# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 11:10:34 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 3-(4H-selenopheno[3,2-b]pyrrol-6-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1c[nH]c2cc[se]c12)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
 32S  32S  3-(4H-selenopheno[3,2-b]pyrrol-6-yl)-L-alanine  L-peptide  23  14  .  2022-07-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_32S
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
 32S  N    N   NH2    0  -0.797   1.7328   0.8261   1.2827
 32S  CA   C   CH1    0  -0.192   2.4351  -0.1397   0.4600
 32S  CB   C   CH2    0  -0.539   1.6276  -0.6808  -0.7446
 32S  CG   C   CR5    0  -0.006   0.2935  -1.2392  -0.3736
 32S  CD2  C   CR55   0  -0.292  -0.9362  -0.5495  -0.2171
 32S  CE2  C   CR55   0   0.335  -1.9124  -1.4557   0.1688
 32S  SEL  SE  SE     0   0.225  -1.6666   1.1537  -0.3871
 32S  CD1  C   CR15   0  -0.093   0.0007  -2.5518  -0.0661
 32S  NE1  N   NR15   0  -0.666  -1.3194  -2.6761   0.2592
 32S  CZ2  C   CR15   0  -0.203  -3.2279  -0.9420   0.3576
 32S  CZ3  C   CR15   0  -0.519  -3.3069   0.3898   0.1174
 32S  C    C   C      0   0.399   3.7560   0.4428  -0.0844
 32S  O    O   O      0  -0.605   3.8518   1.6839  -0.1476
 32S  OXT  O   OC    -1  -0.623   4.6046  -0.3898  -0.4646
 32S  H    H   HNH2   0   0.325   1.5888   1.6758   0.7514
 32S  HN2  H   HNH2   0   0.340   0.8166   0.4705   1.5272
 32S  HA   H   HCH1   0   0.208   2.6749  -1.0021   1.0918
 32S  HB1  H   HCH2   0   0.225   1.4933   0.1273  -1.4728
 32S  HB2  H   HCH2   0   0.235   2.2227  -1.4501  -1.2408
 32S  HD1  H   HCR5   0   0.274   0.6531  -3.4110  -0.0650
 32S  HE1  H   HNR5   0   0.409  -1.7745  -3.5392   0.5041
 32S  HZ2  H   HCR5   0   0.272  -4.0795  -1.5366   0.6596
 32S  HZ3  H   HCR5   0   0.288  -4.1944   1.0015   0.1964

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
 32S  N    CA   single    1.458  0.019  1.458
 32S  N    H    single    0.860  0.020  0.860
 32S  N    HN2  single    0.890  0.020  1.040
 32S  CA   CB   single    1.521  0.033  1.521
 32S  CA   C    single    1.525  0.021  1.525
 32S  CA   HA   single    0.970  0.020  0.970
 32S  CB   CG   single    1.493  0.020  1.493
 32S  CB   HB1  single    0.970  0.020  1.090
 32S  CB   HB2  single    0.970  0.020  1.090
 32S  CG   CD2  aromatic  1.419  0.020  1.419
 32S  CG   CD1  aromatic  1.380  0.020  1.380
 32S  CD2  CE2  aromatic  1.387  0.020  1.387
 32S  CD2  SEL  aromatic  1.861  0.020  1.861
 32S  CE2  NE1  aromatic  1.360  0.020  1.360
 32S  CE2  CZ2  aromatic  1.425  0.020  1.425
 32S  SEL  CZ3  aromatic  1.878  0.020  1.878
 32S  CD1  NE1  aromatic  1.365  0.020  1.365
 32S  CD1  HD1  single    0.930  0.020  1.080
 32S  NE1  HE1  single    0.860  0.020  1.020
 32S  CZ2  CZ3  aromatic  1.356  0.020  1.356
 32S  CZ2  HZ2  single    0.930  0.020  1.080
 32S  CZ3  HZ3  single    0.930  0.020  1.080
 32S  C    O    deloc     1.231  0.020  1.231
 32S  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
 32S  HN2  N    H    107.02  3.000
 32S  HN2  N    CA   109.95  3.000
 32S  H    N    CA   114.00  3.000
