# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 20:25:47 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-[(3S)-3-amino-3-carboxypropyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN[C@@H](CCC(O)=O)C(O)=O)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
 3O3  3O3  'N-[(3S)-3-amino-3-carboxypropyl]-L-glutamic acid'  L-peptide  30  17  .  2022-07-22  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_3O3
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
 3O3  N2    N  NH2    0  -0.780  -3.4171   0.5750  -1.8156
 3O3  N3    N  NH1    0  -0.615   0.2618  -0.2851   0.2255
 3O3  O3    O  O      0  -0.466  -5.1954   1.7380  -0.0406
 3O3  C4    C  CH1    0  -0.214  -3.4867   0.1017  -0.4405
 3O3  OXT   O  OC    -1  -0.814  -4.7473   0.2641   1.5694
 3O3  C5    C  C      0   0.364  -4.5788   0.7650   0.4371
 3O3  C6    C  CH2    0  -0.440  -2.1235   0.2555   0.2344
 3O3  C7    C  CH2    0  -0.262  -0.9961  -0.4844  -0.4686
 3O3  O7    O  OC    -1  -0.821   4.2903   3.0149   0.0965
 3O3  C8    C  CH1    0  -0.214   1.3940  -0.9244  -0.4206
 3O3  O8    O  O      0  -0.510   4.8613   1.1387   1.1450
 3O3  C9    C  CH2    0  -0.395   2.7077  -0.3412   0.1153
 3O3  C10   C  CH2    0  -0.527   2.8625   1.1426  -0.1684
 3O3  C11   C  C      0   0.394   1.4322  -2.4642  -0.2699
 3O3  C12   C  C      0   0.404   4.1185   1.8155   0.4099
 3O3  HN2   H  HNH2   0   0.332  -4.3460   0.5281  -2.2169
 3O3  HNXT  H  HNH2   0   0.333  -3.2070   1.5671  -1.7959
 3O3  HN3   H  HNH1   0   0.313   0.1782  -0.6939   1.1505
 3O3  H4    H  HCH1   0   0.243  -3.7151  -0.9717  -0.4775
 3O3  H6    H  HCH2   0   0.213  -1.8647   1.3198   0.2974
 3O3  H6A   H  HCH2   0   0.209  -2.2093  -0.1033   1.2627
 3O3  H7    H  HCH2   0   0.199  -0.8892  -0.1015  -1.4865
 3O3  H7A   H  HCH2   0   0.205  -1.2735  -1.5472  -0.5681
 3O3  H8    H  HCH1   0   0.182   1.3368  -0.6894  -1.4909
 3O3  H9    H  HCH2   0   0.181   2.7640  -0.5232   1.1936
 3O3  H9A   H  HCH2   0   0.209   3.5405  -0.8927  -0.3281
 3O3  H10   H  HCH2   0   0.206   2.8518   1.3115  -1.2519
 3O3  H10A  H  HCH2   0   0.260   1.9808   1.6716   0.2072
 3O3  O5    O  OC    -1  -0.740   2.0802  -3.0937  -1.1327
 3O3  O6    O  O      0  -0.452   0.8556  -2.9542   0.7233

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
 3O3  C4   N2    single  1.456  0.020  1.456
 3O3  N2   HN2   single  0.890  0.020  1.040
 3O3  N2   HNXT  single  0.890  0.020  1.040
 3O3  C8   N3    single  1.452  0.020  1.452
 3O3  N3   C7    single  1.450  0.020  1.450
 3O3  N3   HN3   single  0.890  0.020  1.040
 3O3  O3   C5    deloc   1.247  0.020  1.247
 3O3  C6   C4    single  1.529  0.020  1.529
 3O3  C4   C5    single  1.550  0.020  1.550
 3O3  C4   H4    single  0.970  0.020  1.090
 3O3  C5   OXT   deloc   1.250  0.020  1.250
 3O3  O5   C11   deloc   1.249  0.020  1.249
 3O3  C7   C6    single  1.521  0.020  1.521
 3O3  C6   H6    single  0.970  0.020  1.090
 3O3  C6   H6A   single  0.970  0.020  1.090
 3O3  O6   C11   deloc   1.249  0.020  1.249
 3O3  C7   H7    single  0.970  0.020  1.090
 3O3  C7   H7A   single  0.970  0.020  1.090
