# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:10:56 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(2-carboxyethyl)-5-chloro-4-nitro-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(Cl)c(cc1CCC(O)=O)[N+]([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
 TZG  TZG  2-(2-carboxyethyl)-5-chloro-4-nitro-L-phenylalanine  ligand  32  21  .  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_TZG
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
 TZG  N1    N   N      1   0.321   3.7611   1.3189   0.0131
 TZG  C4    C   CR16   0  -0.253   1.0072  -1.2093   0.0311
 TZG  C5    C   CR6    0  -0.068   2.2827  -0.6801   0.1367
 TZG  C6    C   CR6    0   0.308   2.4643   0.6798  -0.0843
 TZG  C7    C   CH2    0  -0.510  -1.4895  -0.9900  -0.2951
 TZG  C8    C   CH1    0  -0.256  -1.6433  -2.4841  -0.0390
 TZG  C10   C   CH2    0  -0.584  -1.6512   2.4509   0.5391
 TZG  C12   C   C      0   0.409  -3.1357  -2.8509   0.2055
 TZG  O5    O   OC    -1  -0.610  -3.7821  -2.0872   0.9511
 TZG  N2    N   NH2    0  -0.784  -0.9854  -3.2466  -1.0880
 TZG  C3    C   CR6    0   0.083  -0.0990  -0.4136  -0.2501
 TZG  O1    O   O     -1  -0.378   3.9918   2.2327  -0.7453
 TZG  O2    O   O      0  -0.370   4.5308   0.9234   0.8543
 TZG  C1    C   CR16   0  -0.333   1.3764   1.4783  -0.4058
 TZG  C2    C   CR6    0   0.114   0.0933   0.9609  -0.4793
 TZG  C9    C   CH2    0  -0.522  -1.0472   1.9017  -0.7521
 TZG  C11   C   C      0   0.418  -2.8231   3.4319   0.3471
 TZG  O7    O   O      0  -0.605  -3.1350   3.7431  -0.8185
 TZG  O6    O   OC    -1  -0.627  -3.3612   3.8426   1.3955
 TZG  H4    H   HCR6   0   0.289   0.8831  -2.2760   0.1447
 TZG  H7    H   HCH2   0   0.247  -1.9355  -0.7490  -1.2674
 TZG  H7A   H   HCH2   0   0.265  -2.1015  -0.4604   0.4370
 TZG  H8    H   HCH1   0   0.224  -1.1335  -2.7185   0.9071
 TZG  H10   H   HCH2   0   0.234  -1.9893   1.6295   1.1789
 TZG  H10A  H   HCH2   0   0.236  -0.8700   2.9571   1.1166
 TZG  HN2   H   HNH2   0   0.337  -1.2383  -4.2207  -0.9755
 TZG  HN2A  H   HNH2   0   0.329  -1.3871  -2.9816  -1.9808
 TZG  H1    H   HCR6   0   0.285   1.5271   2.5364  -0.5775
 TZG  H9    H   HCH2   0   0.241  -1.8186   1.4099  -1.3462
 TZG  H9A   H   HCH2   0   0.244  -0.6836   2.7337  -1.3579
 TZG  O4    O   O      0  -0.603  -3.5546  -3.8974  -0.3252
 TZG  CL1   CL  CL     0  -0.082   3.5829  -1.7705   0.4415

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
 TZG  N1   C6    single    1.449  0.020  1.449
 TZG  N1   O1    single    1.210  0.020  1.210
 TZG  N1   O2    double    1.207  0.020  1.207
 TZG  C4   C5    aromatic  1.385  0.020  1.385
 TZG  C4   C3    aromatic  1.391  0.020  1.391
 TZG  C5   C6    aromatic  1.390  0.020  1.390
 TZG  C5   CL1   single    1.724  0.020  1.724
 TZG  C6   C1    aromatic  1.387  0.020  1.387
 TZG  C7   C8    single    1.524  0.020  1.524
 TZG  C7   C3    single    1.506  0.020  1.506
 TZG  C8   C12   single    1.556  0.020  1.556
 TZG  C8   N2    single    1.454  0.020  1.454
 TZG  C10  C9    single    1.528  0.020  1.528
 TZG  C10  C11   single    1.540  0.020  1.540
 TZG  O4   C12   deloc     1.246  0.020  1.246
 TZG  C12  O5    deloc     1.248  0.020  1.248
 TZG  C3   C2    aromatic  1.407  0.020  1.407
 TZG  C1   C2    aromatic  1.385  0.020  1.385
 TZG  C2   C9    single    1.503  0.020  1.503
 TZG  C11  O7    deloc     1.246  0.020  1.246
 TZG  C11  O6    deloc     1.248  0.020  1.248
 TZG  C4   H4    single    0.930  0.020  1.080
 TZG  C7   H7    single    0.970  0.020  1.090
 TZG  C7   H7A   single    0.970  0.020  1.090
 TZG  C8   H8    single    0.970  0.020  1.090
 TZG  C10  H10   single    0.970  0.020  1.090
 TZG  C10  H10A  single    0.970  0.020  1.090
 TZG  N2   HN2   single    0.890  0.020  1.040
 TZG  N2   HN2A  single    0.890  0.020  1.040
 TZG  C1   H1    single    0.930  0.020  1.080
 TZG  C9   H9    single    0.970  0.020  1.090
