# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 05:31:51 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S,6E)-2-amino-2-methylnon-6-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C\CCC[C@](C)(N)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
 UZA  UZA  '(2S,6E)-2-amino-2-methylnon-6-enoic acid'  L-peptide  32  13  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UZA
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
 UZA  N    N  NH2   0  -0.784  -2.2165  -13.1653   -4.6379
 UZA  CA   C  CT    0  -0.045  -1.4444  -14.3483   -4.9803
 UZA  C    C  C     0   0.560   0.0699  -14.1004   -4.9786
 UZA  O    O  O     0  -0.442   0.8984  -14.8719   -4.5606
 UZA  CB1  C  CH3   0  -0.653  -1.7619  -15.4486   -3.9724
 UZA  C05  C  CH3   0  -0.658  -7.5627  -16.0288  -10.7300
 UZA  C06  C  CH2   0  -0.481  -7.2831  -15.7328   -9.2578
 UZA  C07  C  C1    0  -0.213  -5.8787  -15.2698   -9.0287
 UZA  C08  C  C1    0  -0.209  -4.9636  -15.9206   -8.3162
 UZA  C09  C  CH2   0  -0.481  -3.5572  -15.4613   -8.0962
 UZA  C11  C  CH2   0  -0.420  -1.8017  -14.7837   -6.4167
 UZA  OXT  O  OH1   0  -0.596   0.3925  -12.9328   -5.5254
 UZA  H1   H  HNH2  0   0.350  -1.9664  -12.8269   -3.7164
 UZA  H2   H  HNH2  0   0.349  -2.0336  -12.4092   -5.2855
 UZA  H4   H  HCH3  0   0.237  -1.4224  -15.1785   -2.9711
 UZA  H5   H  HCH3  0   0.242  -2.8374  -15.6070   -3.9241
 UZA  H6   H  HCH3  0   0.232  -1.2929  -16.3930   -4.2443
 UZA  H7   H  HCH3  0   0.228  -8.6002  -16.3293  -10.8803
 UZA  H8   H  HCH3  0   0.221  -7.3790  -15.1522  -11.3532
 UZA  H9   H  HCH3  0   0.222  -6.9237  -16.8336  -11.0953
 UZA  H10  H  HCH2  0   0.228  -7.9806  -14.9626   -8.9135
 UZA  H11  H  HCH2  0   0.228  -7.4838  -16.6241   -8.6577
 UZA  H12  H  H     0   0.225  -5.6000  -14.3327   -9.5084
 UZA  H13  H  H     0   0.226  -5.2412  -16.8585   -7.8378
 UZA  H14  H  HCH2  0   0.225  -2.8651  -16.2395   -8.4384
 UZA  H15  H  HCH2  0   0.228  -3.3534  -14.5755   -8.7051
 UZA  H16  H  HCH2  0   0.228  -3.9064  -14.3380   -6.2903
 UZA  H17  H  HCH2  0   0.224  -3.5265  -16.0264   -6.0214
 UZA  H18  H  HCH2  0   0.236  -1.1711  -15.6335   -6.6977
 UZA  H19  H  HCH2  0   0.236  -1.5428  -13.9728   -7.1059
 UZA  H20  H  HOH1  0   0.480   1.3552  -12.8251   -5.5313
 UZA  C10  C  CH2   0  -0.420  -3.2643  -15.1543   -6.6266

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
 UZA  C05  C06  single  1.527  0.020  1.527
 UZA  C06  C07  single  1.496  0.020  1.496
 UZA  C07  C08  double  1.330  0.020  1.330
 UZA  C08  C09  single  1.496  0.020  1.496
 UZA  C09  C10  single  1.530  0.020  1.530
 UZA  C10  C11  single  1.523  0.020  1.523
 UZA  C11  CA   single  1.543  0.020  1.543
 UZA  CA   N    single  1.458  0.019  1.458
 UZA  CA   C    single  1.525  0.021  1.525
 UZA  CA   CB1  single  1.526  0.020  1.526
 UZA  C    O    double  1.231  0.020  1.231
 UZA  C    OXT  single  1.329  0.020  1.329
 UZA  N    H1   single  0.890  0.020  1.040
 UZA  N    H2   single  0.890  0.020  1.040
 UZA  CB1  H4   single  0.970  0.020  1.090
 UZA  CB1  H5   single  0.970  0.020  1.090
 UZA  CB1  H6   single  0.970  0.020  1.090
 UZA  C05  H7   single  0.970  0.020  1.090
 UZA  C05  H8   single  0.970  0.020  1.090
 UZA  C05  H9   single  0.970  0.020  1.090
