# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 11:03:46 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: N-carbamoyl-L-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC(N)=O)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
 W9J  W9J  'N-carbamoyl-L-methionine '  ligand  23  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W9J
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
 W9J  NT   N  NH2    0  -0.845  62.0969  61.5110  22.6547
 W9J  CT   C  C      0   0.655  61.7565  62.1767  23.7993
 W9J  OT   O  O      0  -0.540  62.6050  62.6054  24.5736
 W9J  N    N  NH1    0  -0.638  60.4245  62.4104  23.9551
 W9J  CA   C  CH1    0  -0.195  59.9011  62.8100  25.2408
 W9J  CB   C  CH2    0  -0.446  58.4977  63.3916  25.0679
 W9J  CG   C  CH2    0  -0.535  58.4780  64.6221  24.1734
 W9J  SD   S  S2     0  -0.051  56.7961  65.3043  24.1000
 W9J  CE   C  CH3    0  -0.761  57.0799  66.7063  22.9970
 W9J  C    C  C      0   0.410  59.8983  61.6622  26.2907
 W9J  O    O  O      0  -0.591  60.2719  60.5391  25.9118
 W9J  OXT  O  OC    -1  -0.609  59.5139  61.9924  27.4301
 W9J  H1   H  HNH2   0   0.387  63.0421  61.1709  22.6022
 W9J  H2   H  HNH2   0   0.386  61.4190  60.9425  22.1741
 W9J  H3   H  HNH1   0   0.372  59.7992  61.8396  23.4057
 W9J  H4   H  HCH1   0   0.235  60.5420  63.6073  25.6268
 W9J  H5   H  HCH2   0   0.243  58.1174  63.6502  26.0564
 W9J  H6   H  HCH2   0   0.229  57.8252  62.6276  24.6624
 W9J  H7   H  HCH2   0   0.257  58.8038  64.3785  23.1611
 W9J  H8   H  HCH2   0   0.252  59.1540  65.3853  24.5670
 W9J  H9   H  HCH3   0   0.270  56.1296  67.2181  22.8561
 W9J  H10  H  HCH3   0   0.258  57.7928  67.4077  23.4284
 W9J  H11  H  HCH3   0   0.258  57.4442  66.3751  22.0254

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
 W9J  NT  CT   single  1.367  0.020  1.367
 W9J  CE  SD   single  1.806  0.020  1.806
 W9J  CG  SD   single  1.817  0.020  1.817
 W9J  CG  CB   single  1.521  0.020  1.521
 W9J  CT  N    single  1.361  0.020  1.361
 W9J  CT  OT   double  1.226  0.020  1.226
 W9J  N   CA   single  1.445  0.020  1.445
 W9J  CB  CA   single  1.529  0.020  1.529
 W9J  CA  C    single  1.555  0.020  1.555
 W9J  O   C    deloc   1.243  0.020  1.243
 W9J  C   OXT  deloc   1.247  0.020  1.247
 W9J  NT  H1   single  0.890  0.020  1.040
 W9J  NT  H2   single  0.890  0.020  1.040
 W9J  N   H3   single  0.890  0.020  1.040
 W9J  CA  H4   single  0.970  0.020  1.090
 W9J  CB  H5   single  0.970  0.020  1.090
 W9J  CB  H6   single  0.970  0.020  1.090
 W9J  CG  H7   single  0.970  0.020  1.090
 W9J  CG  H8   single  0.970  0.020  1.090
 W9J  CE  H9   single  0.970  0.020  1.090
 W9J  CE  H10  single  0.970  0.020  1.090
 W9J  CE  H11  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
 W9J  H2   NT  H1   114.63  3.000
 W9J  H2   NT  CT   120.47  3.000
 W9J  H1   NT  CT   116.25  3.000
 W9J  N    CT  OT   123.01  3.000
 W9J  OT   CT  NT   121.78  3.000
 W9J  N    CT  NT   115.03  3.000
 W9J  H3   N   CA   114.61  3.000
 W9J  H3   N   CT   116.54  3.000
 W9J  CA   N   CT   120.26  3.000
 W9J  H4   CA  C    107.51  3.000
 W9J  H4   CA  CB   107.49  3.000
 W9J  C    CA  CB   110.82  3.000
 W9J  H4   CA  N    107.67  3.000
 W9J  C    CA  N    113.41  3.000
 W9J  CB   CA  N    109.70  3.000
 W9J  H6   CB  H5   106.68  3.000
 W9J  H6   CB  CG   109.78  3.000
 W9J  H5   CB  CG   109.67  3.000
 W9J  H6   CB  CA   109.88  3.000
 W9J  H5   CB  CA   107.93  3.000
 W9J  CG   CB  CA   112.71  3.000
 W9J  H8   CG  H7   107.78  3.000
 W9J  H8   CG  SD   108.96  3.000
 W9J  H7   CG  SD   108.84  3.000
 W9J  H8   CG  CB   110.19  3.000
 W9J  H7   CG  CB   111.17  3.000
 W9J  SD   CG  CB   109.85  3.000
 W9J  CE   SD  CG    99.83  3.000
 W9J  H11  CE  H10  109.28  3.000
 W9J  H11  CE  H9   108.64  3.000
 W9J  H10  CE  H9   108.66  3.000
 W9J  H11  CE  SD   111.18  3.000
 W9J  H10  CE  SD   111.15  3.000
 W9J  H9   CE  SD   107.86  3.000
 W9J  OXT  C   O    127.62  3.000
 W9J  OXT  C   CA   114.96  3.000
 W9J  O    C   CA   117.42  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
 W9J  CONST_02  CA  N   CT  NT   180.00   0.0  0
 W9J  CONST_05  H3  N   CT  OT   180.00   0.0  0
 W9J  Var_01    SD  CG  CB  CA  -176.70  30.0  1
 W9J  Var_02    H9  CE  SD  CG   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
 W9J  chir_01  CA  N  CB  C  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
 W9J  plan-1  NT   0.020
 W9J  plan-1  CT   0.020
 W9J  plan-1  OT   0.020
 W9J  plan-1  N    0.020
 W9J  plan-1  CA   0.020
 W9J  plan-1  H1   0.020
 W9J  plan-1  H2   0.020
 W9J  plan-1  H3   0.020
 W9J  plan-2  CA   0.020
 W9J  plan-2  C    0.020
 W9J  plan-2  O    0.020
 W9J  plan-2  OXT  0.020

