# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 10:11:59 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: O-(2-aminoethyl)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCOC[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
 OLZ  OLZ  O-(2-aminoethyl)-L-serine  L-peptide  21  10  .  2012-08-28  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_OLZ
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
 OLZ  OXT   O  OC    -1  -0.612  32.9781  17.6764  23.1455
 OLZ  C     C  C      0   0.379  33.2569  17.0060  22.1293
 OLZ  O     O  O      0  -0.597  34.3743  16.5577  21.8124
 OLZ  CA    C  CH1    0  -0.265  32.0728  16.7216  21.1588
 OLZ  N     N  NH2    0  -0.781  32.4009  15.9441  19.9730
 OLZ  CB    C  CH2    0  -0.115  30.9393  16.0553  21.9242
 OLZ  OG    O  O2     0  -0.485  29.7930  15.9533  21.1139
 OLZ  CD    C  CH2    0  -0.145  28.7187  15.3142  21.7527
 OLZ  CE    C  CH2    0  -0.333  27.5850  15.1406  20.7571
 OLZ  NZ    N  NH2    0  -0.786  27.8808  14.3098  19.6016
 OLZ  HA    H  HCH1   0   0.218  31.7054  17.6989  20.8196
 OLZ  HN    H  HNH2   0   0.332  33.1252  16.4346  19.4626
 OLZ  HNA   H  HNH2   0   0.321  32.8511  15.0856  20.2725
 OLZ  HB    H  HCH2   0   0.180  31.2584  15.0534  22.2576
 OLZ  HBA   H  HCH2   0   0.197  30.7190  16.6346  22.8280
 OLZ  HD    H  HCH2   0   0.185  29.0238  14.3282  22.1375
 OLZ  HDA   H  HCH2   0   0.188  28.3692  15.8966  22.6191
 OLZ  HE    H  HCH2   0   0.223  26.7318  14.7123  21.2886
 OLZ  HEA   H  HCH2   0   0.219  27.2626  16.1250  20.4059
 OLZ  HNZ   H  HNH2   0   0.338  28.7071  14.6659  19.1372
 OLZ  HNZA  H  HNH2   0   0.337  28.1240  13.3767  19.9125

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
 OLZ  C   OXT   deloc   1.249  0.020  1.249
 OLZ  CA  C     single  1.525  0.021  1.525
 OLZ  O   C     deloc   1.231  0.020  1.231
 OLZ  N   CA    single  1.458  0.019  1.458
 OLZ  CA  CB    single  1.530  0.020  1.530
 OLZ  CA  HA    single  0.970  0.020  0.970
 OLZ  N   HN    single  0.890  0.020  1.040
 OLZ  N   HNA   single  0.890  0.020  1.040
 OLZ  OG  CB    single  1.408  0.020  1.408
 OLZ  CB  HB    single  0.970  0.020  1.090
 OLZ  CB  HBA   single  0.970  0.020  1.090
 OLZ  OG  CD    single  1.404  0.020  1.404
 OLZ  CE  CD    single  1.519  0.020  1.519
 OLZ  CD  HD    single  0.970  0.020  1.090
 OLZ  CD  HDA   single  0.970  0.020  1.090
 OLZ  NZ  CE    single  1.454  0.020  1.454
 OLZ  CE  HE    single  0.970  0.020  1.090
 OLZ  CE  HEA   single  0.970  0.020  1.090
 OLZ  NZ  HNZ   single  0.890  0.020  1.040
 OLZ  NZ  HNZA  single  0.890  0.020  1.040

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
 OLZ  CA    C   O    120.80  1.700
 OLZ  O     C   OXT  126.93  3.000
 OLZ  CA    C   OXT  115.81  3.000
 OLZ  HA    CA  CB   109.00  3.000
 OLZ  HA    CA  N    110.00  3.000
 OLZ  CB    CA  N    110.50  1.700
 OLZ  HA    CA  C    109.00  3.000
 OLZ  CB    CA  C    110.10  1.900
 OLZ  N     CA  C    111.00  2.800
 OLZ  HNA   N   HN   103.96  3.000
 OLZ  HNA   N   CA   108.15  3.000
 OLZ  HN    N   CA   108.25  3.000
 OLZ  HBA   CB  HB   106.80  3.000
 OLZ  HBA   CB  OG   110.45  3.000
 OLZ  HB    CB  OG   110.11  3.000
 OLZ  HBA   CB  CA   109.46  3.000
 OLZ  HB    CB  CA   109.53  3.000
 OLZ  OG    CB  CA   110.42  3.000
 OLZ  CD    OG  CB   113.22  3.000
 OLZ  HDA   CD  HD   106.65  3.000
 OLZ  HDA   CD  CE   109.84  3.000
 OLZ  HD    CD  CE   109.47  3.000
 OLZ  HDA   CD  OG   111.12  3.000
 OLZ  HD    CD  OG   110.77  3.000
 OLZ  CE    CD  OG   108.96  3.000
 OLZ  HEA   CE  HE   106.18  3.000
 OLZ  HEA   CE  NZ   108.61  3.000
 OLZ  HE    CE  NZ   108.76  3.000
 OLZ  HEA   CE  CD   109.13  3.000
 OLZ  HE    CE  CD   107.99  3.000
 OLZ  NZ    CE  CD   115.76  3.000
 OLZ  HNZA  NZ  HNZ  105.59  3.000
 OLZ  HNZA  NZ  CE   109.35  3.000
 OLZ  HNZ   NZ  CE   109.25  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
 OLZ  Var_01  CE   CD  OG  CB  -174.77  30.0  3
 OLZ  Var_02  NZ   CE  CD  OG    62.10  30.0  1
 OLZ  Var_03  HB   CB  OG  CD    57.37  30.0  3
 OLZ  Var_04  HNZ  NZ  CE  CD   -54.65  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
 OLZ  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
 OLZ  plan-1  OXT  0.020
 OLZ  plan-1  C    0.020
 OLZ  plan-1  O    0.020
 OLZ  plan-1  CA   0.020

