# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 01:03:29 2022
#   Inital geometry file: a 48 line input string
#   Ligand name: (2R)-2-aminopent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC=C)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
 DYL  DYL  '(2R)-2-aminopent-4-enoic acid'  D-peptide  16  8  .  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_DYL
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
 DYL  N   N  NH2    0  -0.810  -26.9059  25.7609  -3.7479
 DYL  CA  C  CH1    0  -0.202  -26.0068  24.6402  -3.5094
 DYL  C   C  C      0   0.406  -25.8193  24.3759  -1.9970
 DYL  O   O  O      0  -0.602  -26.2736  25.2233  -1.2027
 DYL  CB  C  CH2    0  -0.473  -26.5481  23.4154  -4.2571
 DYL  CG  C  C1     0  -0.115  -25.6283  22.2404  -4.3457
 DYL  CD  C  C2     0  -0.566  -26.0047  20.9667  -4.2953
 DYL  O1  O  OC    -1  -0.595  -25.1895  23.3411  -1.7046
 DYL  H1  H  HNH2   0   0.332  -26.7237  26.4754  -3.0563
 DYL  H2  H  HNH2   0   0.328  -26.7129  26.1673  -4.6544
 DYL  H4  H  HCH1   0   0.194  -24.9931  24.8340  -3.9032
 DYL  H5  H  HCH2   0   0.228  -26.7616  23.7403  -5.2836
 DYL  H6  H  HCH2   0   0.221  -27.5104  23.1147  -3.8327
 DYL  H7  H  H      0   0.218  -24.5816  22.4665  -4.5324
 DYL  H8  H  H      0   0.221  -25.2957  20.1589  -4.4243
 DYL  H9  H  H      0   0.217  -27.0353  20.6828  -4.1140

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
 DYL  CG  CD  double  1.329  0.020  1.329
 DYL  CG  CB  single  1.495  0.020  1.495
 DYL  CB  CA  single  1.521  0.033  1.521
 DYL  N   CA  single  1.458  0.019  1.458
 DYL  CA  C   single  1.525  0.021  1.525
 DYL  C   O   deloc   1.231  0.020  1.231
 DYL  C   O1  deloc   1.246  0.020  1.246
 DYL  N   H1  single  0.890  0.020  1.040
 DYL  N   H2  single  0.890  0.020  1.040
 DYL  CA  H4  single  0.970  0.020  1.090
 DYL  CB  H5  single  0.970  0.020  1.090
 DYL  CB  H6  single  0.970  0.020  1.090
 DYL  CG  H7  single  0.930  0.020  1.080
 DYL  CD  H8  single  0.930  0.020  1.080
 DYL  CD  H9  single  0.930  0.020  1.080

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
 DYL  H2  N   H1  107.14  3.000
 DYL  H2  N   CA  109.75  3.000
 DYL  H1  N   CA  108.69  3.000
 DYL  H4  CA  CB  106.87  3.000
 DYL  H4  CA  C   105.51  3.000
 DYL  CB  CA  C   110.50  1.500
 DYL  H4  CA  N   111.91  3.000
 DYL  C   CA  N   111.00  2.800
 DYL  CB  CA  N   110.40  1.500
 DYL  O1  C   O   126.78  3.000
 DYL  O1  C   CA  115.63  3.000
 DYL  O   C   CA  120.80  1.700
 DYL  H6  CB  H5  105.85  3.000
 DYL  H6  CB  CG  110.38  3.000
 DYL  H5  CB  CG  107.28  3.000
 DYL  H6  CB  CA  109.93  3.000
 DYL  H5  CB  CA  106.75  3.000
 DYL  CG  CB  CA  116.07  3.000
 DYL  H7  CG  CD  118.59  3.000
 DYL  H7  CG  CB  116.05  3.000
 DYL  CD  CG  CB  125.22  3.000
 DYL  H9  CD  H8  116.56  3.000
 DYL  H9  CD  CG  121.77  3.000
 DYL  H8  CD  CG  121.68  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
 DYL  Var_01  CD  CG  CB  CA  143.95  30.0  2
 DYL  Var_02  H8  CD  CG  CB  176.30   0.0  2

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
 DYL  chir_01  CA  CB  N  C  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
 DYL  plan-1  CA  0.020
 DYL  plan-1  C   0.020
 DYL  plan-1  O   0.020
 DYL  plan-1  O1  0.020
 DYL  plan-2  CB  0.020
 DYL  plan-2  CG  0.020
 DYL  plan-2  CD  0.020
 DYL  plan-2  H7  0.020
 DYL  plan-2  H8  0.020
 DYL  plan-2  H9  0.020