 TZG  C9   H9A   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
 TZG  O2    N1   O1   124.25  3.000
 TZG  O2    N1   C6   118.23  3.000
 TZG  O1    N1   C6   117.50  3.000
 TZG  H4    C4   C3   119.66  3.000
 TZG  H4    C4   C5   118.38  3.000
 TZG  C3    C4   C5   121.94  3.000
 TZG  CL1   C5   C6   123.26  3.000
 TZG  CL1   C5   C4   117.80  3.000
 TZG  C6    C5   C4   118.83  3.000
 TZG  C1    C6   C5   119.84  3.000
 TZG  C1    C6   N1   117.61  3.000
 TZG  C5    C6   N1   122.54  3.000
 TZG  H7A   C7   H7   105.07  3.000
 TZG  H7A   C7   C3   108.18  3.000
 TZG  H7    C7   C3   108.54  3.000
 TZG  H7A   C7   C8   107.85  3.000
 TZG  H7    C7   C8   108.87  3.000
 TZG  C3    C7   C8   117.62  3.000
 TZG  H8    C8   N2   107.40  3.000
 TZG  H8    C8   C12  105.02  3.000
 TZG  N2    C8   C12  115.07  3.000
 TZG  H8    C8   C7   107.86  3.000
 TZG  N2    C8   C7   110.32  3.000
 TZG  C12   C8   C7   110.76  3.000
 TZG  H10A  C10  H10  105.00  3.000
 TZG  H10A  C10  C11  108.29  3.000
 TZG  H10   C10  C11  108.40  3.000
 TZG  H10A  C10  C9   109.26  3.000
 TZG  H10   C10  C9   110.27  3.000
 TZG  C11   C10  C9   115.11  3.000
 TZG  O5    C12  O4   126.48  3.000
 TZG  O5    C12  C8   116.51  3.000
 TZG  O4    C12  C8   116.97  3.000
 TZG  HN2A  N2   HN2  104.49  3.000
 TZG  HN2A  N2   C8   108.59  3.000
 TZG  HN2   N2   C8   108.13  3.000
 TZG  C2    C3   C7   119.70  3.000
 TZG  C2    C3   C4   118.88  3.000
 TZG  C7    C3   C4   121.41  3.000
 TZG  H1    C1   C2   119.05  3.000
 TZG  H1    C1   C6   119.35  3.000
 TZG  C2    C1   C6   121.57  3.000
 TZG  C9    C2   C1   118.58  3.000
 TZG  C9    C2   C3   122.50  3.000
 TZG  C1    C2   C3   118.88  3.000
 TZG  H9A   C9   H9   106.08  3.000
 TZG  H9A   C9   C2   108.97  3.000
 TZG  H9    C9   C2   110.68  3.000
 TZG  H9A   C9   C10  109.07  3.000
 TZG  H9    C9   C10  110.05  3.000
 TZG  C2    C9   C10  111.81  3.000
 TZG  O6    C11  O7   126.57  3.000
 TZG  O6    C11  C10  115.66  3.000
 TZG  O7    C11  C10  117.78  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
 TZG  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 TZG  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 TZG  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 TZG  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 TZG  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 TZG  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 TZG  CONST_07  C4   C5   C6   N1   180.00   0.0  0
 TZG  CONST_08  C2   C1   C6   N1   180.00   0.0  0
 TZG  CONST_09  C9   C2   C3   C4   180.00   0.0  0
 TZG  CONST_10  C7   C3   C4   C5   180.00   0.0  0
 TZG  CONST_11  C9   C2   C1   C6   180.00   0.0  0
 TZG  CONST_12  C1   C2   C3   C7   180.00   0.0  0
 TZG  CONST_13  CL1  C5   C4   C3   180.00   0.0  0
 TZG  CONST_14  C1   C6   C5   CL1  180.00   0.0  0
 TZG  CONST_15  H1   C1   C6   C5   180.00   0.0  0
 TZG  CONST_16  H4   C4   C5   C6   180.00   0.0  0
 TZG  Var_01    C8   C7   C3   C4    -0.78  30.0  3
 TZG  Var_02    C3   C2   C9   C10   87.06  30.0  1
 TZG  Var_03    C11  C10  C9   C2   179.65  30.0  1
 TZG  Var_04    O7   C11  C10  C9    -3.38  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
 TZG  chir_01  C8  C7  C12  N2  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
 TZG  plan-1  N1   0.020
 TZG  plan-1  C4   0.020
 TZG  plan-1  C5   0.020
 TZG  plan-1  C6   0.020
 TZG  plan-1  C7   0.020
 TZG  plan-1  C3   0.020
 TZG  plan-1  C1   0.020
 TZG  plan-1  C2   0.020
 TZG  plan-1  C9   0.020
 TZG  plan-1  H4   0.020
 TZG  plan-1  H1   0.020
 TZG  plan-1  CL1  0.020
 TZG  plan-2  N1   0.020
 TZG  plan-2  C6   0.020
 TZG  plan-2  O1   0.020
 TZG  plan-2  O2   0.020
 TZG  plan-3  C8   0.020
 TZG  plan-3  C12  0.020
 TZG  plan-3  O5   0.020
 TZG  plan-3  O4   0.020
 TZG  plan-4  C10  0.020
 TZG  plan-4  C11  0.020
 TZG  plan-4  O7   0.020
 TZG  plan-4  O6   0.020

