# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 18:22:41 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)CC[C@H](C[C@H](N)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
 3ZA  3ZA  '(4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid'  ligand  31  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3ZA
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
 3ZA  O6   O  OH1    0  -0.548  -4.5587  -0.8205   0.6555
 3ZA  C5   C  CH2    0  -0.578  -2.0526   0.0123   0.1058
 3ZA  C3   C  CH1    0  -0.340   0.4637  -0.1462   0.2873
 3ZA  O2   O  OC    -1  -0.629   4.5737   0.8045  -1.1393
 3ZA  O1   O  O      0  -0.612   4.7264   1.5624   0.9495
 3ZA  C7   C  C      0   0.418   0.5106  -1.6429  -0.0700
 3ZA  C8   C  C      0   0.554  -3.2393   0.8232  -0.3655
 3ZA  C1   C  CH1    0  -0.213   3.0585  -0.0783   0.4594
 3ZA  C2   C  CH2    0  -0.421   1.7724   0.5349  -0.1262
 3ZA  C4   C  CH2    0  -0.390  -0.7178   0.5777  -0.3539
 3ZA  N1   N  NH2    0  -0.803   3.0303  -0.3145   1.8939
 3ZA  C6   C  C      0   0.401   4.2350   0.8357   0.0633
 3ZA  O5   O  O      0  -0.495  -3.1303   1.8162  -1.0699
 3ZA  N2   N  NT     0  -0.209  -4.4579   0.4149   0.0672
 3ZA  C9   C  CH3    0  -0.515  -5.7124   0.9619  -0.3877
 3ZA  H1   H  HOH1   0   0.476  -4.6334  -0.6624   1.6064
 3ZA  H2   H  HCH2   0   0.254  -2.0748  -0.0466   1.1990
 3ZA  H3   H  HCH2   0   0.266  -2.1634  -1.0172  -0.2448
 3ZA  H4   H  HCH1   0   0.189   0.3572  -0.0519   1.3745
 3ZA  H6   H  HCH1   0   0.203   3.2196  -1.0498  -0.0210
 3ZA  H7   H  HCH2   0   0.205   1.8488   0.5299  -1.2170
 3ZA  H8   H  HCH2   0   0.202   1.7143   1.5899   0.1723
 3ZA  H9   H  HCH2   0   0.211  -0.6382   0.5164  -1.4414
 3ZA  H10  H  HCH2   0   0.212  -0.6558   1.6390  -0.0985
 3ZA  H11  H  HNH2   0   0.319   2.8463   0.5585   2.3724
 3ZA  H12  H  HNH2   0   0.333   2.2545  -0.9321   2.1019
 3ZA  H15  H  HCH3   0   0.242  -6.1380   0.3715  -1.2019
 3ZA  H16  H  HCH3   0   0.247  -6.4213   0.9860   0.4390
 3ZA  H17  H  HCH3   0   0.254  -5.5592   1.9787  -0.7348
 3ZA  O3   O  O      0  -0.614   0.3435  -1.9407  -1.2708
 3ZA  O4   O  OC    -1  -0.616   0.7403  -2.4477   0.8596

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
 3ZA  C5  C4   single  1.521  0.020  1.521
 3ZA  C5  C8   single  1.513  0.020  1.513
 3ZA  C4  C3   single  1.527  0.020  1.527
 3ZA  C8  O5   double  1.222  0.020  1.222
 3ZA  C8  N2   single  1.356  0.020  1.356
 3ZA  N2  O6   single  1.372  0.020  1.372
 3ZA  N2  C9   single  1.442  0.020  1.442
 3ZA  C3  C2   single  1.532  0.020  1.532
 3ZA  C3  C7   single  1.539  0.020  1.539
 3ZA  C2  C1   single  1.541  0.020  1.541
 3ZA  C7  O3   deloc   1.248  0.020  1.248
 3ZA  C7  O4   deloc   1.251  0.020  1.251
 3ZA  O1  C6   deloc   1.247  0.020  1.247
 3ZA  C1  C6   single  1.541  0.020  1.541
 3ZA  C1  N1   single  1.454  0.020  1.454
 3ZA  C6  O2   deloc   1.250  0.020  1.250
 3ZA  O6  H1   single  0.850  0.020  0.980
 3ZA  C5  H2   single  0.970  0.020  1.090
 3ZA  C5  H3   single  0.970  0.020  1.090
 3ZA  C3  H4   single  0.970  0.020  1.090
