# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:51:29 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[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[Se]C[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
 BYY  BYY  '5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid'  ligand  32  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYY
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
 BYY  O3   O   O     0  -0.528   3.6233  -2.9753  -1.0072
 BYY  C3   C   CR5   0   0.645   3.2652  -2.0084  -0.3520
 BYY  N1   N   NR15  0  -0.661   3.9798  -0.8829  -0.1150
 BYY  N2   N   NR15  0  -0.658   2.0609  -1.8565   0.2679
 BYY  C4   C   C     0  -0.066   1.9873  -0.6706   1.0855
 BYY  C5   C   C     0  -0.045   3.3336   0.0513   0.7678
 BYY  C6   C   CH2   0  -0.592   3.0782   1.4114   0.1158
 BYY  SE1  SE  SE    0   0.016   1.3825   1.2470  -0.8399
 BYY  C2   C   CR15  0  -0.375   0.7967   0.2302   0.7406
 BYY  C7   C   CH2   0  -0.426  -0.5079  -0.5201   0.5456
 BYY  C8   C   CH2   0  -0.420  -1.7233   0.3815   0.3722
 BYY  C9   C   CH2   0  -0.419  -3.0189  -0.4160   0.2872
 BYY  C10  C   CH2   0  -0.581  -4.2280   0.4907   0.1314
 BYY  C11  C   C     0   0.550  -5.5341  -0.2479   0.0410
 BYY  O11  O   OH1   0  -0.598  -6.5631   0.5829  -0.1058
 BYY  O12  O   O     0  -0.446  -5.6628  -1.4457   0.0947
 BYY  H1   H   HNR5  0   0.400   4.9269  -0.7725  -0.4341
 BYY  H2   H   HNR5  0   0.399   1.4938  -2.6652   0.4608
 BYY  H3   H   H     0   0.281   1.9231  -0.9332   2.1462
 BYY  H4   H   H     0   0.279   3.9240   0.2015   1.6758
 BYY  H5   H   HCH2  0   0.274   2.9874   2.1872   0.8777
 BYY  H6   H   HCH2  0   0.285   3.8845   1.6920  -0.5625
 BYY  H7   H   HCR5  0   0.274   0.6758   0.9518   1.5560
 BYY  H8   H   HCH2  0   0.235  -0.4261  -1.2019  -0.3056
 BYY  H9   H   HCH2  0   0.240  -0.6614  -1.1509   1.4294
 BYY  H10  H   HCH2  0   0.223  -1.7792   1.0851   1.2096
 BYY  H11  H   HCH2  0   0.224  -1.6160   0.9918  -0.5312
 BYY  H12  H   HCH2  0   0.229  -2.9622  -1.1106  -0.5550
 BYY  H13  H   HCH2  0   0.228  -3.1273  -1.0282   1.1866
 BYY  H14  H   HCH2  0   0.277  -4.2934   1.1906   0.9712
 BYY  H15  H   HCH2  0   0.276  -4.1277   1.1177  -0.7604
 BYY  H16  H   HOH1  0   0.478  -7.3895   0.0797  -0.1533

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
 BYY  O12  C11  double  1.206  0.020  1.206
 BYY  C10  C11  single  1.503  0.020  1.503
 BYY  C10  C9   single  1.519  0.020  1.519
 BYY  C11  O11  single  1.331  0.020  1.331
 BYY  C9   C8   single  1.524  0.020  1.524
 BYY  C8   C7   single  1.523  0.020  1.523
 BYY  C7   C2   single  1.518  0.020  1.518
 BYY  SE1  C2   single  1.968  0.020  1.968
 BYY  SE1  C6   single  1.953  0.020  1.953
 BYY  C2   C4   single  1.532  0.020  1.532
 BYY  N2   C4   single  1.442  0.020  1.442
 BYY  N2   C3   single  1.363  0.020  1.363
 BYY  C4   C5   single  1.560  0.020  1.560
 BYY  C6   C5   single  1.530  0.020  1.530
 BYY  C3   O3   double  1.222  0.020  1.222
 BYY  C3   N1   single  1.354  0.020  1.354
 BYY  C5   N1   single  1.439  0.020  1.439
 BYY  N1   H1   single  0.860  0.020  1.020
 BYY  N2   H2   single  0.890  0.020  1.040
 BYY  C4   H3   single  0.970  0.020  1.090
 BYY  C5   H4   single  0.970  0.020  1.090
 BYY  C6   H5   single  0.970  0.020  1.090
 BYY  C6   H6   single  0.970  0.020  1.090
 BYY  C2   H7   single  0.970  0.020  1.090
 BYY  C7   H8   single  0.970  0.020  1.090
 BYY  C7   H9   single  0.970  0.020  1.090
 BYY  C8   H10  single  0.970  0.020  1.090
 BYY  C8   H11  single  0.970  0.020  1.090
 BYY  C9   H12  single  0.970  0.020  1.090
