   C8    179.72  30.0  3
 BN7  Var_10    H7   C11  C9   C8    -63.07  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
 BN7  chir_01  C2   S   C12  C3  positiv
 BN7  chir_02  C12  N   C    C2  negativ
 BN7  chir_03  C    N1  C12  C1  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
 BN7  plan-1  C12  0.020
 BN7  plan-1  N    0.020
 BN7  plan-1  C13  0.020
 BN7  plan-1  O2   0.020
 BN7  plan-1  C    0.020
 BN7  plan-1  N1   0.020
 BN7  plan-1  H20  0.020
 BN7  plan-1  H24  0.020
 BN7  plan-2  O    0.020
 BN7  plan-2  C7   0.020
 BN7  plan-2  O1   0.020
 BN7  plan-2  C6   0.020