 UZA  C06  H10  single  0.970  0.020  1.090
 UZA  C06  H11  single  0.970  0.020  1.090
 UZA  C07  H12  single  0.930  0.020  1.080
 UZA  C08  H13  single  0.930  0.020  1.080
 UZA  C09  H14  single  0.970  0.020  1.090
 UZA  C09  H15  single  0.970  0.020  1.090
 UZA  C10  H16  single  0.970  0.020  1.090
 UZA  C10  H17  single  0.970  0.020  1.090
 UZA  C11  H18  single  0.970  0.020  1.090
 UZA  C11  H19  single  0.970  0.020  1.090
 UZA  OXT  H20  single  0.850  0.020  0.980

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
 UZA  H2   N    H1   106.73  3.000
 UZA  H2   N    CA   111.18  3.000
 UZA  H1   N    CA   110.80  3.000
 UZA  C11  CA   CB1  111.31  3.000
 UZA  CB1  CA   C    108.74  3.000
 UZA  C11  CA   C    105.97  3.000
 UZA  CB1  CA   N    108.71  3.000
 UZA  C    CA   N    111.00  2.800
 UZA  C11  CA   N    109.03  3.000
 UZA  OXT  C    O    122.52  3.000
 UZA  OXT  C    CA   120.80  1.700
 UZA  O    C    CA   120.80  1.700
 UZA  H6   CB1  H5   108.09  3.000
 UZA  H6   CB1  H4   108.05  3.000
 UZA  H5   CB1  H4   107.62  3.000
 UZA  H6   CB1  CA   111.77  3.000
 UZA  H5   CB1  CA   109.88  3.000
 UZA  H4   CB1  CA   111.28  3.000
 UZA  H9   C05  H8   107.63  3.000
 UZA  H9   C05  H7   107.93  3.000
 UZA  H8   C05  H7   107.63  3.000
 UZA  H9   C05  C06  111.01  3.000
 UZA  H8   C05  C06  111.35  3.000
 UZA  H7   C05  C06  111.13  3.000
 UZA  H11  C06  H10  106.50  3.000
 UZA  H11  C06  C07  109.91  3.000
 UZA  H10  C06  C07  109.39  3.000
 UZA  H11  C06  C05  109.73  3.000
 UZA  H10  C06  C05  108.84  3.000
 UZA  C07  C06  C05  112.29  3.000
 UZA  H12  C07  C08  118.75  3.000
 UZA  H12  C07  C06  116.04  3.000
 UZA  C08  C07  C06  125.20  3.000
 UZA  H13  C08  C09  116.08  3.000
 UZA  H13  C08  C07  118.78  3.000
 UZA  C09  C08  C07  125.14  3.000
 UZA  H15  C09  H14  106.47  3.000
 UZA  H15  C09  C10  109.67  3.000
 UZA  H14  C09  C10  108.75  3.000
 UZA  H15  C09  C08  109.99  3.000
 UZA  H14  C09  C08  109.26  3.000
 UZA  C10  C09  C08  112.52  3.000
 UZA  H19  C11  H18  106.08  3.000
 UZA  H19  C11  C10  108.68  3.000
 UZA  H18  C11  C10  109.19  3.000
 UZA  H19  C11  CA   108.79  3.000
 UZA  H18  C11  CA   108.94  3.000
 UZA  C10  C11  CA   114.79  3.000
 UZA  H20  OXT  C    109.96  3.000
 UZA  H17  C10  H16  106.54  3.000
 UZA  H17  C10  C11  110.37  3.000
 UZA  H16  C10  C11  109.90  3.000
 UZA  H17  C10  C09  109.01  3.000
 UZA  H16  C10  C09  109.48  3.000
 UZA  C11  C10  C09  111.41  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
 UZA  CONST_01  H20  OXT  C    CA    180.00   0.0  0
 UZA  Var_01    C09  C08  C07  C06   179.54   0.0  2
 UZA  Var_02    C09  C10  C11  CA    175.31  30.0  2
 UZA  Var_03    C08  C07  C06  C05  -115.79  30.0  3
 UZA  Var_04    C10  C09  C08  C07   115.72  30.0  3
 UZA  Var_05    C11  C10  C09  C08   176.01  30.0  3
 UZA  Var_06    H7   C05  C06  C07  -177.93  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
 UZA  chir_01  CA  N  C  CB1  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
 UZA  plan-1  CA   0.020
 UZA  plan-1  C    0.020
 UZA  plan-1  O    0.020
 UZA  plan-1  OXT  0.020
 UZA  plan-1  H20  0.020
 UZA  plan-2  C06  0.020
 UZA  plan-2  C07  0.020
 UZA  plan-2  C08  0.020
 UZA  plan-2  C09  0.020
 UZA  plan-2  H12  0.020
 UZA  plan-2  H13  0.020

