# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:11:18 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: S-[(2-carbamoylphenyl)selanyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS[Se]c1ccccc1C(N)=O)C(O)=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
 30V  30V  S-[(2-carbamoylphenyl)selanyl]-L-cysteine  L-peptide  28  17  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_30V
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
 30V  N    N   NH2    0  -0.765  -2.8656   0.0004  -1.3264
 30V  CA   C   CH1    0  -0.192  -3.1850  -0.3105   0.0527
 30V  CB   C   CH2    0  -0.566  -1.9214  -0.3370   0.9114
 30V  SG   S   S2     0  -0.081  -0.6581  -1.4847   0.2905
 30V  SE   SE  SE     0   0.088   0.2257  -0.3550  -1.3679
 30V  C06  C   CR6    0  -0.151   1.9633   0.0387  -0.6541
 30V  C07  C   CR6    0  -0.026   2.7704  -0.8600   0.0510
 30V  C08  C   C      0   0.457   2.3917  -2.2977   0.2551
 30V  N09  N   NH2    0  -0.789   2.5998  -2.7666   1.4932
 30V  O16  O   O      0  -0.472   1.9824  -2.9880  -0.6655
 30V  C17  C   CR16   0  -0.256   4.0182  -0.4383   0.5074
 30V  C18  C   CR16   0  -0.255   4.4826   0.8430   0.2499
 30V  C19  C   CR16   0  -0.237   3.6846   1.7278  -0.4570
 30V  C20  C   CR16   0  -0.272   2.4265   1.3309  -0.8892
 30V  C    C   C      0   0.389  -4.2023   0.6402   0.7438
 30V  O    O   O      0  -0.599  -4.4780   1.7052   0.1612
 30V  H    H   HNH2   0   0.344  -3.6625  -0.2314  -1.9064
 30V  H2   H   HNH2   0   0.330  -2.7617   1.0047  -1.4147
 30V  HA   H   HCH1   0   0.227  -3.6051  -1.3208   0.0727
 30V  HB2  H   HCH2   0   0.270  -1.4788   0.6558   1.0179
 30V  HB1  H   HCH2   0   0.283  -2.1625  -0.6974   1.9131
 30V  H7   H   HNH2   0   0.411   2.8119  -2.1563   2.2635
 30V  H8   H   HNH2   0   0.404   2.3710  -3.7228   1.7123
 30V  H9   H   HCR6   0   0.270   4.6505  -1.1305   1.0491
 30V  H10  H   HCR6   0   0.266   5.4600   1.1432   0.6024
 30V  H11  H   HCR6   0   0.267   4.0257   2.7347  -0.6587
 30V  H12  H   HCR6   0   0.271   1.7993   2.0473  -1.4062
 30V  OXT  O   OC    -1  -0.617  -4.6334   0.2536   1.8488

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
 30V  O    C    deloc     1.231  0.020  1.231
 30V  C    CA   single    1.525  0.021  1.525
 30V  CA   CB   single    1.530  0.020  1.530
 30V  CA   N    single    1.458  0.019  1.458
 30V  CB   SG   single    1.816  0.020  1.816
 30V  C19  C18  aromatic  1.385  0.020  1.385
 30V  C19  C20  aromatic  1.388  0.020  1.388
 30V  C18  C17  aromatic  1.387  0.020  1.387
 30V  C20  C06  aromatic  1.393  0.020  1.393
 30V  C17  C07  aromatic  1.394  0.020  1.394
 30V  SG   SE   single    2.193  0.020  2.193
 30V  C06  C07  aromatic  1.399  0.020  1.399
 30V  C06  SE   single    1.919  0.020  1.919
 30V  C07  C08  single    1.501  0.020  1.501
 30V  C08  O16  double    1.221  0.020  1.221
 30V  C08  N09  single    1.340  0.020  1.340
 30V  N    H    single    0.860  0.020  0.860
 30V  N    H2   single    0.890  0.020  1.040
 30V  CA   HA   single    0.970  0.020  0.970
 30V  CB   HB2  single    0.970  0.020  1.090
 30V  CB   HB1  single    0.970  0.020  1.090
 30V  N09  H7   single    0.860  0.020  1.020
 30V  N09  H8   single    0.860  0.020  1.020
 30V  C17  H9   single    0.930  0.020  1.080
 30V  C18  H10  single    0.930  0.020  1.080
 30V  C19  H11  single    0.930  0.020  1.080
 30V  C20  H12  single    0.930  0.020  1.080
 30V  C    OXT  deloc     1.248  0.020  1.248

