# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:18:24 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: methyl (4R)-4-amino-1-methyl-L-prolinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1C[C@@H](N)CN1C
#
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
 SZ8  SZ8  'methyl (4R)-4-amino-1-methyl-L-prolinate'  ligand  25  11  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZ8
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
 SZ8  C1    C  CH1   0  -0.085  -2.0121  -0.7241  -0.4239
 SZ8  N1    N  NH2   0  -0.801  -3.1616  -1.5357  -0.0687
 SZ8  O1    O  O2    0  -0.456   2.2222  -0.7400   0.4221
 SZ8  C2    C  CH2   0  -0.259  -2.1478   0.7188   0.0351
 SZ8  N2    N  NT    0  -0.420  -0.7822   1.1948  -0.0107
 SZ8  C3    C  CH3   0  -0.525  -0.5676   2.4897   0.5823
 SZ8  C4    C  CH1   0  -0.167   0.0598   0.1426   0.5145
 SZ8  C5    C  C     0   0.580   1.4003   0.1050  -0.1889
 SZ8  C6    C  CH3   0  -0.422   3.5189  -0.9283  -0.1428
 SZ8  C7    C  CH2   0  -0.485  -0.7457  -1.1652   0.3137
 SZ8  H1    H  HCH1  0   0.213  -1.8072  -0.7184  -1.5041
 SZ8  HN1   H  HNH2  0   0.346  -3.9588  -1.2443  -0.6219
 SZ8  HN1A  H  HNH2  0   0.347  -2.9894  -2.4963  -0.3394
 SZ8  H2    H  HCH2  0   0.237  -2.7902   1.3226  -0.6111
 SZ8  H2A   H  HCH2  0   0.188  -2.5789   0.7385   1.0508
 SZ8  H3    H  HCH3  0   0.196  -0.7840   2.5115   1.6615
 SZ8  H3A   H  HCH3  0   0.235   0.4656   2.8099   0.4418
 SZ8  H3B   H  HCH3  0   0.236  -1.2055   3.2307   0.0990
 SZ8  H4    H  HCH1  0   0.252   0.2618   0.2727   1.5898
 SZ8  H6    H  HCH3  0   0.238   3.4599  -1.2859  -1.1705
 SZ8  H6A   H  HCH3  0   0.238   4.1023  -0.0082  -0.1158
 SZ8  H6B   H  HCH3  0   0.251   4.0060  -1.6797   0.4715
 SZ8  H7    H  HCH2  0   0.247  -1.0240  -1.5786   1.2842
 SZ8  H7A   H  HCH2  0   0.258  -0.1972  -1.9376  -0.2263
 SZ8  O2    O  O     0  -0.442   1.6983   0.7349  -1.1700

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
 SZ8  C1  N1    single  1.451  0.020  1.451
 SZ8  C1  C2    single  1.520  0.020  1.520
 SZ8  C1  C7    single  1.531  0.020  1.531
 SZ8  O1  C5    single  1.328  0.020  1.328
 SZ8  O1  C6    single  1.427  0.020  1.427
 SZ8  C2  N2    single  1.447  0.020  1.447
 SZ8  N2  C3    single  1.440  0.020  1.440
 SZ8  N2  C4    single  1.446  0.020  1.446
 SZ8  O2  C5    double  1.203  0.020  1.203
 SZ8  C4  C5    single  1.514  0.020  1.514
 SZ8  C4  C7    single  1.549  0.020  1.549
 SZ8  C1  H1    single  0.970  0.020  1.090
 SZ8  N1  HN1   single  0.890  0.020  1.040
 SZ8  N1  HN1A  single  0.890  0.020  1.040
 SZ8  C2  H2    single  0.970  0.020  1.090
 SZ8  C2  H2A   single  0.970  0.020  1.090
 SZ8  C3  H3    single  0.970  0.020  1.090
 SZ8  C3  H3A   single  0.970  0.020  1.090
 SZ8  C3  H3B   single  0.970  0.020  1.090
 SZ8  C4  H4    single  0.970  0.020  1.090
 SZ8  C6  H6    single  0.970  0.020  1.090
 SZ8  C6  H6A   single  0.970  0.020  1.090
 SZ8  C6  H6B   single  0.970  0.020  1.090
 SZ8  C7  H7    single  0.970  0.020  1.090
 SZ8  C7  H7A   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
 SZ8  H1    C1  C7   108.71  3.000
 SZ8  H1    C1  C2   107.96  3.000
 SZ8  C7    C1  C2   101.65  3.000
 SZ8  H1    C1  N1   113.02  3.000
 SZ8  C7    C1  N1   112.10  3.000
 SZ8  C2    C1  N1   112.71  3.000
 SZ8  HN1A  N1  HN1  105.11  3.000
 SZ8  HN1A  N1  C1   109.28  3.000
 SZ8  HN1   N1  C1   109.19  3.000
 SZ8  C6    O1  C5   117.66  3.000
 SZ8  H2A   C2  H2   107.73  3.000
 SZ8  H2A   C2  N2   113.07  3.000
 SZ8  H2    C2  N2   110.75  3.000
 SZ8  H2A   C2  C1   109.25  3.000
 SZ8  H2    C2  C1   113.47  3.000
 SZ8  N2    C2  C1   102.62  3.000
 SZ8  C4    N2  C3   114.70  3.000
 SZ8  C4    N2  C2   107.37  3.000
 SZ8  C3    N2  C2   115.05  3.000
 SZ8  H3B   C3  H3A  107.30  3.000
 SZ8  H3B   C3  H3   107.81  3.000
 SZ8  H3A   C3  H3   107.86  3.000
 SZ8  H3B   C3  N2   109.95  3.000
 SZ8  H3A   C3  N2   110.61  3.000
 SZ8  H3    C3  N2   113.09  3.000
 SZ8  H4    C4  C7   108.76  3.000
 SZ8  H4    C4  C5   107.09  3.000
 SZ8  C7    C4  C5   112.28  3.000
 SZ8  H4    C4  N2   112.03  3.000
 SZ8  C7    C4  N2   105.34  3.000
 SZ8  C5    C4  N2   111.39  3.000
 SZ8  C4    C5  O2   125.80  3.000
 SZ8  C4    C5  O1   110.49  3.000
 SZ8  O2    C5  O1   123.71  3.000
 SZ8  H6B   C6  H6A  109.27  3.000
 SZ8  H6B   C6  H6   109.31  3.000
 SZ8  H6A   C6  H6   109.23  3.000
 SZ8  H6B   C6  O1   105.96  3.000
 SZ8  H6A   C6  O1   111.43  3.000
 SZ8  H6    C6  O1   111.56  3.000
 SZ8  H7A   C7  H7   107.48  3.000
 SZ8  H7A   C7  C4   113.62  3.000
 SZ8  H7    C7  C4   109.71  3.000
 SZ8  H7A   C7  C1   112.44  3.000
 SZ8  H7    C7  C1   109.08  3.000
 SZ8  C4    C7  C1   104.44  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
 SZ8  Var_01  C4  N2  C2  C1  -41.45  30.0  1
 SZ8  Var_02  H3  C3  N2  C2   63.18  30.0  3
 SZ8  Var_03  H6  C6  O1  C5  -58.59  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
 SZ8  chir_01  C1  N1  C2  C7  negativ
 SZ8  chir_02  C4  N2  C5  C7  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
 SZ8  plan-1  O1  0.020
 SZ8  plan-1  C4  0.020
 SZ8  plan-1  C5  0.020
 SZ8  plan-1  O2  0.020