 3ZA  C1  H6   single  0.970  0.020  1.090
 3ZA  C2  H7   single  0.970  0.020  1.090
 3ZA  C2  H8   single  0.970  0.020  1.090
 3ZA  C4  H9   single  0.970  0.020  1.090
 3ZA  C4  H10  single  0.970  0.020  1.090
 3ZA  N1  H11  single  0.890  0.020  1.040
 3ZA  N1  H12  single  0.890  0.020  1.040
 3ZA  C9  H15  single  0.970  0.020  1.090
 3ZA  C9  H16  single  0.970  0.020  1.090
 3ZA  C9  H17  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
 3ZA  H1   O6  N2   106.27  3.000
 3ZA  H3   C5  H2   105.52  3.000
 3ZA  H3   C5  C4   110.01  3.000
 3ZA  H2   C5  C4   109.85  3.000
 3ZA  H3   C5  C8   108.99  3.000
 3ZA  H2   C5  C8   108.90  3.000
 3ZA  C4   C5  C8   113.27  3.000
 3ZA  H4   C3  C4   107.48  3.000
 3ZA  H4   C3  C2   108.20  3.000
 3ZA  C4   C3  C2   109.69  3.000
 3ZA  H4   C3  C7   108.47  3.000
 3ZA  C2   C3  C7   110.09  3.000
 3ZA  C4   C3  C7   112.77  3.000
 3ZA  O4   C7  O3   125.86  3.000
 3ZA  O4   C7  C3   117.30  3.000
 3ZA  O3   C7  C3   116.82  3.000
 3ZA  N2   C8  O5   120.57  3.000
 3ZA  N2   C8  C5   116.37  3.000
 3ZA  O5   C8  C5   123.03  3.000
 3ZA  H6   C1  C6   107.51  3.000
 3ZA  H6   C1  N1   106.94  3.000
 3ZA  C6   C1  N1   111.38  3.000
 3ZA  H6   C1  C2   108.00  3.000
 3ZA  N1   C1  C2   115.06  3.000
 3ZA  C6   C1  C2   107.67  3.000
 3ZA  H8   C2  H7   106.22  3.000
 3ZA  H8   C2  C1   108.86  3.000
 3ZA  H7   C2  C1   108.61  3.000
 3ZA  H8   C2  C3   107.98  3.000
 3ZA  H7   C2  C3   109.08  3.000
 3ZA  C1   C2  C3   115.69  3.000
 3ZA  H10  C4  H9   106.44  3.000
 3ZA  H10  C4  C3   108.56  3.000
 3ZA  H9   C4  C3   109.58  3.000
 3ZA  H10  C4  C5   109.88  3.000
 3ZA  H9   C4  C5   110.13  3.000
 3ZA  C3   C4  C5   112.09  3.000
 3ZA  H12  N1  H11  106.83  3.000
 3ZA  H12  N1  C1   108.44  3.000
 3ZA  H11  N1  C1   109.25  3.000
 3ZA  C1   C6  O1   117.63  3.000
 3ZA  C1   C6  O2   116.06  3.000
 3ZA  O1   C6  O2   126.27  3.000
 3ZA  C9   N2  C8   124.53  3.000
 3ZA  C9   N2  O6   114.38  3.000
 3ZA  C8   N2  O6   118.29  3.000
 3ZA  H17  C9  H16  108.29  3.000
 3ZA  H17  C9  H15  108.85  3.000
 3ZA  H16  C9  H15  108.91  3.000
 3ZA  H17  C9  N2   109.48  3.000
 3ZA  H16  C9  N2   109.58  3.000
 3ZA  H15  C9  N2   111.66  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
 3ZA  CONST_01  C5   C8  N2  O6    0.00   0.0  0
 3ZA  CONST_02  O5   C8  N2  O6  180.00   0.0  0
 3ZA  CONST_03  C9   N2  C8  C5  180.00   0.0  0
 3ZA  CONST_04  C9   N2  C8  O5    0.00   0.0  0
 3ZA  Var_01    C8   C5  C4  C3  172.32  30.0  1
 3ZA  Var_02    O5   C8  C5  C4    1.51  30.0  3
 3ZA  Var_03    H15  C9  N2  O6  -65.72  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
 3ZA  chir_01  C3  C4  C2  C7  positiv
 3ZA  chir_02  C1  N1  C6  C2  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
 3ZA  plan-1  O6  0.020
 3ZA  plan-1  C5  0.020
 3ZA  plan-1  C8  0.020
 3ZA  plan-1  O5  0.020
 3ZA  plan-1  N2  0.020
 3ZA  plan-1  C9  0.020
 3ZA  plan-2  C3  0.020
 3ZA  plan-2  C7  0.020
 3ZA  plan-2  O3  0.020
 3ZA  plan-2  O4  0.020
 3ZA  plan-3  O2  0.020
 3ZA  plan-3  O1  0.020
 3ZA  plan-3  C1  0.020
 3ZA  plan-3  C6  0.020