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
 30V  H2   N    H    104.93  3.000
 30V  H2   N    CA   108.55  3.000
 30V  H    N    CA   114.00  3.000
 30V  HA   CA   C    109.00  3.000
 30V  HA   CA   CB   109.00  3.000
 30V  C    CA   CB   110.10  1.900
 30V  HA   CA   N    110.00  3.000
 30V  CB   CA   N    110.50  1.700
 30V  C    CA   N    111.00  2.800
 30V  HB1  CB   HB2  107.47  3.000
 30V  HB1  CB   SG   105.00  3.000
 30V  HB2  CB   SG   109.02  3.000
 30V  HB1  CB   CA   109.81  3.000
 30V  HB2  CB   CA   111.97  3.000
 30V  SG   CB   CA   113.21  3.000
 30V  SE   SG   CB   102.32  3.000
 30V  C06  SE   SG   100.91  3.000
 30V  C20  C06  C07  119.30  3.000
 30V  C07  C06  SE   125.32  3.000
 30V  C20  C06  SE   115.38  3.000
 30V  C17  C07  C08  118.11  3.000
 30V  C08  C07  C06  122.58  3.000
 30V  C17  C07  C06  119.16  3.000
 30V  O16  C08  N09  123.41  3.000
 30V  N09  C08  C07  114.94  3.000
 30V  O16  C08  C07  121.57  3.000
 30V  H8   N09  H7   117.23  3.000
 30V  H8   N09  C08  119.86  3.000
 30V  H7   N09  C08  121.88  3.000
 30V  H9   C17  C18  119.21  3.000
 30V  H9   C17  C07  119.55  3.000
 30V  C18  C17  C07  121.22  3.000
 30V  H10  C18  C19  120.63  3.000
 30V  H10  C18  C17  119.90  3.000
 30V  C19  C18  C17  119.47  3.000
 30V  H11  C19  C20  119.58  3.000
 30V  H11  C19  C18  120.52  3.000
 30V  C20  C19  C18  119.88  3.000
 30V  H12  C20  C19  118.96  3.000
 30V  H12  C20  C06  120.10  3.000
 30V  C19  C20  C06  120.94  3.000
 30V  OXT  C    O    127.09  3.000
 30V  OXT  C    CA   115.50  3.000
 30V  O    C    CA   120.80  1.700

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
 30V  CONST_01  C18  C19  C20  C06     0.00   0.0  0
 30V  CONST_02  C18  C17  C07  C06     0.00   0.0  0
 30V  CONST_03  C19  C18  C17  C07     0.00   0.0  0
 30V  CONST_04  C19  C20  C06  C07     0.00   0.0  0
 30V  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 30V  CONST_06  C20  C06  C07  C17     0.00   0.0  0
 30V  CONST_07  C19  C20  C06  SE    180.00   0.0  0
 30V  CONST_08  C17  C07  C06  SE    180.00   0.0  0
 30V  CONST_09  C18  C17  C07  C08   180.00   0.0  0
 30V  CONST_10  C20  C06  C07  C08   180.00   0.0  0
 30V  CONST_11  H11  C19  C20  C06   180.00   0.0  0
 30V  CONST_12  H9   C17  C07  C06   180.00   0.0  0
 30V  CONST_13  H10  C18  C17  C07   180.00   0.0  0
 30V  CONST_14  H12  C20  C06  C07   180.00   0.0  0
 30V  CONST_15  H7   N09  C08  C07     0.00   0.0  0
 30V  CONST_16  H8   N09  C08  C07   180.00   0.0  0
 30V  Var_01    C20  C06  SE   SG   -137.93  30.0  1
 30V  Var_02    O16  C08  C07  C06    46.73  30.0  2
 30V  Var_03    HB2  CB   SG   SE    -47.21  30.0  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
 30V  chir_01  CA  C  CB  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
 30V  plan-1  SE   0.020
 30V  plan-1  C06  0.020
 30V  plan-1  C07  0.020
 30V  plan-1  C08  0.020
 30V  plan-1  C17  0.020
 30V  plan-1  C18  0.020
 30V  plan-1  C19  0.020
 30V  plan-1  C20  0.020
 30V  plan-1  H9   0.020
 30V  plan-1  H10  0.020
 30V  plan-1  H11  0.020
 30V  plan-1  H12  0.020
 30V  plan-2  C07  0.020
 30V  plan-2  C08  0.020
 30V  plan-2  N09  0.020
 30V  plan-2  O16  0.020
 30V  plan-2  H7   0.020
 30V  plan-2  H8   0.020
 30V  plan-3  CA   0.020
 30V  plan-3  C    0.020
 30V  plan-3  O    0.020
 30V  plan-3  OXT  0.020

