# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:01:58 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[2-(selanylmethyl)acryloyl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN1C(=O)C(=C)C[SeH]
#
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
 SLC  SLC  1-[2-(selanylmethyl)acryloyl]-L-proline  ligand  26  14  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SLC
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
 SLC  C4    C   C      0   0.524   0.4540  -0.6958  -0.4775
 SLC  O1    O   O      0  -0.506   0.8547  -1.8466  -0.3359
 SLC  C2    C   C      0  -0.018  -1.0004  -0.4182  -0.7337
 SLC  C3    C   C2     0  -0.523  -1.5596  -0.7837  -1.8830
 SLC  C1    C   CH2    0  -0.620  -1.7821   0.1945   0.3829
 SLC  SE    SE  SE     0  -0.176  -2.1157  -1.2092   1.7362
 SLC  N     N   NR5    0  -0.451   1.2603   0.3659  -0.4245
 SLC  C8    C   CR15   0  -0.148   2.6652   0.2144  -0.0754
 SLC  C9    C   C      0   0.402   2.8768  -0.3075   1.3602
 SLC  O3    O   O      0  -0.591   1.9881  -0.0529   2.1886
 SLC  C7    C   CH2    0  -0.492   3.2223   1.6408  -0.2269
 SLC  C6    C   CH2    0  -0.457   2.2328   2.3361  -1.1567
 SLC  C5    C   CH2    0  -0.280   0.9018   1.7445  -0.7159
 SLC  O2    O   OC    -1  -0.621   3.9647  -0.8852   1.5610
 SLC  H31C  H   H      0   0.253  -2.6133  -0.6212  -2.0729
 SLC  H32C  H   H      0   0.256  -0.9854  -1.2444  -2.6764
 SLC  H11C  H   HCH2   0   0.289  -1.2349   1.0002   0.8719
 SLC  H12C  H   HCH2   0   0.285  -2.7360   0.5805   0.0265
 SLC  HSE   H   H      0   0.188  -2.5526  -0.2977   2.7837
 SLC  H8    H   HCR5   0   0.232   3.1499  -0.4570  -0.7904
 SLC  H71C  H   HCH2   0   0.234   3.2280   2.1530   0.7389
 SLC  H72C  H   HCH2   0   0.250   4.2442   1.6414  -0.6032
 SLC  H61C  H   HCH2   0   0.246   2.2537   3.4223  -1.0711
 SLC  H62C  H   HCH2   0   0.236   2.4284   2.0747  -2.1989
 SLC  H51C  H   HCH2   0   0.233   0.5336   2.2567   0.1795
 SLC  H52C  H   HCH2   0   0.256   0.1316   1.8056  -1.4840

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
 SLC  O2  C9    deloc   1.248  0.020  1.248
 SLC  C9  O3    deloc   1.241  0.020  1.241
 SLC  C9  C8    single  1.542  0.020  1.542
 SLC  C8  C7    single  1.539  0.020  1.539
 SLC  C8  N     single  1.456  0.020  1.456
 SLC  C7  C6    single  1.526  0.020  1.526
 SLC  C6  C5    single  1.522  0.020  1.522
 SLC  C5  N     single  1.454  0.020  1.454
 SLC  N   C4    single  1.334  0.020  1.334
 SLC  C4  O1    double  1.227  0.020  1.227
 SLC  C4  C2    single  1.503  0.020  1.503
 SLC  C2  C3    double  1.329  0.020  1.329
 SLC  C2  C1    single  1.494  0.020  1.494
 SLC  C1  SE    single  1.978  0.020  1.978
 SLC  SE  HSE   single  1.444  0.020  1.000
 SLC  C7  H71C  single  0.939  0.020  1.096
 SLC  C7  H72C  single  0.939  0.020  1.096
 SLC  C6  H61C  single  0.939  0.020  1.096
 SLC  C6  H62C  single  0.939  0.020  1.096
 SLC  C5  H51C  single  0.939  0.020  1.096
 SLC  C5  H52C  single  0.939  0.020  1.096
 SLC  C3  H31C  single  0.930  0.020  1.086
 SLC  C3  H32C  single  0.930  0.020  1.086
 SLC  C1  H11C  single  0.939  0.020  1.096
 SLC  C1  H12C  single  0.939  0.020  1.096
 SLC  C8  H8    single  0.939  0.020  1.096

