# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 06:56:46 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: N-methyl-D-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@H](CC(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
 OEM  OEM  'N-methyl-D-aspartic acid '  D-peptide  17  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 GRAND
;

data_comp_OEM
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
 OEM  C     C  C      0   0.405   7.7612  36.6691   9.9196
 OEM  N     N  NH1    0  -0.584   9.4195  38.4949   9.5367
 OEM  O     O  O      0  -0.612   8.5770  35.9188   9.3517
 OEM  CA    C  CH1    0  -0.204   8.0865  38.1823  10.0261
 OEM  CB    C  CH2    0  -0.583   7.7677  38.7323  11.4192
 OEM  CG    C  C      0   0.404   8.6600  38.2218  12.5659
 OEM  CAA   C  CH3    0  -0.515   9.7070  39.9079   9.4374
 OEM  OD1   O  O      0  -0.601   9.3734  37.2187  12.3492
 OEM  OD2   O  OC    -1  -0.626   8.5781  38.8466  13.6449
 OEM  OXT   O  OC    -1  -0.628   6.6484  36.3317  10.3817
 OEM  HA    H  HCH1   0   0.196   7.3857  38.6726   9.3319
 OEM  HB    H  HCH2   0   0.202   7.8017  39.8267  11.4169
 OEM  HBA   H  HCH2   0   0.219   6.7311  38.4841  11.6636
 OEM  HAA   H  HCH3   0   0.217  10.7096  40.0513   9.0294
 OEM  HAAA  H  HCH3   0   0.205   9.0078  40.3803   8.7421
 OEM  H8    H  HNH1   0   0.322  10.0880  38.0562  10.1564
 OEM  H9    H  HCH3   0   0.183   9.6565  40.4775  10.3764

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
 OEM  C    CA    single  1.525  0.021  1.525
 OEM  C    OXT   deloc   1.251  0.020  1.251
 OEM  N    CA    single  1.458  0.019  1.458
 OEM  O    C     deloc   1.231  0.020  1.231
 OEM  CA   CB    single  1.521  0.033  1.521
 OEM  CA   HA    single  0.970  0.020  0.970
 OEM  CB   CG    single  1.540  0.020  1.540
 OEM  CB   HB    single  0.970  0.020  1.090
 OEM  CB   HBA   single  0.970  0.020  1.090
 OEM  CG   OD2   deloc   1.250  0.020  1.250
 OEM  CAA  N     single  1.445  0.020  1.445
 OEM  CAA  HAA   single  0.970  0.020  1.090
 OEM  CAA  HAAA  single  0.970  0.020  1.090
 OEM  OD1  CG    deloc   1.250  0.020  1.250
 OEM  N    H8    single  0.890  0.020  1.040
 OEM  CAA  H9    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
 OEM  OXT   C    CA    120.80  1.700
 OEM  OXT   C    O     126.05  3.000
 OEM  CA    C    O     120.80  1.700
 OEM  H8    N    CAA   109.55  3.000
 OEM  H8    N    CA    107.85  3.000
 OEM  CAA   N    CA    114.56  3.000
 OEM  HA    CA   CB    109.00  3.000
 OEM  HA    CA   N     110.00  3.000
 OEM  CB    CA   N     110.40  1.500
 OEM  HA    CA   C     110.00  3.000
 OEM  CB    CA   C     110.50  1.500
 OEM  N     CA   C     111.00  2.800
 OEM  HBA   CB   HB    104.88  3.000
 OEM  HBA   CB   CG    107.91  3.000
 OEM  HB    CB   CG    108.35  3.000
 OEM  HBA   CB   CA    108.61  3.000
 OEM  HB    CB   CA    110.53  3.000
 OEM  CG    CB   CA    115.96  3.000
 OEM  OD2   CG   OD1   126.05  3.000
 OEM  OD1   CG   CB    117.88  3.000
 OEM  OD2   CG   CB    116.06  3.000
 OEM  H9    CAA  HAAA  106.86  3.000
 OEM  H9    CAA  HAA   107.05  3.000
 OEM  HAAA  CAA  HAA   107.03  3.000
 OEM  H9    CAA  N     116.02  3.000
 OEM  HAAA  CAA  N     109.81  3.000
 OEM  HAA   CAA  N     109.67  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
 OEM  Var_01  OD2  CG   CB  CA   166.86  30.0  3
 OEM  Var_02  HAA  CAA  N   CA  -177.93  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
 OEM  chir_01  CA  C  N  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
 OEM  plan-1  C    0.020
 OEM  plan-1  O    0.020
 OEM  plan-1  CA   0.020
 OEM  plan-1  OXT  0.020
 OEM  plan-2  CB   0.020
 OEM  plan-2  CG   0.020
 OEM  plan-2  OD1  0.020
 OEM  plan-2  OD2  0.020

