# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 11:54:28 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (2~{S})-2-(methylamino)butanedioic 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
 SOQ  SOQ  "N-methyl-L-aspartic acid"  ligand  17  10  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SOQ
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
 SOQ  CA   C  CH1    0  -0.221  16.4680  13.1503  2.8339
 SOQ  CB   C  CH2    0  -0.574  15.6360  14.1240  3.6571
 SOQ  CG   C  C      0   0.406  16.4065  14.8473  4.7764
 SOQ  N    N  NH1    0  -0.584  17.5623  13.8325  2.1514
 SOQ  C    C  C      0   0.400  15.6111  12.2388  1.9054
 SOQ  O    O  O      0  -0.609  16.1088  11.9303  0.8019
 SOQ  OD1  O  OC    -1  -0.624  16.1353  16.0541  4.9584
 SOQ  OD2  O  O      0  -0.615  17.2109  14.1658  5.4463
 SOQ  C1   C  CH3    0  -0.523  17.1518  14.9163  1.2806
 SOQ  O1   O  OC    -1  -0.611  14.5196  11.8334  2.3584
 SOQ  H1   H  HCH1   0   0.207  16.9415  12.4669  3.5522
 SOQ  H2   H  HCH2   0   0.194  15.1522  14.8590  3.0078
 SOQ  H3   H  HCH2   0   0.222  14.8197  13.5620  4.1180
 SOQ  H4   H  HNH1   0   0.325  18.0187  13.1385  1.5739
 SOQ  H7   H  HCH3   0   0.216  17.9976  15.2108  0.6572
 SOQ  H8   H  HCH3   0   0.182  16.3163  14.6816  0.6073
 SOQ  H9   H  HCH3   0   0.209  16.8675  15.7959  1.8611

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
 SOQ  O   C    deloc   1.249  0.020  1.249
 SOQ  C1  N    single  1.450  0.020  1.450
 SOQ  N   CA   single  1.459  0.020  1.459
 SOQ  C   CA   single  1.558  0.020  1.558
 SOQ  CA  CB   single  1.522  0.020  1.522
 SOQ  CB  CG   single  1.539  0.020  1.539
 SOQ  CG  OD2  deloc   1.249  0.020  1.249
 SOQ  CG  OD1  deloc   1.250  0.020  1.250
 SOQ  C   O1   deloc   1.249  0.020  1.249
 SOQ  CA  H1   single  0.970  0.020  1.090
 SOQ  CB  H2   single  0.970  0.020  1.090
 SOQ  CB  H3   single  0.970  0.020  1.090
 SOQ  N   H4   single  0.890  0.020  1.040
 SOQ  C1  H7   single  0.970  0.020  1.090
 SOQ  C1  H8   single  0.970  0.020  1.090
 SOQ  C1  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
 SOQ  H1   CA  C    105.23  3.000
 SOQ  H1   CA  N    105.87  3.000
 SOQ  C    CA  N    114.04  3.000
 SOQ  H1   CA  CB   106.25  3.000
 SOQ  C    CA  CB   113.31  3.000
 SOQ  N    CA  CB   111.33  3.000
 SOQ  H3   CB  H2   105.40  3.000
 SOQ  H3   CB  CG   107.99  3.000
 SOQ  H2   CB  CG   109.72  3.000
 SOQ  H3   CB  CA   107.90  3.000
 SOQ  H2   CB  CA   110.52  3.000
 SOQ  CG   CB  CA   114.84  3.000
 SOQ  OD2  CG  OD1  126.03  3.000
 SOQ  OD1  CG  CB   116.80  3.000
 SOQ  OD2  CG  CB   117.12  3.000
 SOQ  H4   N   C1   107.32  3.000
 SOQ  H4   N   CA   106.54  3.000
 SOQ  C1   N   CA   114.72  3.000
 SOQ  O1   C   O    126.03  3.000
 SOQ  O1   C   CA   117.02  3.000
 SOQ  O    C   CA   116.86  3.000
 SOQ  H9   C1  H8   107.46  3.000
 SOQ  H9   C1  H7   106.75  3.000
 SOQ  H8   C1  H7   107.29  3.000
 SOQ  H9   C1  N    110.90  3.000
 SOQ  H8   C1  N    115.08  3.000
 SOQ  H7   C1  N    108.99  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
 SOQ  Var_01  OD2  CG  CB  CA    -41.76  30.0  3
 SOQ  Var_02  OD1  CG  CB  CA    140.52  30.0  3
 SOQ  Var_03  H7   C1  N   CA   -167.55  30.0  3
 SOQ  Var_04  H8   C1  N   CA    -47.01  30.0  3
 SOQ  Var_05  H9   C1  N   CA     75.21  30.0  3
 SOQ  Var_06  H2   CB  CG  OD1    15.33  30.0  2
 SOQ  Var_07  H3   CB  CG  OD1   -99.06  30.0  2
 SOQ  Var_08  H2   CB  CG  OD2  -166.96  30.0  2
 SOQ  Var_09  H3   CB  CG  OD2    78.65  30.0  2

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
 SOQ  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
 SOQ  plan-1  CB   0.020
 SOQ  plan-1  CG   0.020
 SOQ  plan-1  OD1  0.020
 SOQ  plan-1  OD2  0.020
 SOQ  plan-2  CA   0.020
 SOQ  plan-2  C    0.020
 SOQ  plan-2  O    0.020
 SOQ  plan-2  O1   0.020

