# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:55:30 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (4S)-2-[(1S)-1-amino-2-hydroxyethyl]-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)C1=NCC[C@H](N1)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
 SDB  SDB  '(4S)-2-[(1S)-1-amino-2-hydroxyethyl]-3,4,5,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  25  13  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SDB
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
 SDB  O     O  O      0  -0.599  -2.2036  -1.9955  -0.3305
 SDB  C     C  C      0   0.415  -2.6186  -0.8694   0.0081
 SDB  CA1   C  CH1    0  -0.172  -1.5615   0.1786   0.4175
 SDB  CB1   C  CH2    0  -0.487  -1.7287   1.5109  -0.3000
 SDB  CG    C  CH2    0  -0.315  -0.5264   2.3976  -0.0013
 SDB  NE    N  N      0  -0.474   0.7453   1.7651  -0.2871
 SDB  N1    N  NH1    0  -0.659  -0.2239  -0.3198   0.1800
 SDB  C1    C  C      0   0.400   0.7876   0.4871  -0.2102
 SDB  CA    C  CH1    0  -0.167   2.1217  -0.1964  -0.5079
 SDB  N     N  NH2    0  -0.791   2.0674  -1.5761  -0.9429
 SDB  CB    C  CH2    0  -0.136   2.9961  -0.0652   0.7341
 SDB  OG    O  OH1    0  -0.668   4.2930  -0.5310   0.4495
 SDB  OXT   O  OC    -1  -0.604  -3.8017  -0.4921   0.0764
 SDB  HA1   H  HCH1   0   0.232  -1.6960   0.3566   1.4940
 SDB  HB11  H  HCH2   0   0.221  -1.8012   1.3456  -1.3797
 SDB  HB12  H  HCH2   0   0.233  -2.6528   1.9921   0.0177
 SDB  H1    H  HNH1   0   0.356  -0.1820  -1.3027  -0.0447
 SDB  HG1C  H  HCH2   0   0.216  -0.5944   3.3199  -0.5856
 SDB  HG2C  H  HCH2   0   0.207  -0.5600   2.7124   1.0500
 SDB  HA    H  HCH1   0   0.241   2.5833   0.3944  -1.3046
 SDB  HN1   H  HNH2   0   0.345   1.7676  -2.1946  -0.1998
 SDB  HN2   H  HNH2   0   0.353   1.4310  -1.6955  -1.7199
 SDB  HB1C  H  HCH2   0   0.209   2.9989   0.9878   1.0353
 SDB  HB2C  H  HCH2   0   0.190   2.5333  -0.6322   1.5557
 SDB  HG    H  HOH1   0   0.453   4.8443  -0.3558   1.2173

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
 SDB  O    C     deloc   1.247  0.020  1.247
 SDB  C    CA1   single  1.544  0.020  1.544
 SDB  C    OXT   deloc   1.244  0.020  1.244
 SDB  CA1  CB1   single  1.522  0.020  1.522
 SDB  CA1  N1    single  1.447  0.020  1.447
 SDB  CB1  CG    single  1.524  0.020  1.524
 SDB  CG   NE    single  1.449  0.020  1.449
 SDB  NE   C1    double  1.281  0.020  1.281
 SDB  N1   C1    single  1.352  0.020  1.352
 SDB  C1   CA    single  1.528  0.020  1.528
 SDB  CA   N     single  1.448  0.020  1.448
 SDB  CA   CB    single  1.525  0.020  1.525
 SDB  CB   OG    single  1.407  0.020  1.407
 SDB  CA1  HA1   single  0.970  0.020  1.090
 SDB  CB1  HB11  single  0.970  0.020  1.090
 SDB  CB1  HB12  single  0.970  0.020  1.090
 SDB  N1   H1    single  0.890  0.020  1.040
