# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:51:06 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: methyl L-serinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CO
#
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
 5R5  5R5  'methyl L-serinate        '  L-peptide  17  8  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5R5
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
 5R5  N    N  NH2   0  -0.777  -24.0721  20.3044  -4.9717
 5R5  CA   C  CH1   0  -0.246  -23.0761  19.4578  -4.3355
 5R5  C    C  C     0   0.594  -22.4164  20.1420  -3.1438
 5R5  CB   C  CH2   0  -0.172  -22.0373  19.0009  -5.3534
 5R5  OG   O  OH1   0  -0.665  -21.3789  20.0607  -6.0031
 5R5  O    O  O     0  -0.454  -21.2853  20.5679  -3.1274
 5R5  C1   C  CH3   0  -0.424  -22.7960  20.9592  -0.9654
 5R5  OXT  O  O2    0  -0.449  -23.2511  20.2575  -2.1234
 5R5  H    H  HNH2  0   0.357  -24.7928  20.5729  -4.3148
 5R5  H2   H  HNH2  0   0.348  -23.6438  21.1571  -5.3092
 5R5  HA   H  HCH1  0   0.269  -23.5830  18.5602  -3.9675
 5R5  HB2  H  HCH2  0   0.235  -22.5582  18.4301  -6.1242
 5R5  HB3  H  HCH2  0   0.209  -21.3334  18.3136  -4.8686
 5R5  HG   H  HOH1  0   0.445  -20.8336  20.5067  -5.3465
 5R5  H11  H  HCH3  0   0.252  -23.6232  20.9426  -0.2622
 5R5  H12  H  HCH3  0   0.240  -21.9315  20.4695  -0.5179
 5R5  H13  H  HCH3  0   0.240  -22.5421  21.9925  -1.2009

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
 5R5  OG   CB   single  1.407  0.020  1.407
 5R5  CB   CA   single  1.530  0.020  1.530
 5R5  N    CA   single  1.458  0.019  1.458
 5R5  CA   C    single  1.525  0.021  1.525
 5R5  C    O    double  1.231  0.020  1.231
 5R5  C    OXT  single  1.323  0.020  1.323
 5R5  OXT  C1   single  1.428  0.020  1.428
 5R5  N    H    single  0.860  0.020  0.860
 5R5  N    H2   single  0.890  0.020  1.040
 5R5  CA   HA   single  0.970  0.020  0.970
 5R5  CB   HB2  single  0.970  0.020  1.090
 5R5  CB   HB3  single  0.970  0.020  1.090
 5R5  OG   HG   single  0.850  0.020  0.980
 5R5  C1   H11  single  0.970  0.020  1.090
 5R5  C1   H12  single  0.970  0.020  1.090
 5R5  C1   H13  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
 5R5  H2   N    H    107.12  3.000
 5R5  H2   N    CA   110.28  3.000
 5R5  H    N    CA   114.00  3.000
 5R5  HA   CA   CB   109.00  3.000
 5R5  HA   CA   C    109.00  3.000
 5R5  CB   CA   C    110.10  1.900
 5R5  HA   CA   N    110.00  3.000
 5R5  C    CA   N    111.00  2.800
 5R5  CB   CA   N    110.50  1.700
 5R5  OXT  C    O    123.30  3.000
 5R5  OXT  C    CA   111.65  3.000
 5R5  O    C    CA   120.80  1.700
 5R5  HB3  CB   HB2  106.90  3.000
 5R5  HB3  CB   OG   112.08  3.000
 5R5  HB2  CB   OG   106.93  3.000
 5R5  HB3  CB   CA   109.27  3.000
 5R5  HB2  CB   CA   107.64  3.000
 5R5  OG   CB   CA   113.68  3.000
 5R5  HG   OG   CB   107.40  3.000
 5R5  H13  C1   H12  109.27  3.000
 5R5  H13  C1   H11  109.39  3.000
 5R5  H12  C1   H11  109.37  3.000
 5R5  H13  C1   OXT  111.40  3.000
 5R5  H12  C1   OXT  111.40  3.000
 5R5  H11  C1   OXT  105.94  3.000
 5R5  C1   OXT  C    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
 5R5  Var_01  H11  C1  OXT  C  179.71  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
 5R5  chir_01  CA  CB  N  C  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
 5R5  plan-1  CA   0.020
 5R5  plan-1  C    0.020
 5R5  plan-1  O    0.020
 5R5  plan-1  OXT  0.020

