# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 16:52:59 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-(3H-azepin-5-yl)-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1=CCC=NC=C1)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
 4V0  4V0  3-(3H-azepin-5-yl)-L-alanine  ligand  24  13  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4V0
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
 4V0  N    N  NH2    0  -0.776  -1.5986   1.5130  -0.9400
 4V0  CA   C  CH1    0  -0.209  -1.6867   0.1433  -0.4697
 4V0  CB   C  CH2    0  -0.516  -0.6447  -0.0937   0.6367
 4V0  CG   C  C      0   0.195   0.7725   0.0531   0.1528
 4V0  CD1  C  C1     0  -0.323   1.3358  -1.0418  -0.5951
 4V0  CE1  C  C1     0  -0.132   2.6466  -1.4022  -0.6134
 4V0  NZ1  N  N      0  -0.344   3.6422  -0.8666   0.1588
 4V0  CZ2  C  C1     0  -0.055   3.6919   0.3803   0.4240
 4V0  CE2  C  CH2    0  -0.557   2.8187   1.4024  -0.2348
 4V0  CD2  C  C1     0  -0.319   1.4800   1.1788   0.3869
 4V0  C    C  C      0   0.384  -3.0738  -0.2964   0.0656
 4V0  O    O  O      0  -0.606  -3.8886   0.6004   0.3578
 4V0  H1   H  HNH2   0   0.334  -2.2450   1.6332  -1.7110
 4V0  H2   H  HNH2   0   0.322  -1.9616   2.1173  -0.2111
 4V0  H4   H  HCH1   0   0.219  -1.4400  -0.5150  -1.3110
 4V0  H5   H  HCH2   0   0.234  -0.8286   0.6190   1.4473
 4V0  H6   H  HCH2   0   0.240  -0.7973  -1.0921   1.0501
 4V0  H7   H  H      0   0.246   0.6467  -1.7279  -1.0776
 4V0  H8   H  H      0   0.253   2.9242  -2.3082  -1.1412
 4V0  H9   H  H      0   0.258   4.3938   0.7076   1.1876
 4V0  H10  H  HCH2   0   0.265   3.1877   2.4092  -0.0521
 4V0  H11  H  HCH2   0   0.266   2.7898   1.2243  -1.3157
 4V0  H12  H  H      0   0.246   1.0730   1.9476   1.0341
 4V0  OXT  O  OC    -1  -0.623  -3.2463  -1.5276   0.1845

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
 4V0  NZ1  CE1  single  1.369  0.020  1.369
 4V0  NZ1  CZ2  double  1.276  0.020  1.276
 4V0  CE1  CD1  double  1.360  0.020  1.360
 4V0  CZ2  CE2  single  1.497  0.020  1.497
 4V0  CD1  CG   single  1.441  0.020  1.441
 4V0  CE2  CD2  single  1.493  0.020  1.493
 4V0  CG   CD2  double  1.350  0.020  1.350
 4V0  CG   CB   single  1.505  0.020  1.505
 4V0  CB   CA   single  1.538  0.020  1.538
 4V0  CA   C    single  1.550  0.020  1.550
 4V0  CA   N    single  1.451  0.020  1.451
 4V0  C    O    deloc   1.246  0.020  1.246
 4V0  N    H1   single  0.890  0.020  1.040
 4V0  N    H2   single  0.890  0.020  1.040
 4V0  CA   H4   single  0.970  0.020  1.090
 4V0  CB   H5   single  0.970  0.020  1.090
 4V0  CB   H6   single  0.970  0.020  1.090
 4V0  CD1  H7   single  0.930  0.020  1.080
 4V0  CE1  H8   single  0.930  0.020  1.080
 4V0  CZ2  H9   single  0.930  0.020  1.080
 4V0  CE2  H10  single  0.970  0.020  1.090
 4V0  CE2  H11  single  0.970  0.020  1.090
 4V0  CD2  H12  single  0.930  0.020  1.080
 4V0  C    OXT  deloc   1.249  0.020  1.249

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
 4V0  H2   N    H1   104.35  3.000
 4V0  H2   N    CA   107.93  3.000
 4V0  H1   N    CA   108.66  3.000
 4V0  H4   CA   C    107.22  3.000
 4V0  H4   CA   CB   107.88  3.000
 4V0  C    CA   CB   108.30  3.000
 4V0  H4   CA   N    107.72  3.000
 4V0  C    CA   N    115.72  3.000
 4V0  CB   CA   N    109.72  3.000
 4V0  H6   CB   H5   106.96  3.000
 4V0  H6   CB   CG   110.04  3.000
 4V0  H5   CB   CG   109.44  3.000
 4V0  H6   CB   CA   108.58  3.000
 4V0  H5   CB   CA   108.57  3.000
 4V0  CG   CB   CA   113.06  3.000
 4V0  CD2  CG   CD1  121.25  3.000
 4V0  CD2  CG   CB   121.27  3.000
 4V0  CD1  CG   CB   117.46  3.000
 4V0  H7   CD1  CE1  116.01  3.000
 4V0  H7   CD1  CG   117.57  3.000
 4V0  CE1  CD1  CG   125.84  3.000
 4V0  H8   CE1  NZ1  114.52  3.000
 4V0  H8   CE1  CD1  118.34  3.000
 4V0  NZ1  CE1  CD1  126.15  3.000
 4V0  CZ2  NZ1  CE1  121.87  3.000
 4V0  H9   CZ2  CE2  118.68  3.000
 4V0  H9   CZ2  NZ1  117.72  3.000
 4V0  CE2  CZ2  NZ1  123.58  3.000
 4V0  H11  CE2  H10  108.97  3.000
 4V0  H11  CE2  CD2  111.27  3.000
 4V0  H10  CE2  CD2  111.89  3.000
 4V0  H11  CE2  CZ2  109.78  3.000
 4V0  H10  CE2  CZ2  111.11  3.000
 4V0  CD2  CE2  CZ2  103.74  3.000
 4V0  H12  CD2  CE2  118.62  3.000
 4V0  H12  CD2  CG   119.87  3.000
 4V0  CE2  CD2  CG   121.51  3.000
 4V0  OXT  C    O    126.63  3.000
 4V0  OXT  C    CA   115.85  3.000
 4V0  O    C    CA   117.50  3.000

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
 4V0  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
 4V0  plan-1  CA   0.020
 4V0  plan-1  C    0.020
 4V0  plan-1  O    0.020
 4V0  plan-1  OXT  0.020

