# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 14:22:43 2022
#   Inital geometry file: a 40 line input string
#   Ligand name: (3S)-3-aminopyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCNC1=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
 YV4  YV4  (3S)-3-aminopyrrolidin-2-one  ligand  15  7  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YV4
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
 YV4  N01   N  NH2   0  -0.783   9.7136  21.6834  -33.2789
 YV4  C02   C  CH1   0  -0.221   9.0247  22.5206  -32.3268
 YV4  C03   C  CH2   0  -0.476   9.7931  23.7802  -31.9390
 YV4  C04   C  CH2   0  -0.260   8.6988  24.7446  -31.4811
 YV4  N05   N  NH1   0  -0.625   7.5578  24.3136  -32.2643
 YV4  C06   C  C     0   0.512   7.6649  23.0727  -32.7650
 YV4  O07   O  O     0  -0.486   6.8346  22.4806  -33.4342
 YV4  H012  H  HNH2  0   0.349   9.1484  20.8718  -33.4958
 YV4  H1    H  HNH2  0   0.342   9.8344  22.1830  -34.1523
 YV4  H021  H  HCH1  0   0.267   8.8337  21.9228  -31.4264
 YV4  H032  H  HCH2  0   0.256  10.5452  23.6069  -31.1716
 YV4  H031  H  HCH2  0   0.244  10.2976  24.1830  -32.8214
 YV4  H042  H  HCH2  0   0.235   8.5022  24.6487  -30.4093
 YV4  H041  H  HCH2  0   0.251   8.9422  25.7869  -31.6842
 YV4  H051  H  HNH1  0   0.394   6.7041  24.8476  -32.3194

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
 YV4  C02  N01   single  1.443  0.020  1.443
 YV4  C03  C02   single  1.526  0.020  1.526
 YV4  C04  C03   single  1.529  0.020  1.529
 YV4  N05  C04   single  1.449  0.020  1.449
 YV4  C06  N05   single  1.342  0.020  1.342
 YV4  O07  C06   double  1.220  0.020  1.220
 YV4  C02  C06   single  1.532  0.020  1.532
 YV4  N01  H012  single  0.890  0.020  1.040
 YV4  N01  H1    single  0.890  0.020  1.040
 YV4  C02  H021  single  0.970  0.020  1.090
 YV4  C03  H032  single  0.970  0.020  1.090
 YV4  C03  H031  single  0.970  0.020  1.090
 YV4  C04  H042  single  0.970  0.020  1.090
 YV4  C04  H041  single  0.970  0.020  1.090
 YV4  N05  H051  single  0.860  0.020  1.020

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
 YV4  H1    N01  H012  106.08  3.000
 YV4  H1    N01  C02   109.85  3.000
 YV4  H012  N01  C02   109.87  3.000
 YV4  H021  C02  C06   106.06  3.000
 YV4  H021  C02  C03   109.20  3.000
 YV4  C06   C02  C03   102.84  3.000
 YV4  H021  C02  N01   107.96  3.000
 YV4  C06   C02  N01   116.37  3.000
 YV4  C03   C02  N01   113.97  3.000
 YV4  H031  C03  H032  107.99  3.000
 YV4  H031  C03  C04   109.86  3.000
 YV4  H032  C03  C04   112.58  3.000
 YV4  H031  C03  C02   109.36  3.000
 YV4  H032  C03  C02   113.31  3.000
 YV4  C04   C03  C02   103.67  3.000
 YV4  H041  C04  H042  107.86  3.000
 YV4  H041  C04  N05   111.08  3.000
 YV4  H042  C04  N05   111.22  3.000
 YV4  H041  C04  C03   112.81  3.000
 YV4  H042  C04  C03   111.52  3.000
 YV4  N05   C04  C03   102.36  3.000
 YV4  H051  N05  C06   122.45  3.000
 YV4  H051  N05  C04   122.58  3.000
 YV4  C06   N05  C04   114.43  3.000
 YV4  O07   C06  N05   126.80  3.000
 YV4  O07   C06  C02   125.90  3.000
 YV4  N05   C06  C02   107.30  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
 YV4  CONST_01  C04   N05  C06  C02    0.00   0.0  0
 YV4  CONST_02  O07   C06  N05  C04  180.00   0.0  0
 YV4  CONST_03  H051  N05  C06  C02  180.00   0.0  0
 YV4  Var_01    N05   C04  C03  C02  -29.03  30.0  1
 YV4  Var_02    C06   N05  C04  C03   19.08  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
 YV4  chir_01  C02  N01  C03  C06  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
 YV4  plan-1  C02   0.020
 YV4  plan-1  C04   0.020
 YV4  plan-1  N05   0.020
 YV4  plan-1  C06   0.020
 YV4  plan-1  O07   0.020
 YV4  plan-1  H051  0.020

