# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 04:31:17 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (4-{(2S)-2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}phenyl)methaneseleninic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1ccc(C[Se](O)=O)cc1)NC(=O)OC(C)(C)C
#
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
 ZYZ  ZYZ  '(4-{(2S)-2-[(tert-butoxycarbonyl)amino]-3-methoxy-3-oxopropyl}phenyl)methaneseleninic acid'  ligand  47  24  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZYZ
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
 ZYZ  SE    SE  SE    0   1.098  -5.2235   0.2273   0.0323
 ZYZ  C1    C   CH2   0  -0.735  -3.7191  -0.7904  -0.7193
 ZYZ  N1    N   NH1   0  -0.651   2.5601   0.0139   0.3778
 ZYZ  C2    C   CR6   0   0.081  -2.4490  -0.0930  -0.3670
 ZYZ  C3    C   CR16  0  -0.263  -1.8294  -0.3155   0.8604
 ZYZ  C4    C   CR16  0  -0.307  -0.6651   0.3595   1.1957
 ZYZ  C5    C   CR6   0   0.149  -0.0961   1.2815   0.3230
 ZYZ  O5    O   O     0  -0.513   3.8127  -0.5669  -1.4142
 ZYZ  C6    C   CR16  0  -0.288  -0.7233   1.5100  -0.8994
 ZYZ  O6    O   O2    0  -0.501   3.5256  -1.9659   0.3477
 ZYZ  C7    C   CR16  0  -0.272  -1.8835   0.8340  -1.2406
 ZYZ  C8    C   CH2   0  -0.564   1.1789   1.9993   0.6648
 ZYZ  C9    C   CH1   0  -0.186   2.3890   1.3719  -0.0456
 ZYZ  C10   C   C     0   0.596   3.6511   2.1873   0.2163
 ZYZ  C12   C   CH3   0  -0.425   4.6914   4.2572  -0.2086
 ZYZ  C13   C   CT    0   0.185   4.2815  -3.0859  -0.1886
 ZYZ  C14   C   CH3   0  -0.670   5.7382  -2.7036  -0.4222
 ZYZ  C15   C   CH3   0  -0.659   4.1950  -4.1261   0.9215
 ZYZ  C16   C   CH3   0  -0.672   3.6287  -3.6276  -1.4545
 ZYZ  H1    H   HCH2  0   0.313  -3.7844  -1.7941  -0.2929
 ZYZ  H1A   H   HCH2  0   0.304  -3.8758  -0.8479  -1.7983
 ZYZ  HN1   H   HNH1  0   0.397   2.3524  -0.2126   1.3384
 ZYZ  H3    H   HCR6  0   0.255  -2.2532  -1.0281   1.5562
 ZYZ  H4    H   HCR6  0   0.251  -0.2001   0.1683   2.1559
 ZYZ  H6    H   HCR6  0   0.253  -0.3015   2.2265  -1.5949
 ZYZ  H7    H   HCR6  0   0.258  -2.3525   1.0277  -2.1982
 ZYZ  H8    H   HCH2  0   0.287   1.1038   3.0464   0.3705
 ZYZ  H8A   H   HCH2  0   0.274   1.3434   1.9871   1.7454
 ZYZ  H9    H   HCH1  0   0.297   2.1997   1.3916  -1.1220
 ZYZ  H12   H   HCH3  0   0.242   4.8372   4.5048   0.8421
 ZYZ  H12A  H   HCH3  0   0.242   5.6110   3.8351  -0.6122
 ZYZ  H12B  H   HCH3  0   0.254   4.4346   5.1569  -0.7593
 ZYZ  H14   H   HCH3  0   0.235   6.1816  -2.2783   0.4795
 ZYZ  H14A  H   HCH3  0   0.234   6.3039  -3.6013  -0.6756
 ZYZ  H14B  H   HCH3  0   0.247   5.8585  -1.9941  -1.2375
