# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:25:07 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: O-(diazoacetyl)-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](COC(=O)C=[N+]=[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
 AZS  AZS  'O-(diazoacetyl)-L-serine '  L-peptide  18  12  .  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_AZS
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
 AZS  OXT  O  OC     0  -0.391  12.3393  -33.6887  -22.7884
 AZS  C    C  C      0   0.335  13.5524  -33.8782  -22.9873
 AZS  O    O  O     -1  -0.669  14.5102  -33.2871  -22.4521
 AZS  CA   C  CH1    0  -0.226  13.9374  -34.9407  -24.0539
 AZS  N    N  NH2    0  -0.751  12.8138  -35.7955  -24.3839
 AZS  CB   C  CH2    0  -0.226  14.5303  -34.1868  -25.2395
 AZS  OG   O  O2     0  -0.365  14.9640  -35.1542  -26.2087
 AZS  CH   C  C      0   0.543  15.4085  -34.7095  -27.3775
 AZS  CI   C  C1     0  -0.199  15.7786  -35.8187  -28.2309
 AZS  NJ   N  N      1  -0.077  16.2331  -35.5251  -29.4123
 AZS  NK   N  N     -1  -0.096  16.6248  -35.2587  -30.4249
 AZS  OH   O  O      0  -0.442  15.4951  -33.5418  -27.6879
 AZS  HA   H  HCH1   0   0.136  14.7344  -35.5605  -23.6261
 AZS  HN1  H  HNH2   0   0.297  11.9955  -35.2188  -24.5317
 AZS  HN2  H  HNH2   0   0.357  12.9874  -36.2987  -25.2446
 AZS  HB1  H  HCH2   0   0.203  13.7785  -33.5299  -25.6875
 AZS  HB2  H  HCH2   0   0.231  15.3804  -33.5792  -24.9257
 AZS  HI   H  H      0   0.340  15.7073  -36.8649  -27.9786

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
 AZS  OXT  C    deloc   1.244  0.020  1.244
 AZS  C    O    deloc   1.231  0.020  1.231
 AZS  C    CA   single  1.525  0.021  1.525
 AZS  CA   HA   single  0.970  0.020  0.970
 AZS  CA   N    single  1.458  0.019  1.458
 AZS  CA   CB   single  1.530  0.020  1.530
 AZS  N    HN1  single  0.890  0.020  1.040
 AZS  N    HN2  single  0.890  0.020  1.040
 AZS  CB   HB1  single  0.970  0.020  1.090
 AZS  CB   HB2  single  0.970  0.020  1.090
 AZS  CB   OG   single  1.436  0.020  1.436
 AZS  OG   CH   single  1.327  0.020  1.327
 AZS  CH   OH   double  1.211  0.020  1.211
 AZS  CH   CI   single  1.448  0.020  1.448
 AZS  CI   HI   single  0.930  0.020  1.080
 AZS  CI   NJ   double  1.299  0.020  1.299
 AZS  NJ   NK   double  1.118  0.020  1.118

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
 AZS  CA   C   O    120.80  1.700
 AZS  CA   C   OXT  117.10  3.000
 AZS  O    C   OXT  127.49  3.000
 AZS  HA   CA  CB   109.00  3.000
 AZS  CB   CA  N    110.50  1.700
 AZS  HA   CA  N    110.00  3.000
 AZS  CB   CA  C    110.10  1.900
 AZS  N    CA  C    111.00  2.800
 AZS  HA   CA  C    109.00  3.000
 AZS  HN2  N   HN1  107.33  3.000
 AZS  HN2  N   CA   110.72  3.000
 AZS  HN1  N   CA   108.90  3.000
 AZS  HB2  CB  HB1  108.59  3.000
 AZS  HB2  CB  OG   109.50  3.000
 AZS  HB1  CB  OG   109.60  3.000
 AZS  OG   CB  CA   108.00  3.000
 AZS  HB2  CB  CA   110.78  3.000
 AZS  HB1  CB  CA   110.37  3.000
 AZS  CH   OG  CB   118.01  3.000
 AZS  OH   CH  CI   124.70  3.000
 AZS  CI   CH  OG   110.37  3.000
 AZS  OH   CH  OG   124.93  3.000
 AZS  HI   CI  NJ   117.06  3.000
 AZS  NJ   CI  CH   116.89  3.000
 AZS  HI   CI  CH   126.05  3.000
 AZS  NK   NJ  CI   180.00  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
 AZS  Var_01  OH  CH  OG  CB     1.06  30.0  3
 AZS  Var_02  NJ  CI  CH  OG  -179.99  30.0  2
 AZS  Var_03  HI  CI  NJ  NK  -170.60   0.0  2

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
 AZS  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
 AZS  plan-1  OXT  0.020
 AZS  plan-1  C    0.020
 AZS  plan-1  O    0.020
 AZS  plan-1  CA   0.020
 AZS  plan-2  OG   0.020
 AZS  plan-2  CH   0.020
 AZS  plan-2  CI   0.020
 AZS  plan-2  OH   0.020
 AZS  plan-3  CH   0.020
 AZS  plan-3  CI   0.020
 AZS  plan-3  NJ   0.020
 AZS  plan-3  NK   0.020
 AZS  plan-3  HI   0.020

