# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 14:41:06 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-[(2S)-2-amino-3-hydroxypropyl]pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)CC1=CC=CNC1=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
 YOP  YOP  "3-[(2S)-2-amino-3-hydroxypropyl]pyridin-2(5H)-one"
  ligand  24  12  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YOP
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
 YOP  CA   C  CH1   0  -0.151  13.1676  -2.2972  16.5018
 YOP  CB   C  CH2   0  -0.452  14.0134  -3.1260  15.5432
 YOP  C    C  CH2   0  -0.146  12.9129  -0.9019  15.9344
 YOP  CG   C  CR6   0  -0.127  14.5426  -4.4299  16.0654
 YOP  CD1  C  CR16  0  -0.170  14.4041  -4.8722  17.3470
 YOP  CE1  C  CR16  0  -0.380  14.9565  -6.1021  17.7853
 YOP  CF   C  CR16  0   0.033  15.6360  -6.8533  16.8877
 YOP  CD2  C  CR6   0   0.522  15.2725  -5.2402  15.1087
 YOP  N    N  NH2   0  -0.786  11.9240  -2.9942  16.7958
 YOP  NE2  N  NR16  0  -0.657  15.7740  -6.4216  15.6118
 YOP  OD2  O  O     0  -0.498  15.4586  -4.9415  13.9302
 YOP  O    O  OH1   0  -0.666  14.1308  -0.2042  15.8059
 YOP  HA   H  HCH1  0   0.225  13.7076  -2.1716  17.4476
 YOP  HB1  H  HCH2  0   0.251  14.8603  -2.5233  15.2032
 YOP  HB2  H  HCH2  0   0.233  13.4225  -3.3163  14.6386
 YOP  HC2  H  HCH2  0   0.198  12.2225  -0.3781  16.6103
 YOP  HC1  H  HCH2  0   0.184  12.3972  -1.0043  14.9681
 YOP  HD1  H  HCR6  0   0.266  13.8478  -4.2787  18.0599
 YOP  HE1  H  HCR6  0   0.268  14.8396  -6.4380  18.8043
 YOP  HF   H  HCR6  0   0.303  16.0915  -7.8047  17.1203
 YOP  H    H  HNH2  0   0.345  11.3541  -2.4364  17.4203
 YOP  H42  H  HOH1  0   0.453  13.9526   0.6427  15.3880
 YOP  H2   H  HNH2  0   0.338  11.3859  -3.1003  15.9431
 YOP  HE2  H  HNR6  0   0.415  16.2865  -7.0008  14.9601

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
 YOP  OD2  CD2  double  1.230  0.020  1.230
 YOP  CD2  NE2  single  1.379  0.020  1.379
 YOP  CD2  CG   single  1.451  0.020  1.451
 YOP  CB   CG   single  1.501  0.020  1.501
 YOP  CB   CA   single  1.524  0.020  1.524
 YOP  NE2  CF   single  1.354  0.020  1.354
 YOP  CG   CD1  double  1.363  0.020  1.363
 YOP  O    C    single  1.409  0.020  1.409
 YOP  C    CA   single  1.528  0.020  1.528
 YOP  CA   N    single  1.456  0.020  1.456
 YOP  CF   CE1  double  1.353  0.020  1.353
 YOP  CD1  CE1  single  1.418  0.020  1.418
 YOP  CA   HA   single  0.970  0.020  1.090
 YOP  CB   HB1  single  0.970  0.020  1.090
 YOP  CB   HB2  single  0.970  0.020  1.090
 YOP  C    HC2  single  0.970  0.020  1.090
 YOP  C    HC1  single  0.970  0.020  1.090
 YOP  CD1  HD1  single  0.930  0.020  1.080
 YOP  CE1  HE1  single  0.930  0.020  1.080
 YOP  CF   HF   single  0.930  0.020  1.080
 YOP  N    H    single  0.860  0.020  1.020
 YOP  O    H42  single  0.850  0.020  0.980
 YOP  N    H2   single  0.890  0.020  1.040
 YOP  NE2  HE2  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
 YOP  HA   CA   N    107.54  3.000
 YOP  HA   CA   C    107.33  3.000
 YOP  N    CA   C    111.71  3.000