 3O3  C12  O7    deloc   1.252  0.020  1.252
 3O3  C11  C8    single  1.548  0.020  1.548
 3O3  C9   C8    single  1.534  0.020  1.534
 3O3  C8   H8    single  0.970  0.020  1.090
 3O3  O8   C12   deloc   1.245  0.020  1.245
 3O3  C10  C9    single  1.519  0.020  1.519
 3O3  C9   H9    single  0.970  0.020  1.090
 3O3  C9   H9A   single  0.970  0.020  1.090
 3O3  C10  C12   single  1.538  0.020  1.538
 3O3  C10  H10   single  0.970  0.020  1.090
 3O3  C10  H10A  single  0.970  0.020  1.090

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
 3O3  HNXT  N2   HN2  104.06  3.000
 3O3  HNXT  N2   C4   108.03  3.000
 3O3  HN2   N2   C4   108.38  3.000
 3O3  HN3   N3   C8   107.01  3.000
 3O3  HN3   N3   C7   108.02  3.000
 3O3  C8    N3   C7   113.75  3.000
 3O3  H4    C4   C6   107.37  3.000
 3O3  H4    C4   C5   106.91  3.000
 3O3  C6    C4   C5   109.59  3.000
 3O3  H4    C4   N2   107.21  3.000
 3O3  C5    C4   N2   115.42  3.000
 3O3  C6    C4   N2   109.98  3.000
 3O3  OXT   C5   C4   115.88  3.000
 3O3  OXT   C5   O3   126.38  3.000
 3O3  C4    C5   O3   117.74  3.000
 3O3  H6A   C6   H6   106.45  3.000
 3O3  H6A   C6   C7   109.48  3.000
 3O3  H6    C6   C7   108.88  3.000
 3O3  H6A   C6   C4   108.21  3.000
 3O3  H6    C6   C4   109.46  3.000
 3O3  C7    C6   C4   114.08  3.000
 3O3  H7A   C7   H7   106.16  3.000
 3O3  H7A   C7   C6   108.91  3.000
 3O3  H7    C7   C6   109.43  3.000
 3O3  H7A   C7   N3   113.19  3.000
 3O3  H7    C7   N3   108.23  3.000
 3O3  C6    C7   N3   110.79  3.000
 3O3  H8    C8   C11  108.02  3.000
 3O3  H8    C8   C9   107.70  3.000
 3O3  C11   C8   C9   108.85  3.000
 3O3  H8    C8   N3   107.41  3.000
 3O3  C9    C8   N3   110.18  3.000
 3O3  C11   C8   N3   114.46  3.000
 3O3  H9A   C9   H9   106.06  3.000
 3O3  H9A   C9   C10  109.85  3.000
 3O3  H9    C9   C10  109.95  3.000
 3O3  H9A   C9   C8   108.60  3.000
 3O3  H9    C9   C8   108.96  3.000
 3O3  C10   C9   C8   113.17  3.000
 3O3  H10A  C10  H10  104.88  3.000
 3O3  H10A  C10  C12  108.51  3.000
 3O3  H10   C10  C12  108.19  3.000
 3O3  H10A  C10  C9   109.02  3.000
 3O3  H10   C10  C9   109.52  3.000
 3O3  C12   C10  C9   116.14  3.000
 3O3  C8    C11  O6   117.16  3.000
 3O3  C8    C11  O5   116.55  3.000
 3O3  O6    C11  O5   126.24  3.000
 3O3  C10   C12  O8   118.13  3.000
 3O3  C10   C12  O7   115.93  3.000
 3O3  O8    C12  O7   125.93  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
 3O3  Var_01  C4   C6   C7   N3   179.71  30.0  3
 3O3  Var_02  C8   N3   C7   C6  -177.83  30.0  1
 3O3  Var_03  C9   C10  C12  O7   175.21  30.0  2
 3O3  Var_04  C12  C10  C9   C8   176.60  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
 3O3  chir_01  C4  N2  C6   C5  negativ
 3O3  chir_02  C8  N3  C11  C9  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
 3O3  plan-1  O3   0.020
 3O3  plan-1  C4   0.020
 3O3  plan-1  OXT  0.020
 3O3  plan-1  C5   0.020
 3O3  plan-2  C8   0.020
 3O3  plan-2  C11  0.020
 3O3  plan-2  O5   0.020
 3O3  plan-2  O6   0.020
 3O3  plan-3  O7   0.020
 3O3  plan-3  O8   0.020
 3O3  plan-3  C10  0.020
 3O3  plan-3  C12  0.020