 ZYZ  H15   H   HCH3  0   0.238   3.1600  -4.3936   1.1388
 ZYZ  H15A  H   HCH3  0   0.231   4.7168  -5.0325   0.6145
 ZYZ  H15B  H   HCH3  0   0.238   4.6593  -3.7682   1.8415
 ZYZ  H16   H   HCH3  0   0.247   3.6913  -2.9302  -2.2869
 ZYZ  H16A  H   HCH3  0   0.235   4.1373  -4.5464  -1.7485
 ZYZ  H16B  H   HCH3  0   0.236   2.5794  -3.8723  -1.2815
 ZYZ  O51   O   O     0  -0.778  -6.3782  -1.0524  -0.4171
 ZYZ  O61   O   O     0  -0.759  -5.0057   0.0860   1.6294
 ZYZ  H23   H   H     0   0.484  -7.2668  -0.6764  -0.5016
 ZYZ  C11   C   C     0   0.767   3.3555  -0.8312  -0.3218
 ZYZ  O3    O   O     0  -0.436   4.5754   1.8134   0.8890
 ZYZ  O4    O   O2    0  -0.452   3.5902   3.3628  -0.3845

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
 ZYZ  SE   O51   single    1.781  0.020  1.781
 ZYZ  C1   SE    single    1.966  0.020  1.966
 ZYZ  C1   H1    single    0.970  0.020  1.090
 ZYZ  C1   H1A   single    0.970  0.020  1.090
 ZYZ  N1   C9    single    1.433  0.020  1.433
 ZYZ  N1   HN1   single    0.890  0.020  1.040
 ZYZ  C2   C1    single    1.491  0.020  1.491
 ZYZ  C3   C2    aromatic  1.393  0.020  1.393
 ZYZ  C3   H3    single    0.930  0.020  1.080
 ZYZ  C4   C3    aromatic  1.387  0.020  1.387
 ZYZ  C4   H4    single    0.930  0.020  1.080
 ZYZ  O4   C12   single    1.429  0.020  1.429
 ZYZ  O4   C10   single    1.322  0.020  1.322
 ZYZ  C5   C4    aromatic  1.391  0.020  1.391
 ZYZ  C5   C6    aromatic  1.393  0.020  1.393
 ZYZ  O5   C11   double    1.213  0.020  1.213
 ZYZ  C6   C7    aromatic  1.385  0.020  1.385
 ZYZ  C6   H6    single    0.930  0.020  1.080
 ZYZ  O6   C11   single    1.328  0.020  1.328
 ZYZ  C7   C2    aromatic  1.394  0.020  1.394
 ZYZ  C7   H7    single    0.930  0.020  1.080
 ZYZ  C8   C5    single    1.503  0.020  1.503
 ZYZ  C8   H8    single    0.970  0.020  1.090
 ZYZ  C8   H8A   single    0.970  0.020  1.090
 ZYZ  C9   C8    single    1.537  0.020  1.537
 ZYZ  C9   C10   single    1.525  0.020  1.525
 ZYZ  C9   H9    single    0.970  0.020  1.090
 ZYZ  C10  O3    double    1.203  0.020  1.203
 ZYZ  C11  N1    single    1.355  0.020  1.355
 ZYZ  C12  H12   single    0.970  0.020  1.090
 ZYZ  C12  H12A  single    0.970  0.020  1.090
 ZYZ  C12  H12B  single    0.970  0.020  1.090
 ZYZ  C13  O6    single    1.454  0.020  1.454
 ZYZ  C13  C14   single    1.524  0.020  1.524
 ZYZ  C14  H14   single    0.970  0.020  1.090
 ZYZ  C14  H14A  single    0.970  0.020  1.090
 ZYZ  C14  H14B  single    0.970  0.020  1.090
 ZYZ  C15  C13   single    1.524  0.020  1.524
 ZYZ  C15  H15   single    0.970  0.020  1.090
 ZYZ  C15  H15A  single    0.970  0.020  1.090
 ZYZ  C15  H15B  single    0.970  0.020  1.090