 YOP  HA   CA   CB   109.37  3.000
 YOP  N    CA   CB   109.93  3.000
 YOP  C    CA   CB   110.84  3.000
 YOP  HB2  CB   HB1  104.85  3.000
 YOP  HB2  CB   CG   109.03  3.000
 YOP  HB1  CB   CG   108.29  3.000
 YOP  HB2  CB   CA   108.31  3.000
 YOP  HB1  CB   CA   109.01  3.000
 YOP  CG   CB   CA   116.70  3.000
 YOP  HC1  C    HC2  106.86  3.000
 YOP  HC1  C    O    111.78  3.000
 YOP  HC2  C    O    111.28  3.000
 YOP  HC1  C    CA   108.63  3.000
 YOP  HC2  C    CA   108.16  3.000
 YOP  O    C    CA   109.99  3.000
 YOP  CD2  CG   CD1  119.34  3.000
 YOP  CD1  CG   CB   124.98  3.000
 YOP  CD2  CG   CB   115.67  3.000
 YOP  HD1  CD1  CE1  118.20  3.000
 YOP  HD1  CD1  CG   119.60  3.000
 YOP  CE1  CD1  CG   122.19  3.000
 YOP  HE1  CE1  CF   120.51  3.000
 YOP  HE1  CE1  CD1  121.32  3.000
 YOP  CF   CE1  CD1  118.17  3.000
 YOP  HF   CF   NE2  116.15  3.000
 YOP  HF   CF   CE1  123.90  3.000
 YOP  NE2  CF   CE1  119.95  3.000
 YOP  OD2  CD2  NE2  120.19  3.000
 YOP  NE2  CD2  CG   114.90  3.000
 YOP  OD2  CD2  CG   124.92  3.000
 YOP  H2   N    H    106.11  3.000
 YOP  H2   N    CA   109.49  3.000
 YOP  H    N    CA   109.97  3.000
 YOP  HE2  NE2  CD2  116.10  3.000
 YOP  HE2  NE2  CF   118.44  3.000
 YOP  CD2  NE2  CF   125.45  3.000
 YOP  H42  O    C    108.40  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
 YOP  CONST_01  CF   NE2  CD2  CG      0.00   0.0  0
 YOP  CONST_02  OD2  CD2  NE2  CF    180.00   0.0  0
 YOP  CONST_03  HE2  NE2  CD2  CG    180.00   0.0  0
 YOP  CONST_04  HE2  NE2  CD2  OD2     0.00   0.0  0
 YOP  Var_01    CF   CE1  CD1  CG     -0.31  30.0  1
 YOP  Var_02    NE2  CD2  CG   CD1    -0.09  30.0  1
 YOP  Var_03    NE2  CF   CE1  CD1     0.11  30.0  1
 YOP  Var_04    CD2  NE2  CF   CE1     0.10  30.0  1
 YOP  Var_05    CD2  CG   CD1  CE1     0.30  30.0  1
 YOP  Var_06    NE2  CD2  CG   CB    178.78  30.0  1
 YOP  Var_07    CE1  CD1  CG   CB   -178.46  30.0  1
 YOP  Var_08    OD2  CD2  CG   CD1   179.97  30.0  1
 YOP  Var_09    HE1  CE1  CD1  CG    179.90  30.0  1
 YOP  Var_10    HF   CF   CE1  CD1  -179.84  30.0  1
 YOP  Var_11    HE2  NE2  CF   CE1   179.97  30.0  1
 YOP  Var_12    HD1  CD1  CE1  CF    179.06  30.0  1
 YOP  Var_13    HF   CF   NE2  CD2  -179.95  30.0  1
 YOP  Var_14    HD1  CD1  CG   CD2  -179.06  30.0  1
 YOP  Var_15    HE1  CE1  CF   NE2   179.90  30.0  1
 YOP  Var_16    CD2  CG   CB   CA    176.22  30.0  3
 YOP  Var_17    CD1  CG   CB   CA     -4.98  30.0  3
 YOP  Var_18    OD2  CD2  CG   CB     -1.16  30.0  1
 YOP  Var_19    HD1  CD1  CG   CB      2.18  30.0  1
 YOP  Var_20    HB1  CB   CG   CD1   118.40  30.0  1
 YOP  Var_21    HB2  CB   CG   CD1  -128.05  30.0  1
 YOP  Var_22    HB1  CB   CG   CD2   -60.40  30.0  1
 YOP  Var_23    HB2  CB   CG   CD2    53.15  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
 YOP  chir_01  CA  CB  C  N  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
 YOP  plan-1  CG   0.020
 YOP  plan-1  CF   0.020
 YOP  plan-1  CD2  0.020
 YOP  plan-1  NE2  0.020
 YOP  plan-1  OD2  0.020
 YOP  plan-1  HE2  0.020

