# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:04:02 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: (2~{R})-5-oxidanylidene-1,2-dihydropyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1NC(=O)C=C1
#
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
 7YL  7YL  '(2~{R})-5-oxidanylidene-1,2-dihydropyrrole-2-carboxylic acid'  peptide  13  9  .  2019-03-22  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_7YL
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
 7YL  C    C  C      0   0.417  4.5175  -31.8050  -26.7491
 7YL  O    O  O      0  -0.574  3.3269  -31.6681  -26.4410
 7YL  CA   C  CR15   0  -0.222  4.8838  -31.6498  -28.2650
 7YL  N    N  NR15   0  -0.637  3.7929  -31.3404  -29.1443
 7YL  CB   C  CR15   0  -0.193  5.3712  -32.9426  -28.8276
 7YL  CG   C  CR15   0  -0.379  4.5997  -33.3301  -29.8433
 7YL  CD   C  CR5    0   0.494  3.5380  -32.3186  -30.0462
 7YL  OE   O  O      0  -0.499  2.6223  -32.3450  -30.8560
 7YL  HA   H  HCR5   0   0.267  5.6726  -30.8899  -28.3316
 7YL  H    H  HNR5   0   0.386  3.1260  -30.6156  -28.9356
 7YL  HB   H  HCR5   0   0.269  6.2337  -33.4557  -28.4285
 7YL  HG   H  HCR5   0   0.261  4.6881  -34.2284  -30.4362
 7YL  OXT  O  OC    -1  -0.592  5.4964  -32.0521  -26.0262

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
 7YL  OE  CD   double  1.223  0.020  1.223
 7YL  CD  CG   single  1.480  0.020  1.480
 7YL  CD  N    single  1.473  0.014  1.473
 7YL  CG  CB   double  1.333  0.020  1.333
 7YL  N   CA   single  1.458  0.019  1.458
 7YL  CB  CA   single  1.521  0.033  1.521
 7YL  CA  C    single  1.525  0.021  1.525
 7YL  C   O    deloc   1.231  0.020  1.231
 7YL  CA  HA   single  0.970  0.020  0.970
 7YL  N   H    single  0.860  0.020  0.860
 7YL  CB  HB   single  0.930  0.020  1.080
 7YL  CG  HG   single  0.930  0.020  1.080
 7YL  C   OXT  deloc   1.242  0.020  1.242

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
 7YL  OXT  C   CA  120.80  1.700
 7YL  OXT  C   O   129.47  3.000
 7YL  CA   C   O   120.80  1.700
 7YL  HA   CA  CB  109.00  3.000
 7YL  HA   CA  N   110.00  3.000
 7YL  CB   CA  N   110.40  1.500
 7YL  HA   CA  C   110.00  3.000
 7YL  CB   CA  C   110.50  1.500
 7YL  N    CA  C   111.00  2.800
 7YL  H    N   CD  122.22  3.000
 7YL  H    N   CA  114.00  3.000
 7YL  CD   N   CA  113.29  3.000
 7YL  HB   CB  CG  127.27  3.000
 7YL  HB   CB  CA  122.23  3.000
 7YL  CG   CB  CA  110.50  3.000
 7YL  HG   CG  CD  123.49  3.000
 7YL  HG   CG  CB  127.79  3.000
 7YL  CD   CG  CB  108.71  3.000
 7YL  OE   CD  CG  127.81  3.000
 7YL  CG   CD  N   103.20  1.500
 7YL  OE   CD  N   126.69  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
 7YL  CONST_01  CG  CD  N   CA    0.00   0.0  0
 7YL  CONST_02  OE  CD  N   CA  180.00   0.0  0
 7YL  CONST_03  H   N   CD  CG  180.00   0.0  0
 7YL  Var_01    CD  CG  CB  CA    0.39  30.0  1
 7YL  Var_02    CB  CG  CD  N     2.56  30.0  1

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
 7YL  chir_01  CA  N  CB  C  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
 7YL  plan-1  CA   0.020
 7YL  plan-1  N    0.020
 7YL  plan-1  CG   0.020
 7YL  plan-1  CD   0.020
 7YL  plan-1  OE   0.020
 7YL  plan-1  H    0.020
 7YL  plan-2  C    0.020
 7YL  plan-2  O    0.020
 7YL  plan-2  CA   0.020
 7YL  plan-2  OXT  0.020

