# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 10:34:27 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: (2S,3S)-3-methylaziridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@@H]1C(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
 3K4  3K4  '(2S,3S)-3-methylaziridine-2-carboxylic acid'  L-peptide  13  7  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3K4
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
 3K4  C5  C  CH1    0  -0.109   1.4477  -0.2637  -0.3333
 3K4  C7  C  CH3    0  -0.677   1.4720  -1.3233   0.7318
 3K4  O   O  O      0  -0.603  -1.2423   0.3869   1.1597
 3K4  C   C  C      0   0.399  -1.1252   0.2556  -0.0720
 3K4  C2  C  CH1    0  -0.271   0.2316   0.5086  -0.7057
 3K4  N6  N  NH1    0  -0.601   1.2964   1.1155   0.0829
 3K4  H1  H  HCH1   0   0.236   2.1341  -0.4510  -1.1564
 3K4  H2  H  HCH3   0   0.217   1.2467  -2.3013   0.3034
 3K4  H3  H  HCH3   0   0.222   2.4612  -1.3857   1.1898
 3K4  H4  H  HCH3   0   0.232   0.7441  -1.1146   1.5118
 3K4  H6  H  HCH1   0   0.228   0.1848   0.7869  -1.7561
 3K4  H7  H  HNH1   0   0.348   1.8546   1.7291  -0.4977
 3K4  O1  O  OC    -1  -0.623  -2.0169  -0.0906  -0.8767

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
 3K4  O   C   deloc   1.231  0.020  1.231
 3K4  C   C2  single  1.519  0.020  1.519
 3K4  C2  N6  single  1.457  0.020  1.457
 3K4  C2  C5  single  1.488  0.020  1.488
 3K4  N6  C5  single  1.449  0.020  1.449
 3K4  C5  C7  single  1.503  0.020  1.503
 3K4  C5  H1  single  0.970  0.020  1.090
 3K4  C7  H2  single  0.970  0.020  1.090
 3K4  C7  H3  single  0.970  0.020  1.090
 3K4  C7  H4  single  0.970  0.020  1.090
 3K4  C2  H6  single  0.970  0.020  1.090
 3K4  N6  H7  single  0.890  0.020  1.040
 3K4  C   O1  deloc   1.250  0.020  1.250

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
 3K4  H1  C5  N6  116.56  3.000
 3K4  H1  C5  C2  114.56  3.000
 3K4  N6  C5  C2   59.49  3.000
 3K4  H1  C5  C7  113.87  3.000
 3K4  N6  C5  C7  118.00  3.000
 3K4  C2  C5  C7  123.82  3.000
 3K4  H4  C7  H3  108.46  3.000
 3K4  H4  C7  H2  108.39  3.000
 3K4  H3  C7  H2  107.49  3.000
 3K4  H4  C7  C5  111.24  3.000
 3K4  H3  C7  C5  110.63  3.000
 3K4  H2  C7  C5  110.52  3.000
 3K4  O1  C   C2  114.51  3.000
 3K4  O1  C   O   126.82  3.000
 3K4  C2  C   O   118.66  3.000
 3K4  H6  C2  N6  116.58  3.000
 3K4  H6  C2  C   114.03  3.000
 3K4  N6  C2  C   119.76  3.000
 3K4  H6  C2  C5  114.18  3.000
 3K4  N6  C2  C5   58.91  3.000
 3K4  C   C2  C5  122.63  3.000
 3K4  H7  N6  C2  110.17  3.000
 3K4  H7  N6  C5  110.77  3.000
 3K4  C2  N6  C5   61.60  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
 3K4  Var_01  C   C2  N6  C5  112.37  30.0  1
 3K4  Var_02  N6  C2  C5  C7  105.14  30.0  1
 3K4  Var_03  O   C   C2  C5   59.53  30.0  3
 3K4  Var_04  H2  C7  C5  C2   90.23  30.0  3

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
 3K4  chir_01  C5  C2  N6  C7  both
 3K4  chir_02  C2  N6  C   C5  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
 3K4  plan-1  O   0.020
 3K4  plan-1  C   0.020
 3K4  plan-1  C2  0.020
 3K4  plan-1  O1  0.020