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
 SLC  N     C4  C2    116.40  3.000
 SLC  C2    C4  O1    120.61  3.000
 SLC  N     C4  O1    122.99  3.000
 SLC  C1    C2  C3    122.59  3.000
 SLC  C1    C2  C4    117.04  3.000
 SLC  C3    C2  C4    120.25  3.000
 SLC  H32C  C3  H31C  116.84  3.000
 SLC  H32C  C3  C2    121.85  3.000
 SLC  H31C  C3  C2    121.31  3.000
 SLC  H12C  C1  H11C  108.94  3.000
 SLC  H12C  C1  SE    109.13  3.000
 SLC  H11C  C1  SE    107.60  3.000
 SLC  H12C  C1  C2    111.04  3.000
 SLC  H11C  C1  C2    112.07  3.000
 SLC  SE    C1  C2    107.96  3.000
 SLC  HSE   SE  C1     95.66  3.000
 SLC  C5    N   C8    112.63  3.000
 SLC  C5    N   C4    126.69  3.000
 SLC  C8    N   C4    120.66  3.000
 SLC  H8    C8  C7    110.13  3.000
 SLC  H8    C8  C9    109.87  3.000
 SLC  C7    C8  C9    110.84  3.000
 SLC  H8    C8  N     109.55  3.000
 SLC  C7    C8  N     103.26  3.000
 SLC  C9    C8  N     113.01  3.000
 SLC  O2    C9  O3    127.71  3.000
 SLC  O3    C9  C8    116.97  3.000
 SLC  O2    C9  C8    115.21  3.000
 SLC  H72C  C7  H71C  107.47  3.000
 SLC  H72C  C7  C6    113.44  3.000
 SLC  H71C  C7  C6    109.16  3.000
 SLC  H72C  C7  C8    111.98  3.000
 SLC  H71C  C7  C8    110.44  3.000
 SLC  C6    C7  C8    104.34  3.000
 SLC  H62C  C6  H61C  108.07  3.000
 SLC  H62C  C6  C5    109.87  3.000
 SLC  H61C  C6  C5    112.43  3.000
 SLC  H62C  C6  C7    110.87  3.000
 SLC  H61C  C6  C7    113.20  3.000
 SLC  C5    C6  C7    102.34  3.000
 SLC  H52C  C5  H51C  108.21  3.000
 SLC  H52C  C5  C6    113.10  3.000
 SLC  H51C  C5  C6    110.43  3.000
 SLC  H52C  C5  N     111.64  3.000
 SLC  H51C  C5  N     111.25  3.000
 SLC  C6    C5  N     102.18  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
 SLC  CONST_01  C8    N   C4  O1    0.00   0.0  0
 SLC  CONST_02  C5    N   C4  O1  180.00   0.0  0
 SLC  CONST_03  C8    N   C4  C2  180.00   0.0  0
 SLC  CONST_04  C5    N   C4  C2    0.00   0.0  0
 SLC  Var_01    C7    C6  C5  N   -37.33  30.0  1
 SLC  Var_02    C5    C6  C7  C8   36.74  30.0  1
 SLC  Var_03    C6    C5  N   C8   25.34  30.0  1
 SLC  Var_04    N     C4  C2  C3  111.48  30.0  2
 SLC  Var_05    SE    C1  C2  C4  -74.62  30.0  3
 SLC  Var_06    H31C  C3  C2  C4  177.99   0.0  2

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
 SLC  chir_01  C8  C9  C7  N  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
 SLC  plan-1  C4    0.020
 SLC  plan-1  O1    0.020
 SLC  plan-1  C2    0.020
 SLC  plan-1  N     0.020
 SLC  plan-1  C8    0.020
 SLC  plan-1  C5    0.020
 SLC  plan-2  C8    0.020
 SLC  plan-2  C9    0.020
 SLC  plan-2  O3    0.020
 SLC  plan-2  O2    0.020
 SLC  plan-3  C4    0.020
 SLC  plan-3  C2    0.020
 SLC  plan-3  C3    0.020
 SLC  plan-3  C1    0.020
 SLC  plan-3  H31C  0.020
 SLC  plan-3  H32C  0.020

