# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 06:11:18 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: N~2~-methyl-D-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](CCC(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
 HJV  HJV  'N~2~-methyl-D-glutamine  '  D-peptide  22  11  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HJV
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
 HJV  CN    C  CH3    0  -0.529   6.9028  83.4842  66.7975
 HJV  N     N  NH1    0  -0.584   8.1426  84.2123  66.9913
 HJV  CA    C  CH1    0  -0.222   9.0876  84.0711  65.8843
 HJV  CB    C  CH2    0  -0.428   8.5175  84.6782  64.6024
 HJV  CG    C  CH2    0  -0.567   9.5800  85.1537  63.6180
 HJV  CD    C  C      0   0.507  10.3539  86.3545  64.1248
 HJV  NE2   N  NH2    0  -0.803  11.6820  86.3093  63.9258
 HJV  OE1   O  O      0  -0.493   9.8031  87.3084  64.6580
 HJV  C     C  C      0   0.404   9.6195  82.6145  65.7222
 HJV  O     O  O      0  -0.614   9.8648  82.0151  66.7898
 HJV  OXT   O  OC    -1  -0.592   9.7889  82.1702  64.5692
 HJV  HN11  H  HCH3   0   0.224   6.3071  83.5370  67.7099
 HJV  HN12  H  HCH3   0   0.218   6.3075  83.9397  66.0046
 HJV  HN13  H  HCH3   0   0.188   7.0257  82.4213  66.5473
 HJV  H2    H  HNH1   0   0.331   8.5986  83.8281  67.8093
 HJV  HA    H  HCH1   0   0.220   9.9620  84.6700  66.1793
 HJV  HB2   H  HCH2   0   0.217   7.8824  85.5272  64.8664
 HJV  HB1   H  HCH2   0   0.223   7.8749  83.9577  64.0931
 HJV  HG2   H  HCH2   0   0.260   9.0970  85.4629  62.6853
 HJV  HG1   H  HCH2   0   0.247  10.2479  84.3317  63.3650
 HJV  H11   H  HNH2   0   0.392  12.2665  87.0832  64.1973
 HJV  H10   H  HNH2   0   0.402  12.1299  85.5172  63.4997

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
 HJV  CG   CD    single  1.516  0.020  1.516
 HJV  CG   CB    single  1.524  0.020  1.524
 HJV  NE2  CD    single  1.344  0.020  1.344
 HJV  CD   OE1   double  1.224  0.020  1.224
 HJV  CB   CA    single  1.521  0.033  1.521
 HJV  C    CA    single  1.525  0.021  1.525
 HJV  C    O     deloc   1.231  0.020  1.231
 HJV  CA   N     single  1.458  0.019  1.458
 HJV  CN   N     single  1.451  0.020  1.451
 HJV  C    OXT   deloc   1.247  0.020  1.247
 HJV  CN   HN11  single  0.970  0.020  1.090
 HJV  CN   HN12  single  0.970  0.020  1.090
 HJV  CN   HN13  single  0.970  0.020  1.090
 HJV  N    H2    single  0.890  0.020  1.040
 HJV  CA   HA    single  0.970  0.020  0.970
 HJV  CB   HB2   single  0.970  0.020  1.090
 HJV  CB   HB1   single  0.970  0.020  1.090
 HJV  CG   HG2   single  0.970  0.020  1.090
 HJV  CG   HG1   single  0.970  0.020  1.090
 HJV  NE2  H11   single  0.860  0.020  1.020
 HJV  NE2  H10   single  0.860  0.020  1.020

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
 HJV  HN13  CN   HN12  107.42  3.000
 HJV  HN13  CN   HN11  107.36  3.000
 HJV  HN12  CN   HN11  106.84  3.000
 HJV  HN13  CN   N     114.85  3.000
 HJV  HN12  CN   N     110.72  3.000
 HJV  HN11  CN   N     109.30  3.000
 HJV  H2    N    CA    106.50  3.000
 HJV  H2    N    CN    107.61  3.000
 HJV  CA    N    CN    113.75  3.000
 HJV  HA    CA   C     110.00  3.000
 HJV  HA    CA   CB    109.00  3.000
 HJV  C     CA   CB    110.50  1.500
 HJV  HA    CA   N     110.00  3.000
 HJV  C     CA   N     111.00  2.800
 HJV  CB    CA   N     110.40  1.500
 HJV  HB1   CB   HB2   106.47  3.000
 HJV  HB1   CB   CG    108.36  3.000
 HJV  HB2   CB   CG    108.59  3.000
 HJV  HB1   CB   CA    110.40  3.000
 HJV  HB2   CB   CA    108.83  3.000
 HJV  CG    CB   CA    113.92  3.000
 HJV  HG1   CG   HG2   106.61  3.000
 HJV  HG1   CG   CD    111.26  3.000
 HJV  HG2   CG   CD    106.63  3.000
 HJV  HG1   CG   CB    110.00  3.000
 HJV  HG2   CG   CB    109.31  3.000
 HJV  CD    CG   CB    112.77  3.000
 HJV  OE1   CD   NE2   122.39  3.000
 HJV  OE1   CD   CG    122.23  3.000
 HJV  NE2   CD   CG    115.37  3.000
 HJV  H10   NE2  H11   117.48  3.000
 HJV  H10   NE2  CD    122.00  3.000
 HJV  H11   NE2  CD    120.52  3.000
 HJV  OXT   C    O     126.35  3.000
 HJV  OXT   C    CA    120.80  1.700
 HJV  O     C    CA    120.80  1.700

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
 HJV  CONST_01  H11   NE2  CD  CG  180.00   0.0  0
 HJV  CONST_02  H10   NE2  CD  CG    0.00   0.0  0
 HJV  Var_01    CD    CG   CB  CA  -68.20  30.0  1
 HJV  Var_02    NE2   CD   CG  CB  136.88  30.0  3
 HJV  Var_03    HN11  CN   N   CA  173.06  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
 HJV  chir_01  CA  CB  C  N  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
 HJV  plan-1  CG   0.020
 HJV  plan-1  CD   0.020
 HJV  plan-1  NE2  0.020
 HJV  plan-1  OE1  0.020
 HJV  plan-1  H11  0.020
 HJV  plan-1  H10  0.020
 HJV  plan-2  CA   0.020
 HJV  plan-2  C    0.020
 HJV  plan-2  O    0.020
 HJV  plan-2  OXT  0.020