 SDB  CG   HG1C  single  0.970  0.020  1.090
 SDB  CG   HG2C  single  0.970  0.020  1.090
 SDB  CA   HA    single  0.970  0.020  1.090
 SDB  N    HN1   single  0.890  0.020  1.040
 SDB  N    HN2   single  0.890  0.020  1.040
 SDB  CB   HB1C  single  0.970  0.020  1.090
 SDB  CB   HB2C  single  0.970  0.020  1.090
 SDB  OG   HG    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
 SDB  OXT   C    CA1   115.53  3.000
 SDB  OXT   C    O     127.27  3.000
 SDB  CA1   C    O     117.20  3.000
 SDB  HA1   CA1  N1    109.25  3.000
 SDB  HA1   CA1  CB1   107.84  3.000
 SDB  N1    CA1  CB1   109.00  3.000
 SDB  HA1   CA1  C     106.60  3.000
 SDB  N1    CA1  C     110.83  3.000
 SDB  CB1   CA1  C     113.20  3.000
 SDB  HB12  CB1  HB11  107.35  3.000
 SDB  HB12  CB1  CG    110.81  3.000
 SDB  HB11  CB1  CG    109.49  3.000
 SDB  HB12  CB1  CA1   110.02  3.000
 SDB  HB11  CB1  CA1   109.87  3.000
 SDB  CG    CB1  CA1   109.28  3.000
 SDB  HG2C  CG   HG1C  105.53  3.000
 SDB  HG2C  CG   NE    109.94  3.000
 SDB  HG1C  CG   NE    108.50  3.000
 SDB  HG2C  CG   CB1   109.29  3.000
 SDB  HG1C  CG   CB1   109.69  3.000
 SDB  NE    CG   CB1   113.57  3.000
 SDB  C1    NE   CG    116.92  3.000
 SDB  H1    N1   C1    119.08  3.000
 SDB  H1    N1   CA1   114.23  3.000
 SDB  C1    N1   CA1   122.25  3.000
 SDB  CA    C1   N1    116.27  3.000
 SDB  CA    C1   NE    117.60  3.000
 SDB  N1    C1   NE    126.03  3.000
 SDB  HA    CA   CB    107.75  3.000
 SDB  HA    CA   N     108.16  3.000
 SDB  CB    CA   N     110.39  3.000
 SDB  HA    CA   C1    105.58  3.000
 SDB  CB    CA   C1    107.67  3.000
 SDB  N     CA   C1    116.87  3.000
 SDB  HN2   N    HN1   107.78  3.000
 SDB  HN2   N    CA    111.53  3.000
 SDB  HN1   N    CA    111.89  3.000
 SDB  HB2C  CB   HB1C  106.93  3.000
 SDB  HB2C  CB   OG    111.60  3.000
 SDB  HB1C  CB   OG    111.81  3.000
 SDB  HB2C  CB   CA    108.83  3.000
 SDB  HB1C  CB   CA    107.95  3.000
 SDB  OG    CB   CA    109.59  3.000
 SDB  HG    OG   CB    107.86  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
 SDB  CONST_01  NE  C1  N1   CA1    0.00   0.0  0
 SDB  CONST_02  N1  C1  NE   CG     0.00   0.0  0
 SDB  CONST_03  CA  C1  N1   CA1  180.00   0.0  0
 SDB  CONST_04  CA  C1  NE   CG   180.00   0.0  0
 SDB  Var_01    NE  CG  CB1  CA1   53.25  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
 SDB  chir_01  CA1  C  CB1  N1  positiv
 SDB  chir_02  CA   N  CB   C1  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
 SDB  plan-1  CA1  0.020
 SDB  plan-1  CG   0.020
 SDB  plan-1  NE   0.020
 SDB  plan-1  N1   0.020
 SDB  plan-1  C1   0.020
 SDB  plan-1  CA   0.020
 SDB  plan-1  H1   0.020
 SDB  plan-2  O    0.020
 SDB  plan-2  C    0.020
 SDB  plan-2  CA1  0.020
 SDB  plan-2  OXT  0.020

