# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:21:24 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: N-carbamoyl-D-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
 CDT  CDT  'N-carbamoyl-D-methionine '  ligand  23  12  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CDT
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
 CDT  NT   N  NH2    0  -0.846   2.5348  -0.8267  -2.4866
 CDT  CT   C  C      0   0.660   1.6110   0.0778  -2.0433
 CDT  OT   O  O      0  -0.548   1.4834   1.1833  -2.5590
 CDT  N    N  NH1    0  -0.641   0.8630  -0.3404  -0.9880
 CDT  CA   C  CH1    0  -0.192  -0.3803   0.3196  -0.6635
 CDT  CB   C  CH2    0  -0.450  -0.8350  -0.1099   0.7317
 CDT  CG   C  CH2    0  -0.536   0.1610   0.2720   1.8164
 CDT  SD   S  S2     0  -0.051  -0.4471  -0.2843   3.4345
 CDT  CE   C  CH3    0  -0.763   0.9225   0.2533   4.4815
 CDT  C    C  C      0   0.411  -1.5019   0.0663  -1.7061
 CDT  O    O  O      0  -0.617  -2.5620   0.6925  -1.5046
 CDT  OXT  O  OC    -1  -0.595  -1.2593  -0.7242  -2.6335
 CDT  HT1  H  HNH2   0   0.388   3.2810  -0.4591  -3.0530
 CDT  HT2  H  HNH2   0   0.388   2.8084  -1.5891  -1.8881
 CDT  HN1  H  HNH1   0   0.375   0.8798  -1.3309  -0.7953
 CDT  HA   H  HCH1   0   0.237  -0.1922   1.3965  -0.6382
 CDT  HB1  H  HCH2   0   0.230  -1.0032  -1.1926   0.7476
 CDT  HB2  H  HCH2   0   0.247  -1.7978   0.3594   0.9358
 CDT  HG1  H  HCH2   0   0.254   0.2972   1.3560   1.8383
 CDT  HG2  H  HCH2   0   0.259   1.1354  -0.1826   1.6307
 CDT  HE1  H  HCH3   0   0.272   0.6968  -0.0435   5.5041
 CDT  HE2  H  HCH3   0   0.259   1.8561  -0.2198   4.1792
 CDT  HE3  H  HCH3   0   0.259   1.0410   1.3356   4.4510

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
 CDT  NT  CT   single  1.367  0.020  1.367
 CDT  NT  HT1  single  0.890  0.020  1.040
 CDT  NT  HT2  single  0.890  0.020  1.040
 CDT  CT  OT   double  1.226  0.020  1.226
 CDT  CT  N    single  1.359  0.020  1.359
 CDT  N   CA   single  1.444  0.020  1.444
 CDT  N   HN1  single  0.890  0.020  1.040
 CDT  CA  CB   single  1.529  0.020  1.529
 CDT  CA  C    single  1.552  0.020  1.552
 CDT  CA  HA   single  0.970  0.020  1.090
 CDT  CB  CG   single  1.521  0.020  1.521
 CDT  CB  HB1  single  0.970  0.020  1.090
 CDT  CB  HB2  single  0.970  0.020  1.090
 CDT  CG  SD   single  1.816  0.020  1.816
 CDT  CG  HG1  single  0.970  0.020  1.090
 CDT  CG  HG2  single  0.970  0.020  1.090
 CDT  SD  CE   single  1.806  0.020  1.806
 CDT  CE  HE1  single  0.970  0.020  1.090
 CDT  CE  HE2  single  0.970  0.020  1.090
 CDT  CE  HE3  single  0.970  0.020  1.090
 CDT  C   O    deloc   1.248  0.020  1.248
 CDT  C   OXT  deloc   1.243  0.020  1.243

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
 CDT  HT2  NT  HT1  114.18  3.000
 CDT  HT2  NT  CT   119.46  3.000
 CDT  HT1  NT  CT   116.23  3.000
 CDT  N    CT  OT   123.12  3.000
 CDT  N    CT  NT   114.84  3.000
 CDT  OT   CT  NT   122.04  3.000
 CDT  HN1  N   CA   114.83  3.000
 CDT  HN1  N   CT   116.16  3.000
 CDT  CA   N   CT   120.49  3.000
 CDT  HA   CA  C    107.49  3.000
 CDT  HA   CA  CB   107.86  3.000
 CDT  C    CA  CB   110.62  3.000
 CDT  HA   CA  N    107.88  3.000
 CDT  C    CA  N    113.36  3.000
 CDT  CB   CA  N    109.43  3.000
 CDT  HB2  CB  HB1  106.68  3.000
 CDT  HB2  CB  CG   109.67  3.000
 CDT  HB1  CB  CG   109.77  3.000
 CDT  HB2  CB  CA   108.21  3.000
 CDT  HB1  CB  CA   109.66  3.000
 CDT  CG   CB  CA   112.67  3.000
 CDT  HG2  CG  HG1  107.79  3.000
 CDT  HG2  CG  SD   108.85  3.000
 CDT  HG1  CG  SD   109.13  3.000
 CDT  HG2  CG  CB   111.02  3.000
 CDT  HG1  CG  CB   110.17  3.000
 CDT  SD   CG  CB   109.83  3.000
 CDT  CE   SD  CG    99.87  3.000
 CDT  HE3  CE  HE2  109.30  3.000
 CDT  HE3  CE  HE1  108.66  3.000
 CDT  HE2  CE  HE1  108.66  3.000
 CDT  HE3  CE  SD   111.23  3.000
 CDT  HE2  CE  SD   111.09  3.000
 CDT  HE1  CE  SD   107.84  3.000
 CDT  OXT  C   O    127.28  3.000
 CDT  OXT  C   CA   117.65  3.000
 CDT  O    C   CA   115.07  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
 CDT  Var_01  SD   CG  CB  CA  -179.55  30.0  3
 CDT  Var_02  HE1  CE  SD  CG  -178.73  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
 CDT  chir_01  CA  N  CB  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
 CDT  plan-1  NT   0.020
 CDT  plan-1  CT   0.020
 CDT  plan-1  OT   0.020
 CDT  plan-1  N    0.020
 CDT  plan-1  CA   0.020
 CDT  plan-1  HT1  0.020
 CDT  plan-1  HT2  0.020
 CDT  plan-1  HN1  0.020
 CDT  plan-2  CA   0.020
 CDT  plan-2  C    0.020
 CDT  plan-2  O    0.020
 CDT  plan-2  OXT  0.020

