# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 00:08:59 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (1R,2S)-1-amino-2-ethenylcyclopropanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@]1(C[C@H]1C=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
 0Y9  0Y9  '(1R,2S)-1-amino-2-ethenylcyclopropanecarboxylic acid'  peptide  17  9  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_0Y9
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
 0Y9  N20  N  NH2    0  -0.805  -1.2804   1.5609  -0.7904
 0Y9  C21  C  CT     0   0.009  -0.5513   0.6652   0.0722
 0Y9  C22  C  CH1    0  -0.322   0.9586   0.7756  -0.0340
 0Y9  C23  C  CH2    0  -0.486   0.2433   1.2031   1.2254
 0Y9  C24  C  C1     0  -0.135   1.8753  -0.3748  -0.0620
 0Y9  C25  C  C2     0  -0.567   2.9512  -0.4459  -0.8438
 0Y9  C26  C  C      0   0.411  -1.2084  -0.7042   0.2399
 0Y9  O27  O  O      0  -0.602  -0.6957  -1.4901   1.0616
 0Y9  H12  H  HNH2   0   0.335  -2.2490   1.5895  -0.4984
 0Y9  H13  H  HCH1   0   0.247   1.2744   1.5943  -0.6778
 0Y9  H14  H  HCH2   0   0.246   0.1965   2.2667   1.4308
 0Y9  H15  H  HCH2   0   0.240   0.3627   0.5778   2.1014
 0Y9  H16  H  H      0   0.242   1.6412  -1.1976   0.6018
 0Y9  H17  H  H      0   0.226   3.2199   0.3530  -1.5259
 0Y9  H18  H  H      0   0.228   3.6017  -1.3105  -0.8305
 0Y9  H2   H  HNH2   0   0.335  -0.9262   2.5044  -0.6858
 0Y9  OXT  O  OC    -1  -0.602  -2.2231  -0.9160  -0.4509

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
 0Y9  C25  C24  double  1.332  0.020  1.332
 0Y9  C24  C22  single  1.471  0.020  1.471
 0Y9  C22  C21  single  1.518  0.020  1.518
 0Y9  C22  C23  single  1.510  0.020  1.510
 0Y9  O27  C26  deloc   1.247  0.020  1.247
 0Y9  C21  C26  single  1.528  0.020  1.528
 0Y9  C21  C23  single  1.500  0.020  1.500
 0Y9  C21  N20  single  1.441  0.020  1.441
 0Y9  N20  H12  single  0.890  0.020  1.040
 0Y9  C22  H13  single  0.970  0.020  1.090
 0Y9  C23  H14  single  0.970  0.020  1.090
 0Y9  C23  H15  single  0.970  0.020  1.090
 0Y9  C24  H16  single  0.930  0.020  1.080
 0Y9  C25  H17  single  0.930  0.020  1.080
 0Y9  C25  H18  single  0.930  0.020  1.080
 0Y9  N20  H2   single  0.890  0.020  1.040
 0Y9  C26  OXT  deloc   1.246  0.020  1.246

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
 0Y9  H2   N20  H12  106.17  3.000
 0Y9  H2   N20  C21  109.88  3.000
 0Y9  H12  N20  C21  109.21  3.000
 0Y9  C26  C21  C23  117.69  3.000
 0Y9  C23  C21  C22   60.05  3.000
 0Y9  C26  C21  C22  120.04  3.000
 0Y9  C23  C21  N20  120.34  3.000
 0Y9  C26  C21  N20  113.89  3.000
 0Y9  C22  C21  N20  114.59  3.000
 0Y9  H13  C22  C24  113.34  3.000
 0Y9  H13  C22  C23  114.70  3.000
 0Y9  C24  C22  C23  122.16  3.000
 0Y9  H13  C22  C21  112.63  3.000
 0Y9  C23  C22  C21   59.40  3.000
 0Y9  C24  C22  C21  124.36  3.000
 0Y9  H15  C23  H14  114.70  3.000
 0Y9  H15  C23  C22  117.33  3.000
 0Y9  H14  C23  C22  117.14  3.000
 0Y9  H15  C23  C21  118.25  3.000
 0Y9  H14  C23  C21  118.32  3.000
 0Y9  C22  C23  C21   60.55  3.000
 0Y9  H16  C24  C25  119.60  3.000
 0Y9  H16  C24  C22  116.60  3.000
 0Y9  C25  C24  C22  123.80  3.000
 0Y9  H18  C25  H17  116.58  3.000
 0Y9  H18  C25  C24  121.41  3.000
 0Y9  H17  C25  C24  122.01  3.000
 0Y9  OXT  C26  O27  126.37  3.000
 0Y9  OXT  C26  C21  116.22  3.000
 0Y9  O27  C26  C21  117.40  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
 0Y9  Var_01  C23  C22  C21  N20   112.18  30.0  1
 0Y9  Var_02  C24  C22  C23  C21  -113.74  30.0  1
 0Y9  Var_03  C25  C24  C22  C21   140.19  30.0  1
 0Y9  Var_04  O27  C26  C21  C22    44.58  30.0  3
 0Y9  Var_05  H12  N20  C21  C22  -166.06  30.0  3
 0Y9  Var_06  H17  C25  C24  C22    -0.38   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
 0Y9  chir_01  C21  C26  C23  N20  both
 0Y9  chir_02  C22  C24  C21  C23  both

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
 0Y9  plan-1  C21  0.020
 0Y9  plan-1  C26  0.020
 0Y9  plan-1  O27  0.020
 0Y9  plan-1  OXT  0.020
 0Y9  plan-2  C22  0.020
 0Y9  plan-2  C24  0.020
 0Y9  plan-2  C25  0.020
 0Y9  plan-2  H16  0.020
 0Y9  plan-2  H17  0.020
 0Y9  plan-2  H18  0.020

