# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:33:39 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: O-tert-butyl-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC[C@H](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
 RZ4  RZ4  'O-tert-butyl-L-serine    '  L-peptide  25  11  .  2016-04-26  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_RZ4
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
 RZ4  C    C  C      0   0.396  24.1788  43.1890  -4.0053
 RZ4  N    N  NH2    0  -0.814  24.6390  45.4246  -4.9310
 RZ4  O    O  O      0  -0.608  22.9402  43.2691  -3.8828
 RZ4  C1   C  CH3    0  -0.681  24.6045  46.0402   0.2316
 RZ4  C2   C  CH3    0  -0.663  22.9220  44.2281  -0.1886
 RZ4  C3   C  CH3    0  -0.657  25.1605  43.6639   0.7531
 RZ4  CA   C  CH1    0  -0.215  24.9802  44.5059  -3.8453
 RZ4  CB   C  CH2    0  -0.128  24.6392  45.1963  -2.5361
 RZ4  CE   C  CT     0   0.212  24.4089  44.5872  -0.1997
 RZ4  OG   O  O2     0  -0.503  24.9831  44.3337  -1.4785
 RZ4  OXT  O  OC    -1  -0.608  24.8396  42.1624  -4.2607
 RZ4  HN   H  HNH2   0   0.336  25.2514  46.2312  -4.8893
 RZ4  HNA  H  HNH2   0   0.340  24.8413  44.9859  -5.8209
 RZ4  H1   H  HCH3   0   0.229  25.6578  46.3256   0.1947
 RZ4  H1A  H  HCH3   0   0.231  24.0414  46.7363  -0.3925
 RZ4  H1B  H  HCH3   0   0.233  24.2599  46.1750   1.2578
 RZ4  H2   H  HCH3   0   0.226  22.7710  43.1920  -0.4960
 RZ4  H2A  H  HCH3   0   0.223  22.5163  44.3445   0.8168
 RZ4  H2B  H  HCH3   0   0.227  22.3363  44.8678  -0.8505
 RZ4  H3   H  HCH3   0   0.227  25.0538  42.6198   0.4529
 RZ4  H3A  H  HCH3   0   0.226  26.2247  43.9051   0.7775
 RZ4  H3B  H  HCH3   0   0.219  24.7715  43.7614   1.7672
 RZ4  HA   H  HCH1   0   0.174  26.0518  44.2577  -3.8339
 RZ4  HB   H  HCH2   0   0.191  25.1939  46.1441  -2.4652
 RZ4  HBA  H  HCH2   0   0.187  23.5736  45.4479  -2.5452

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
 RZ4  OXT  C    deloc   1.247  0.020  1.247
 RZ4  C    O    deloc   1.231  0.020  1.231
 RZ4  C    CA   single  1.525  0.021  1.525
 RZ4  N    CA   single  1.458  0.019  1.458
 RZ4  N    HN   single  0.890  0.020  1.040
 RZ4  N    HNA  single  0.890  0.020  1.040
 RZ4  CE   C1   single  1.528  0.020  1.528
 RZ4  C1   H1   single  0.970  0.020  1.090
 RZ4  C1   H1A  single  0.970  0.020  1.090
 RZ4  C1   H1B  single  0.970  0.020  1.090
 RZ4  C2   CE   single  1.530  0.020  1.530
 RZ4  C2   H2   single  0.970  0.020  1.090
 RZ4  C2   H2A  single  0.970  0.020  1.090
 RZ4  C2   H2B  single  0.970  0.020  1.090
 RZ4  CE   C3   single  1.525  0.020  1.525
 RZ4  C3   H3   single  0.970  0.020  1.090
 RZ4  C3   H3A  single  0.970  0.020  1.090
 RZ4  C3   H3B  single  0.970  0.020  1.090
 RZ4  CA   CB   single  1.530  0.020  1.530
 RZ4  CA   HA   single  0.970  0.020  0.970
 RZ4  CB   OG   single  1.407  0.020  1.407
 RZ4  CB   HB   single  0.970  0.020  1.090
 RZ4  CB   HBA  single  0.970  0.020  1.090
 RZ4  OG   CE   single  1.425  0.020  1.425

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
 RZ4  OXT  C   CA   116.52  3.000
 RZ4  CA   C   O    120.80  1.700
 RZ4  OXT  C   O    126.81  3.000
 RZ4  HNA  N   HN   105.09  3.000
 RZ4  HNA  N   CA   109.49  3.000
 RZ4  HN   N   CA   109.17  3.000
 RZ4  H1B  C1  H1A  107.22  3.000
 RZ4  H1B  C1  H1   107.70  3.000
 RZ4  H1A  C1  H1   108.16  3.000
 RZ4  H1B  C1  CE   110.04  3.000
 RZ4  H1A  C1  CE   112.27  3.000
 RZ4  H1   C1  CE   111.25  3.000
 RZ4  H2B  C2  H2A  107.29  3.000
 RZ4  H2B  C2  H2   108.15  3.000
 RZ4  H2A  C2  H2   108.03  3.000
 RZ4  H2B  C2  CE   112.32  3.000
 RZ4  H2A  C2  CE   110.07  3.000
 RZ4  H2   C2  CE   110.81  3.000
 RZ4  H3B  C3  H3A  107.89  3.000
 RZ4  H3B  C3  H3   107.84  3.000
 RZ4  H3A  C3  H3   108.23  3.000
 RZ4  H3B  C3  CE   110.55  3.000
 RZ4  H3A  C3  CE   111.14  3.000
 RZ4  H3   C3  CE   111.05  3.000
 RZ4  HA   CA  CB   109.00  3.000
 RZ4  HA   CA  N    110.00  3.000
 RZ4  CB   CA  N    110.50  1.700
 RZ4  HA   CA  C    109.00  3.000
 RZ4  CB   CA  C    110.10  1.900
 RZ4  N    CA  C    111.00  2.800
 RZ4  HBA  CB  HB   107.04  3.000
 RZ4  HBA  CB  OG   112.63  3.000
 RZ4  HB   CB  OG   110.87  3.000
 RZ4  HBA  CB  CA   108.41  3.000
 RZ4  HB   CB  CA   109.51  3.000
 RZ4  OG   CB  CA   108.32  3.000
 RZ4  OG   CE  C3   104.74  3.000
 RZ4  OG   CE  C2   110.89  3.000
 RZ4  C3   CE  C2   109.42  3.000
 RZ4  OG   CE  C1   111.77  3.000
 RZ4  C3   CE  C1   109.65  3.000
 RZ4  C2   CE  C1   110.22  3.000
 RZ4  CE   OG  CB   117.84  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
 RZ4  Var_01  H2  C2  CE  C1   179.96  30.0  3
 RZ4  Var_02  H3  C3  CE  C1  -178.77  30.0  3
 RZ4  Var_03  H1  C1  CE  C2  -177.93  30.0  3
 RZ4  Var_04  HB  CB  OG  CE    77.82  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
 RZ4  chir_01  CA  C  N  CB  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
 RZ4  plan-1  C    0.020
 RZ4  plan-1  O    0.020
 RZ4  plan-1  CA   0.020
 RZ4  plan-1  OXT  0.020

