# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:43:06 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: N-methyl-L-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C[C@H](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
 MEN  MEN  'N-methyl-L-asparagine    '  L-peptide  19  10  .  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_MEN
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
 MEN  N     N  NH2    0  -0.792  -15.6821  -22.4521  22.5031
 MEN  CA    C  CH1    0  -0.186  -14.9577  -21.4966  21.6854
 MEN  C     C  C      0   0.405  -14.7397  -22.0471  20.2579
 MEN  O     O  O      0  -0.602  -14.7078  -21.2028  19.3428
 MEN  CB    C  CH2    0  -0.583  -13.5788  -21.1244  22.2812
 MEN  CG    C  C      0   0.518  -12.8172  -20.1027  21.4661
 MEN  OD1   O  O      0  -0.503  -11.8063  -20.3751  20.8304
 MEN  ND2   N  NH1    0  -0.615  -13.3248  -18.8580  21.4945
 MEN  CE2   C  CH3    0  -0.509  -12.7723  -17.7765  20.7176
 MEN  OXT   O  OC    -1  -0.600  -14.5661  -23.2776  20.1571
 MEN  H     H  HNH2   0   0.332  -15.6319  -22.1863  23.4793
 MEN  H2    H  HNH2   0   0.328  -15.2259  -23.3526  22.4213
 MEN  HA    H  HCH1   0   0.207  -15.5571  -20.5834  21.6190
 MEN  HB2   H  HCH2   0   0.252  -13.7287  -20.7427  23.2966
 MEN  HB3   H  HCH2   0   0.243  -12.9715  -22.0282  22.3579
 MEN  HD2   H  HNH1   0   0.399  -14.1626  -18.6841  22.0234
 MEN  HE21  H  HCH3   0   0.244  -13.3547  -16.8796  20.9096
 MEN  HE22  H  HCH3   0   0.232  -11.7357  -17.5733  20.9885
 MEN  HE23  H  HCH3   0   0.231  -12.8092  -17.9846  19.6468

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
 MEN  N    CA    single  1.458  0.019  1.458
 MEN  N    H     single  0.860  0.020  0.860
 MEN  N    H2    single  0.890  0.020  1.040
 MEN  CA   C     single  1.525  0.021  1.525
 MEN  CA   CB    single  1.530  0.020  1.530
 MEN  CA   HA    single  0.970  0.020  0.970
 MEN  C    O     deloc   1.231  0.020  1.231
 MEN  C    OXT   deloc   1.247  0.020  1.247
 MEN  CB   CG    single  1.513  0.020  1.513
 MEN  CB   HB2   single  0.970  0.020  1.090
 MEN  CB   HB3   single  0.970  0.020  1.090
 MEN  CG   OD1   double  1.225  0.020  1.225
 MEN  CG   ND2   single  1.345  0.020  1.345
 MEN  ND2  CE2   single  1.442  0.020  1.442
 MEN  ND2  HD2   single  0.860  0.020  1.020
 MEN  CE2  HE21  single  0.970  0.020  1.090
 MEN  CE2  HE22  single  0.970  0.020  1.090
 MEN  CE2  HE23  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
 MEN  H2    N    H     106.79  3.000
 MEN  H2    N    CA    108.36  3.000
 MEN  H     N    CA    114.00  3.000
 MEN  HA    CA   CB    109.00  3.000
 MEN  HA    CA   C     109.00  3.000
 MEN  CB    CA   C     110.10  1.900
 MEN  HA    CA   N     110.00  3.000
 MEN  CB    CA   N     110.50  1.700
 MEN  C     CA   N     111.00  2.800
 MEN  OXT   C    O     127.30  3.000
 MEN  OXT   C    CA    116.48  3.000
 MEN  O     C    CA    120.80  1.700
 MEN  HB3   CB   HB2   107.43  3.000
 MEN  HB3   CB   CG    108.48  3.000
 MEN  HB2   CB   CG    109.46  3.000
 MEN  HB3   CB   CA    108.89  3.000
 MEN  HB2   CB   CA    108.60  3.000
 MEN  CG    CB   CA    113.80  3.000
 MEN  ND2   CG   OD1   121.90  3.000
 MEN  ND2   CG   CB    115.07  3.000
 MEN  OD1   CG   CB    123.03  3.000
 MEN  HD2   ND2  CE2   118.22  3.000
 MEN  HD2   ND2  CG    119.05  3.000
 MEN  CE2   ND2  CG    122.57  3.000
 MEN  HE23  CE2  HE22  108.14  3.000
 MEN  HE23  CE2  HE21  108.22  3.000
 MEN  HE22  CE2  HE21  108.17  3.000
 MEN  HE23  CE2  ND2   111.88  3.000
 MEN  HE22  CE2  ND2   111.73  3.000
 MEN  HE21  CE2  ND2   108.58  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
 MEN  CONST_01  CE2   ND2  CG   CB    180.00   0.0  0
 MEN  CONST_02  CE2   ND2  CG   OD1     0.00   0.0  0
 MEN  CONST_03  HD2   ND2  CG   CB      0.00   0.0  0
 MEN  Var_01    OD1   CG   CB   CA   -109.98  30.0  3
 MEN  Var_02    HE21  CE2  ND2  CG    179.87  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
 MEN  chir_01  CA  N  C  CB  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
 MEN  plan-1  CB   0.020
 MEN  plan-1  CG   0.020
 MEN  plan-1  OD1  0.020
 MEN  plan-1  ND2  0.020
 MEN  plan-1  CE2  0.020
 MEN  plan-1  HD2  0.020
 MEN  plan-2  CA   0.020
 MEN  plan-2  C    0.020
 MEN  plan-2  O    0.020
 MEN  plan-2  OXT  0.020

