# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:36:14 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: N-carboxy-L-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC(O)=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
 CXM  CXM  'N-carboxy-L-methionine   '  L-peptide  21  12  .  2016-04-22  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CXM
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
 CXM  N    N  NH1    0  -0.661  39.2878  48.2225  36.4019
 CXM  CA   C  CH1    0  -0.185  37.9705  47.9369  36.9089
 CXM  CB   C  CH2    0  -0.392  37.1001  47.2076  35.8717
 CXM  CG   C  CH2    0  -0.555  36.9334  47.9996  34.5870
 CXM  SD   S  S2     0  -0.057  35.9027  47.1753  33.3371
 CXM  CE   C  CH3    0  -0.765  37.0048  45.8375  32.8232
 CXM  C    C  C      0   0.401  38.0222  47.0963  38.2136
 CXM  O    O  O      0  -0.598  39.1364  46.6765  38.5877
 CXM  CN   C  C      0   0.487  39.7378  49.5217  36.1125
 CXM  ON1  O  O      0  -0.662  40.9801  49.6521  36.0116
 CXM  ON2  O  OC    -1  -0.646  38.8777  50.4173  35.9561
 CXM  OXT  O  OC    -1  -0.611  36.9268  46.9004  38.7771
 CXM  H    H  HNH1   0   0.328  39.9875  47.6276  36.8189
 CXM  HA   H  HCH1   0   0.202  37.4727  48.8821  37.1480
 CXM  HB2  H  HCH2   0   0.209  37.5563  46.2374  35.6477
 CXM  HB3  H  HCH2   0   0.211  36.1165  47.0046  36.2980
 CXM  HG2  H  HCH2   0   0.257  36.4406  48.9532  34.7862
 CXM  HG3  H  HCH2   0   0.256  37.9008  48.2270  34.1373
 CXM  HE1  H  HCH3   0   0.268  36.5339  45.3257  31.9855
 CXM  HE2  H  HCH3   0   0.256  37.9656  46.2317  32.4938
 CXM  HE3  H  HCH3   0   0.257  37.1681  45.1145  33.6204

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
 CXM  N   CA   single  1.458  0.019  1.458
 CXM  N   CN   single  1.405  0.020  1.405
 CXM  N   H    single  0.860  0.020  0.860
 CXM  CA  CB   single  1.530  0.020  1.530
 CXM  CA  C    single  1.525  0.021  1.525
 CXM  CA  HA   single  0.970  0.020  0.970
 CXM  CB  CG   single  1.518  0.020  1.518
 CXM  CB  HB2  single  0.970  0.020  1.090
 CXM  CB  HB3  single  0.970  0.020  1.090
 CXM  CG  SD   single  1.818  0.020  1.818
 CXM  CG  HG2  single  0.970  0.020  1.090
 CXM  CG  HG3  single  0.970  0.020  1.090
 CXM  SD  CE   single  1.808  0.020  1.808
 CXM  CE  HE1  single  0.970  0.020  1.090
 CXM  CE  HE2  single  0.970  0.020  1.090
 CXM  CE  HE3  single  0.970  0.020  1.090
 CXM  C   O    deloc   1.231  0.020  1.231
 CXM  C   OXT  deloc   1.247  0.020  1.247
 CXM  CN  ON1  deloc   1.253  0.020  1.253
 CXM  CN  ON2  deloc   1.252  0.020  1.252

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
 CXM  H    N   CN   114.10  3.000
 CXM  H    N   CA   114.00  3.000
 CXM  CN   N   CA   123.29  3.000
 CXM  HA   CA  C    110.00  3.000
 CXM  HA   CA  CB   109.00  3.000
 CXM  C    CA  CB   110.10  1.900
 CXM  HA   CA  N    110.00  3.000
 CXM  C    CA  N    111.00  2.800
 CXM  CB   CA  N    110.50  1.700
 CXM  HB3  CB  HB2  106.89  3.000
 CXM  HB3  CB  CG   109.18  3.000
 CXM  HB2  CB  CG   109.56  3.000
 CXM  HB3  CB  CA   109.57  3.000
 CXM  HB2  CB  CA   108.80  3.000
 CXM  CG   CB  CA   112.67  3.000
 CXM  HG3  CG  HG2  107.06  3.000
 CXM  HG3  CG  SD   108.29  3.000
 CXM  HG2  CG  SD   105.41  3.000
 CXM  HG3  CG  CB   111.11  3.000
 CXM  HG2  CG  CB   110.54  3.000
 CXM  SD   CG  CB   114.05  3.000
 CXM  CE   SD  CG   100.68  3.000
 CXM  HE3  CE  HE2  109.24  3.000
 CXM  HE3  CE  HE1  108.42  3.000
 CXM  HE2  CE  HE1  108.59  3.000
 CXM  HE3  CE  SD   112.01  3.000
 CXM  HE2  CE  SD   110.84  3.000
 CXM  HE1  CE  SD   107.64  3.000
 CXM  OXT  C   O    126.57  3.000
 CXM  OXT  C   CA   115.81  3.000
 CXM  O    C   CA   120.80  1.700
 CXM  ON2  CN  ON1  126.64  3.000
 CXM  ON2  CN  N    117.86  3.000
 CXM  ON1  CN  N    115.48  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
 CXM  Var_01  ON1  CN  N   CA   162.49  30.0  2
 CXM  Var_02  SD   CG  CB  CA  -179.69  30.0  3
 CXM  Var_03  HE1  CE  SD  CG  -173.97  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
 CXM  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
 CXM  plan-1  CA   0.020
 CXM  plan-1  C    0.020
 CXM  plan-1  O    0.020
 CXM  plan-1  OXT  0.020
 CXM  plan-2  N    0.020
 CXM  plan-2  CN   0.020
 CXM  plan-2  ON1  0.020
 CXM  plan-2  ON2  0.020