 32S  HA   CA   C    110.00  3.000
 32S  HA   CA   CB   109.00  3.000
 32S  C    CA   CB   110.50  1.500
 32S  HA   CA   N    110.00  3.000
 32S  C    CA   N    111.00  2.800
 32S  CB   CA   N    110.40  1.500
 32S  HB2  CB   HB1  106.52  3.000
 32S  HB2  CB   CG   109.66  3.000
 32S  HB1  CB   CG   109.36  3.000
 32S  HB2  CB   CA   108.39  3.000
 32S  HB1  CB   CA   108.86  3.000
 32S  CG   CB   CA   113.79  3.000
 32S  CD1  CG   CD2  104.72  3.000
 32S  CD1  CG   CB   126.94  3.000
 32S  CD2  CG   CB   128.32  3.000
 32S  SEL  CD2  CE2  110.32  3.000
 32S  SEL  CD2  CG   140.82  3.000
 32S  CE2  CD2  CG   108.86  3.000
 32S  CZ2  CE2  NE1  135.84  3.000
 32S  CZ2  CE2  CD2  116.82  3.000
 32S  NE1  CE2  CD2  107.34  3.000
 32S  CZ3  SEL  CD2   86.90  3.000
 32S  HD1  CD1  NE1  120.79  3.000
 32S  HD1  CD1  CG   129.02  3.000
 32S  NE1  CD1  CG   110.18  3.000
 32S  HE1  NE1  CD1  125.00  3.000
 32S  HE1  NE1  CE2  126.08  3.000
 32S  CD1  NE1  CE2  108.91  3.000
 32S  HZ2  CZ2  CZ3  122.94  3.000
 32S  HZ2  CZ2  CE2  124.45  3.000
 32S  CZ3  CZ2  CE2  112.62  3.000
 32S  HZ3  CZ3  CZ2  126.22  3.000
 32S  HZ3  CZ3  SEL  120.44  3.000
 32S  CZ2  CZ3  SEL  113.34  3.000
 32S  OXT  C    O    126.61  3.000
 32S  OXT  C    CA   120.80  1.700
 32S  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
 32S  CONST_01  NE1  CE2  CD2  CG     0.00   0.0  0
 32S  CONST_02  CZ2  CE2  CD2  CG   180.00   0.0  0
 32S  CONST_03  CZ3  SEL  CD2  CG   180.00   0.0  0
 32S  CONST_04  CE2  NE1  CD1  CG     0.00   0.0  0
 32S  CONST_05  NE1  CD1  CG   CD2    0.00   0.0  0
 32S  CONST_06  CD1  NE1  CE2  CD2    0.00   0.0  0
 32S  CONST_07  CZ3  CZ2  CE2  CD2    0.00   0.0  0
 32S  CONST_08  CZ2  CZ3  SEL  CD2    0.00   0.0  0
 32S  CONST_09  CD1  CG   CD2  CE2    0.00   0.0  0
 32S  CONST_10  CZ3  SEL  CD2  CE2    0.00   0.0  0
 32S  CONST_11  SEL  CZ3  CZ2  CE2    0.00   0.0  0
 32S  CONST_12  CD1  CG   CD2  SEL  180.00   0.0  0
 32S  CONST_13  NE1  CE2  CD2  SEL  180.00   0.0  0
 32S  CONST_14  CZ2  CE2  CD2  SEL    0.00   0.0  0
 32S  CONST_15  CZ2  CE2  NE1  CD1  180.00   0.0  0
 32S  CONST_16  CZ3  CZ2  CE2  NE1  180.00   0.0  0
 32S  CONST_17  CE2  CD2  CG   CB   180.00   0.0  0
 32S  CONST_18  SEL  CD2  CG   CB     0.00   0.0  0
 32S  CONST_19  NE1  CD1  CG   CB   180.00   0.0  0
 32S  CONST_20  HE1  NE1  CD1  CG   180.00   0.0  0
 32S  CONST_21  HD1  CD1  CG   CD2  180.00   0.0  0
 32S  CONST_22  HZ2  CZ2  CE2  CD2  180.00   0.0  0
 32S  CONST_23  HZ3  CZ3  SEL  CD2  180.00   0.0  0
 32S  Var_01    CD2  CG   CB   CA    85.71  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
 32S  chir_01  CA  N  CB  C  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
 32S  plan-1  CB   0.020
 32S  plan-1  CG   0.020
 32S  plan-1  CD2  0.020
 32S  plan-1  CE2  0.020
 32S  plan-1  SEL  0.020
 32S  plan-1  CD1  0.020
 32S  plan-1  NE1  0.020
 32S  plan-1  CZ2  0.020
 32S  plan-1  CZ3  0.020
 32S  plan-1  HD1  0.020
 32S  plan-1  HE1  0.020
 32S  plan-1  HZ2  0.020
 32S  plan-1  HZ3  0.020
 32S  plan-2  CA   0.020
 32S  plan-2  C    0.020
 32S  plan-2  O    0.020
 32S  plan-2  OXT  0.020

