# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 05:05:36 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 3-cyclobutyl-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCC1)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
 2JH  2JH  '3-cyclobutyl-L-alanine   '  L-peptide  22  10  .  2022-08-09  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_2JH
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
 2JH  N    N  NH2    0  -0.799   0.7615   1.7351   0.4248
 2JH  CA   C  CH1    0  -0.212   0.9343   0.2923   0.4971
 2JH  CB   C  CH2    0  -0.426  -0.1590  -0.5286  -0.2057
 2JH  C1   C  C      0   0.403   2.3064  -0.1266  -0.0736
 2JH  O    O  O      0  -0.608   2.8690   0.6625  -0.8578
 2JH  CG   C  CH1    0  -0.219  -1.5616  -0.3313   0.3371
 2JH  CD1  C  CH2    0  -0.454  -2.3840   0.9293  -0.0216
 2JH  CD2  C  CH2    0  -0.433  -2.6969  -1.1733  -0.2818
 2JH  CE   C  CH2    0  -0.453  -3.6341   0.0382  -0.1281
 2JH  H1   H  HNH2   0   0.324   0.8869   2.0315  -0.5349
 2JH  H2   H  HNH2   0   0.344  -0.1839   1.9846   0.6837
 2JH  H4   H  HCH1   0   0.199   0.9162   0.0110   1.5574
 2JH  H5   H  HCH2   0   0.200  -0.1539  -0.2972  -1.2789
 2JH  H6   H  HCH2   0   0.215   0.0946  -1.5897  -0.1151
 2JH  H8   H  HCH1   0   0.217  -1.5583  -0.4687   1.4245
 2JH  H9   H  HCH2   0   0.223  -2.4084   1.7548   0.6924
 2JH  H10  H  HCH2   0   0.219  -2.0945   1.3253  -0.9984
 2JH  H11  H  HCH2   0   0.216  -2.4918  -1.3865  -1.3341
 2JH  H12  H  HCH2   0   0.224  -2.9707  -2.1064   0.2128
 2JH  H13  H  HCH2   0   0.222  -4.1891   0.0045   0.8108
 2JH  H14  H  HCH2   0   0.224  -4.3383   0.2427  -0.9353
 2JH  O1   O  OC    -1  -0.625   2.7222  -1.2528   0.2701

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
 2JH  N    CA   single  1.458  0.019  1.458
 2JH  CA   C1   single  1.544  0.020  1.544
 2JH  CA   CB   single  1.521  0.033  1.521
 2JH  O    C1   deloc   1.247  0.020  1.247
 2JH  CB   CG   single  1.517  0.020  1.517
 2JH  CG   CD2  single  1.543  0.020  1.543
 2JH  CG   CD1  single  1.547  0.020  1.547
 2JH  CD2  CE   single  1.539  0.020  1.539
 2JH  CD1  CE   single  1.539  0.020  1.539
 2JH  N    H1   single  0.890  0.020  1.040
 2JH  N    H2   single  0.890  0.020  1.040
 2JH  CA   H4   single  0.970  0.020  1.090
 2JH  CB   H5   single  0.970  0.020  1.090
 2JH  CB   H6   single  0.970  0.020  1.090
 2JH  CG   H8   single  0.970  0.020  1.090
 2JH  CD1  H9   single  0.970  0.020  1.090
 2JH  CD1  H10  single  0.970  0.020  1.090
 2JH  CD2  H11  single  0.970  0.020  1.090
 2JH  CD2  H12  single  0.970  0.020  1.090
 2JH  CE   H13  single  0.970  0.020  1.090
 2JH  CE   H14  single  0.970  0.020  1.090
 2JH  C1   O1   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
 2JH  H2   N    H1   106.63  3.000
 2JH  H2   N    CA   110.05  3.000
 2JH  H1   N    CA   108.84  3.000
 2JH  H4   CA   C1   107.60  3.000
 2JH  H4   CA   CB   107.05  3.000
 2JH  C1   CA   CB   108.55  3.000
 2JH  H4   CA   N    107.48  3.000
 2JH  CB   CA   N    110.40  1.500
 2JH  C1   CA   N    110.87  3.000
 2JH  H6   CB   H5   106.50  3.000
 2JH  H6   CB   CG   108.10  3.000
 2JH  H5   CB   CG   109.06  3.000
 2JH  H6   CB   CA   108.36  3.000
 2JH  H5   CB   CA   109.34  3.000
 2JH  CG   CB   CA   115.13  3.000
 2JH  O1   C1   O    126.43  3.000
 2JH  O1   C1   CA   116.03  3.000
 2JH  O    C1   CA   117.50  3.000
 2JH  H8   CG   CD2  109.38  3.000
 2JH  H8   CG   CD1  109.49  3.000
 2JH  CD2  CG   CD1   87.74  3.000
 2JH  H8   CG   CB   109.63  3.000
 2JH  CD1  CG   CB   120.96  3.000
 2JH  CD2  CG   CB   117.77  3.000
 2JH  H10  CD1  H9   108.45  3.000
 2JH  H10  CD1  CE   111.29  3.000
 2JH  H9   CD1  CE   117.71  3.000
 2JH  H10  CD1  CG   111.19  3.000
 2JH  H9   CD1  CG   118.45  3.000
 2JH  CE   CD1  CG    88.63  3.000
 2JH  H12  CD2  H11  108.46  3.000
 2JH  H12  CD2  CE   118.36  3.000
 2JH  H11  CD2  CE   111.34  3.000
 2JH  H12  CD2  CG   118.00  3.000
 2JH  H11  CD2  CG   110.77  3.000
 2JH  CE   CD2  CG    88.77  3.000
 2JH  H14  CE   H13  108.31  3.000
 2JH  H14  CE   CD2  117.82  3.000
 2JH  H13  CE   CD2  111.80  3.000
 2JH  H14  CE   CD1  117.85  3.000
 2JH  H13  CE   CD1  111.81  3.000
 2JH  CD2  CE   CD1   88.17  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
 2JH  Var_01  CD1  CE  CD2  CG  19.47  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
 2JH  chir_01  CA  N   C1   CB   positiv
 2JH  chir_02  CG  CB  CD2  CD1  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
 2JH  plan-1  CA  0.020
 2JH  plan-1  C1  0.020
 2JH  plan-1  O   0.020
 2JH  plan-1  O1  0.020