 ZYZ  C16  C13   single    1.524  0.020  1.524
 ZYZ  C16  H16   single    0.970  0.020  1.090
 ZYZ  C16  H16A  single    0.970  0.020  1.090
 ZYZ  C16  H16B  single    0.970  0.020  1.090
 ZYZ  SE   O61   double    1.618  0.020  1.618
 ZYZ  O51  H23   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
 ZYZ  O61   SE   O51   105.87  3.000
 ZYZ  O61   SE   C1    103.25  3.000
 ZYZ  O51   SE   C1     91.58  3.000
 ZYZ  H1A   C1   H1    109.20  3.000
 ZYZ  H1A   C1   C2    112.35  3.000
 ZYZ  H1    C1   C2    112.85  3.000
 ZYZ  C2    C1   SE    108.62  3.000
 ZYZ  H1A   C1   SE    107.17  3.000
 ZYZ  H1    C1   SE    106.30  3.000
 ZYZ  HN1   N1   C11   118.20  3.000
 ZYZ  C11   N1   C9    120.57  3.000
 ZYZ  HN1   N1   C9    118.02  3.000
 ZYZ  C7    C2   C3    118.57  3.000
 ZYZ  C7    C2   C1    120.57  3.000
 ZYZ  C3    C2   C1    120.82  3.000
 ZYZ  H3    C3   C4    119.58  3.000
 ZYZ  C4    C3   C2    120.58  3.000
 ZYZ  H3    C3   C2    119.84  3.000
 ZYZ  H4    C4   C5    119.81  3.000
 ZYZ  C5    C4   C3    120.95  3.000
 ZYZ  H4    C4   C3    119.24  3.000
 ZYZ  C8    C5   C6    120.22  3.000
 ZYZ  C8    C5   C4    121.40  3.000
 ZYZ  C6    C5   C4    118.36  3.000
 ZYZ  H6    C6   C7    119.36  3.000
 ZYZ  H6    C6   C5    119.76  3.000
 ZYZ  C7    C6   C5    120.88  3.000
 ZYZ  C13   O6   C11   122.60  3.000
 ZYZ  H7    C7   C6    119.53  3.000
 ZYZ  H7    C7   C2    119.81  3.000
 ZYZ  C6    C7   C2    120.66  3.000
 ZYZ  H8A   C8   H8    106.73  3.000
 ZYZ  H8A   C8   C9    109.50  3.000
 ZYZ  H8    C8   C9    108.75  3.000
 ZYZ  C9    C8   C5    111.59  3.000
 ZYZ  H8A   C8   C5    110.32  3.000
 ZYZ  H8    C8   C5    109.81  3.000
 ZYZ  H9    C9   C10   107.63  3.000
 ZYZ  H9    C9   C8    108.14  3.000
 ZYZ  C10   C9   C8    110.73  3.000
 ZYZ  H9    C9   N1    109.19  3.000
 ZYZ  C10   C9   N1    110.93  3.000
 ZYZ  C8    C9   N1    110.14  3.000
 ZYZ  C9    C10  O4    111.06  3.000
 ZYZ  C9    C10  O3    124.46  3.000
 ZYZ  O4    C10  O3    124.48  3.000
 ZYZ  H12B  C12  H12A  109.44  3.000
 ZYZ  H12B  C12  H12   109.43  3.000
 ZYZ  H12A  C12  H12   109.41  3.000
 ZYZ  H12B  C12  O4    105.90  3.000
 ZYZ  H12A  C12  O4    111.24  3.000
 ZYZ  H12   C12  O4    111.35  3.000
 ZYZ  C16   C13  C15   109.77  3.000
 ZYZ  C16   C13  C14   111.79  3.000
 ZYZ  C15   C13  C14   109.70  3.000
 ZYZ  C16   C13  O6    110.95  3.000
 ZYZ  C15   C13  O6    103.16  3.000
 ZYZ  C14   C13  O6    111.12  3.000
 ZYZ  H14B  C14  H14A  107.78  3.000
 ZYZ  H14B  C14  H14   108.68  3.000
 ZYZ  H14A  C14  H14   107.58  3.000
 ZYZ  H14B  C14  C13   112.60  3.000
 ZYZ  H14A  C14  C13   108.96  3.000
 ZYZ  H14   C14  C13   111.07  3.000
