# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:12:10 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: N-methyl-D-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
 MND  MND  'N-methyl-D-asparagine    '  D-peptide  19  10  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MND
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
 MND  N     N  NH2    0  -0.764  8.3419   2.1834  -1.1394
 MND  CA    C  CH1    0  -0.129  8.2645   1.7065  -2.5217
 MND  CB    C  CH2    0  -0.605  7.8874   2.8553  -3.4455
 MND  CG    C  C      0   0.503  6.9155   3.7902  -2.7702
 MND  OD1   O  O      0  -0.535  5.7752   3.4427  -2.4912
 MND  ND2   N  NH1    0  -0.617  7.3495   5.0365  -2.5117
 MND  CE2   C  CH3    0  -0.497  6.5233   5.9953  -1.8201
 MND  C     C  C      0   0.350  7.3129   0.4859  -2.5406
 MND  O     O  O      0  -0.506  6.4548   0.4065  -3.4396
 MND  OXT   O  OC    -1  -0.771  7.6134  -0.3881  -1.6995
 MND  H     H  HNH2   0   0.347  8.5572   1.3872  -0.5520
 MND  H2    H  HNH2   0   0.343  9.1316   2.8123  -1.0477
 MND  HA    H  HCH1   0   0.211  9.2520   1.3415  -2.8581
 MND  HB2   H  HCH2   0   0.292  8.7871   3.3772  -3.7844
 MND  HB3   H  HCH2   0   0.311  7.3991   2.4667  -4.3385
 MND  HD2   H  HNH1   0   0.393  8.3116   5.2743  -2.6768
 MND  HE21  H  HCH3   0   0.221  7.1023   6.8983  -1.6532
 MND  HE22  H  HCH3   0   0.206  5.6401   6.2617  -2.4030
 MND  HE23  H  HCH3   0   0.248  6.1860   5.6217  -0.8513

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
 MND  N    CA    single  1.458  0.019  1.458
 MND  CA   CB    single  1.521  0.033  1.521
 MND  CA   C     single  1.525  0.021  1.525
 MND  CB   CG    single  1.508  0.020  1.508
 MND  CG   OD1   double  1.224  0.020  1.224
 MND  CG   ND2   single  1.345  0.020  1.345
 MND  ND2  CE2   single  1.442  0.020  1.442
 MND  C    O     deloc   1.231  0.020  1.231
 MND  C    OXT   deloc   1.250  0.020  1.250
 MND  N    H     single  0.860  0.020  0.860
 MND  N    H2    single  0.890  0.020  1.040
 MND  CA   HA    single  0.970  0.020  0.970
 MND  CB   HB2   single  0.970  0.020  1.090
 MND  CB   HB3   single  0.970  0.020  1.090
 MND  ND2  HD2   single  0.860  0.020  1.020
 MND  CE2  HE21  single  0.970  0.020  1.090
 MND  CE2  HE22  single  0.970  0.020  1.090
 MND  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
 MND  H2    N    H     105.65  3.000
 MND  H2    N    CA    109.18  3.000
 MND  H     N    CA    114.00  3.000
 MND  HA    CA   C     110.00  3.000
 MND  HA    CA   CB    109.00  3.000
 MND  C     CA   CB    110.50  1.500
 MND  HA    CA   N     110.00  3.000
 MND  C     CA   N     111.00  2.800
 MND  CB    CA   N     110.40  1.500
 MND  HB3   CB   HB2   106.55  3.000
 MND  HB3   CB   CG    107.42  3.000
 MND  HB2   CB   CG    111.90  3.000
 MND  HB3   CB   CA    109.84  3.000
 MND  HB2   CB   CA    110.14  3.000
 MND  CG    CB   CA    110.84  3.000
 MND  ND2   CG   OD1   121.32  3.000
 MND  ND2   CG   CB    116.91  3.000
 MND  OD1   CG   CB    121.76  3.000
 MND  HD2   ND2  CE2   118.03  3.000
 MND  HD2   ND2  CG    119.79  3.000
 MND  CE2   ND2  CG    121.57  3.000
 MND  HE23  CE2  HE22  107.90  3.000
 MND  HE23  CE2  HE21  108.24  3.000
 MND  HE22  CE2  HE21  108.11  3.000
 MND  HE23  CE2  ND2   112.02  3.000
 MND  HE22  CE2  ND2   111.70  3.000
 MND  HE21  CE2  ND2   108.74  3.000
 MND  OXT   C    O     127.37  3.000
 MND  OXT   C    CA    120.80  1.700
 MND  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
 MND  CONST_01  CE2   ND2  CG   CB   180.00   0.0  0
 MND  CONST_02  CE2   ND2  CG   OD1    0.00   0.0  0
 MND  CONST_03  HD2   ND2  CG   CB     0.00   0.0  0
 MND  Var_01    OD1   CG   CB   CA   -67.12  30.0  3
 MND  Var_02    HE21  CE2  ND2  CG   175.51  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
 MND  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
 MND  plan-1  CB   0.020
 MND  plan-1  CG   0.020
 MND  plan-1  OD1  0.020
 MND  plan-1  ND2  0.020
 MND  plan-1  CE2  0.020
 MND  plan-1  HD2  0.020
 MND  plan-2  CA   0.020
 MND  plan-2  C    0.020
 MND  plan-2  O    0.020
 MND  plan-2  OXT  0.020