 BYY  C9   H13  single  0.970  0.020  1.090
 BYY  C10  H14  single  0.970  0.020  1.090
 BYY  C10  H15  single  0.970  0.020  1.090
 BYY  O11  H16  single  0.850  0.020  0.980

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
 BYY  N2   C3   N1   107.10  3.000
 BYY  N1   C3   O3   126.66  3.000
 BYY  N2   C3   O3   126.23  3.000
 BYY  H1   N1   C5   123.13  3.000
 BYY  H1   N1   C3   122.19  3.000
 BYY  C5   N1   C3   114.21  3.000
 BYY  H2   N2   C4   121.55  3.000
 BYY  H2   N2   C3   119.71  3.000
 BYY  C4   N2   C3   113.24  3.000
 BYY  H3   C4   C2   108.28  3.000
 BYY  H3   C4   C5   111.03  3.000
 BYY  C2   C4   C5   110.65  3.000
 BYY  H3   C4   N2   110.80  3.000
 BYY  C5   C4   N2   102.76  3.000
 BYY  C2   C4   N2   113.29  3.000
 BYY  H4   C5   C6   108.78  3.000
 BYY  H4   C5   C4   111.12  3.000
 BYY  C6   C5   C4   110.73  3.000
 BYY  H4   C5   N1   110.87  3.000
 BYY  C6   C5   N1   113.00  3.000
 BYY  C4   C5   N1   102.25  3.000
 BYY  H6   C6   H5   108.23  3.000
 BYY  H6   C6   SE1  111.05  3.000
 BYY  H5   C6   SE1  109.22  3.000
 BYY  H6   C6   C5   111.75  3.000
 BYY  H5   C6   C5   110.39  3.000
 BYY  SE1  C6   C5   106.18  3.000
 BYY  C2   SE1  C6    84.78  3.000
 BYY  H7   C2   C7   109.05  3.000
 BYY  H7   C2   SE1  106.87  3.000
 BYY  C7   C2   SE1  114.08  3.000
 BYY  H7   C2   C4   107.78  3.000
 BYY  SE1  C2   C4   104.67  3.000
 BYY  C7   C2   C4   113.97  3.000
 BYY  H9   C7   H8   106.21  3.000
 BYY  H9   C7   C8   108.69  3.000
 BYY  H8   C7   C8   109.88  3.000
 BYY  H9   C7   C2   107.53  3.000
 BYY  H8   C7   C2   110.12  3.000
 BYY  C8   C7   C2   114.07  3.000
 BYY  H11  C8   H10  106.12  3.000
 BYY  H11  C8   C9   109.20  3.000
 BYY  H10  C8   C9   109.61  3.000
 BYY  H11  C8   C7   110.21  3.000
 BYY  H10  C8   C7   109.51  3.000
 BYY  C9   C8   C7   112.02  3.000
 BYY  H13  C9   H12  106.45  3.000
 BYY  H13  C9   C10  109.86  3.000
 BYY  H12  C9   C10  109.97  3.000
 BYY  H13  C9   C8   109.35  3.000
 BYY  H12  C9   C8   109.35  3.000
 BYY  C10  C9   C8   111.72  3.000
 BYY  H15  C10  H14  105.31  3.000
 BYY  H15  C10  C11  108.18  3.000
 BYY  H14  C10  C11  107.95  3.000
 BYY  H15  C10  C9   110.64  3.000
 BYY  H14  C10  C9   110.51  3.000
 BYY  C11  C10  C9   113.86  3.000
 BYY  O12  C11  O11  122.86  3.000
 BYY  O11  C11  C10  111.83  3.000
 BYY  O12  C11  C10  125.31  3.000
 BYY  H16  O11  C11  109.92  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
 BYY  CONST_01  C4   N2   C3   N1      0.00   0.0  0
 BYY  CONST_02  C5   N1   C3   N2      0.00   0.0  0
 BYY  CONST_03  C4   N2   C3   O3    180.00   0.0  0
 BYY  CONST_04  C5   N1   C3   O3    180.00   0.0  0
 BYY  CONST_06  H1   N1   C3   N2    180.00   0.0  0
 BYY  CONST_07  H16  O11  C11  C10   180.00   0.0  0
 BYY  Var_01    H5   C6   SE1  C2    -78.46  30.0  1
 BYY  Var_02    C9   C8   C7   C2   -175.62  30.0  1
 BYY  Var_03    C10  C9   C8   C7    179.31  30.0  1
 BYY  Var_04    C11  C10  C9   C8    179.93  30.0  1
 BYY  Var_05    O12  C11  C10  C9      0.68  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
 BYY  chir_01  C4  C2   N2  C5  negativ
 BYY  chir_02  C5  N1   C4  C6  positiv
 BYY  chir_03  C2  SE1  C7  C4  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
 BYY  plan-1  O3   0.020
 BYY  plan-1  C3   0.020
 BYY  plan-1  N1   0.020
 BYY  plan-1  N2   0.020
 BYY  plan-1  C4   0.020
 BYY  plan-1  C5   0.020
 BYY  plan-1  H1   0.020
 BYY  plan-1  H2   0.020
 BYY  plan-2  C10  0.020
 BYY  plan-2  C11  0.020
 BYY  plan-2  O11  0.020
 BYY  plan-2  O12  0.020
 BYY  plan-2  H16  0.020