 ZYZ  H15B  C15  H15A  107.86  3.000
 ZYZ  H15B  C15  H15   108.43  3.000
 ZYZ  H15A  C15  H15   107.84  3.000
 ZYZ  H15B  C15  C13   111.48  3.000
 ZYZ  H15A  C15  C13   109.60  3.000
 ZYZ  H15   C15  C13   111.49  3.000
 ZYZ  H16B  C16  H16A  107.60  3.000
 ZYZ  H16B  C16  H16   108.69  3.000
 ZYZ  H16A  C16  H16   107.88  3.000
 ZYZ  H16B  C16  C13   111.09  3.000
 ZYZ  H16A  C16  C13   108.88  3.000
 ZYZ  H16   C16  C13   112.53  3.000
 ZYZ  H23   O51  SE    109.75  3.000
 ZYZ  O6    C11  O5    126.27  3.000
 ZYZ  O6    C11  N1    110.34  3.000
 ZYZ  O5    C11  N1    123.38  3.000
 ZYZ  C12   O4   C10   117.72  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
 ZYZ  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 ZYZ  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 ZYZ  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 ZYZ  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 ZYZ  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 ZYZ  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 ZYZ  CONST_07  C4   C3   C2   C1    180.00   0.0  0
 ZYZ  CONST_08  C6   C7   C2   C1    180.00   0.0  0
 ZYZ  CONST_09  C8   C5   C4   C3    180.00   0.0  0
 ZYZ  CONST_10  C8   C5   C6   C7    180.00   0.0  0
 ZYZ  CONST_11  H4   C4   C3   C2    180.00   0.0  0
 ZYZ  CONST_12  H6   C6   C7   C2    180.00   0.0  0
 ZYZ  CONST_13  H7   C7   C2   C3    180.00   0.0  0
 ZYZ  CONST_14  H3   C3   C4   C5    180.00   0.0  0
 ZYZ  Var_01    C3   C2   C1   SE     84.54  30.0  2
 ZYZ  Var_02    C9   C8   C5   C4    100.87  30.0  1
 ZYZ  Var_03    O51  SE   C1   C2   -172.38  30.0  3
 ZYZ  Var_04    C9   N1   C11  O5    -10.32  30.0  2
 ZYZ  Var_05    C14  C13  O6   C11    62.47  30.0  3
 ZYZ  Var_06    H14  C14  C13  O6     53.04  30.0  3
 ZYZ  Var_07    H15  C15  C13  O6     59.39  30.0  3
 ZYZ  Var_08    H16  C16  C13  O6     68.31  30.0  3
 ZYZ  Var_09    H12  C12  O4   C10   -60.03  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
 ZYZ  chir_01  C9  N1  C8  C10  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
 ZYZ  plan-1  C1   0.020
 ZYZ  plan-1  C2   0.020
 ZYZ  plan-1  C3   0.020
 ZYZ  plan-1  C4   0.020
 ZYZ  plan-1  C5   0.020
 ZYZ  plan-1  C6   0.020
 ZYZ  plan-1  C7   0.020
 ZYZ  plan-1  C8   0.020
 ZYZ  plan-1  H3   0.020
 ZYZ  plan-1  H4   0.020
 ZYZ  plan-1  H6   0.020
 ZYZ  plan-1  H7   0.020
 ZYZ  plan-2  N1   0.020
 ZYZ  plan-2  O5   0.020
 ZYZ  plan-2  O6   0.020
 ZYZ  plan-2  C11  0.020
 ZYZ  plan-3  C9   0.020
 ZYZ  plan-3  C10  0.020
 ZYZ  plan-3  O3   0.020
 ZYZ  plan-3  O4   0.020
 ZYZ  plan-4  SE   0.020
 ZYZ  plan-4  C1   0.020
 ZYZ  plan-4  O51  0.020
 ZYZ  plan-4  O61  0.020

